Contacts of the helix formed by residues 425 - 448 (chain G) in PDB entry 6S7T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 425 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D PRO* 3.6 21.1 - - + -
55D SER* 4.2 8.3 - - - +
422G ILE* 3.6 18.1 + - + +
423G PRO 2.8 1.6 + - - -
424G SER* 1.3 78.9 - - - +
426G TYR* 1.3 62.9 + - - +
427G PRO* 3.3 2.2 - - - -
428G TYR* 3.5 30.1 + - + -
429G TYR* 3.2 27.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 426 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539F THR* 6.2 1.1 - - + -
542F SER* 3.9 6.5 - - - +
543F ASN* 4.7 12.8 - - - +
546F THR* 3.6 19.1 + - + +
594F TRP* 6.5 0.4 - + - -
421G PHE* 4.1 17.5 + + + +
422G ILE 4.2 6.7 - - - -
423G PRO* 3.0 38.8 + - + +
425G ALA* 1.3 74.8 - - - +
427G PRO* 1.3 71.7 - - + +
429G TYR* 4.0 20.6 - + + +
430G ALA* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 427 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLN* 5.9 0.2 - - + -
44D TYR* 3.4 37.2 - - + +
542F SER* 3.6 20.0 - - - +
545F PHE* 4.0 16.6 - - + -
546F THR* 3.9 7.6 - - - +
549F ILE* 3.4 27.6 - - + +
424G SER 4.1 6.3 - - - +
425G ALA 3.5 3.6 - - - -
426G TYR* 1.3 88.3 - - + +
428G TYR* 1.3 65.2 + - + +
430G ALA* 2.9 8.1 + - + +
431G SER 2.8 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 428 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLN* 3.6 28.0 - - + +
44D TYR* 3.7 30.7 + + - -
45D CYS* 4.2 13.9 - - + +
48D VAL* 5.6 0.3 - - - +
49D GLY 4.3 9.0 + - - -
50D THR* 5.1 1.9 - - - -
52D PRO* 3.9 17.8 - - + +
55D SER* 3.7 26.5 - - - +
56D PHE* 3.6 41.1 - + + +
59D GLY* 4.8 4.6 - - - -
112D VAL* 5.3 2.7 - - + -
424G SER 4.5 1.1 - - - -
425G ALA* 3.5 34.3 - - + +
426G TYR 3.5 0.2 - - - -
427G PRO* 1.3 73.8 - - + +
429G TYR* 1.3 67.8 + - + +
431G SER* 3.0 18.0 + - - -
432G ALA* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 429 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D SER* 4.0 13.4 + - - -
112D VAL* 3.6 34.9 - - + -
594F TRP* 4.0 37.7 - + + -
420G ARG* 5.1 1.0 - - - -
421G PHE* 3.8 28.7 + + - -
422G ILE* 4.1 25.6 + - - +
425G ALA* 3.2 23.8 - - + +
426G TYR* 4.0 21.8 - + + +
428G TYR* 1.3 78.9 - - + +
430G ALA* 1.3 67.2 + - - +
432G ALA* 3.0 12.5 + - - +
433G PHE* 3.1 24.5 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546F THR* 4.1 20.0 - - + -
549F ILE* 4.3 5.8 - - + -
550F LEU* 4.1 16.8 - - + -
426G TYR 3.3 12.5 + - - +
427G PRO* 2.9 11.1 + - + +
429G TYR* 1.3 78.9 - - - +
431G SER* 1.3 66.8 + - - +
433G PHE* 3.0 6.0 + - - +
434G SER* 2.7 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 431 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D THR* 3.6 13.8 - - - +
41D GLN* 2.5 35.3 + - - -
59D GLY* 4.5 3.3 + - - -
62D SER* 6.1 0.2 - - - -
63D CYS* 3.7 8.8 - - - -
549F ILE* 3.9 18.1 - - - +
427G PRO 2.8 13.6 + - - -
428G TYR 3.2 8.7 - - - -
430G ALA* 1.3 74.2 - - - +
432G ALA* 1.3 67.4 + - - +
434G SER* 3.0 11.4 + - - -
435G MET* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 432 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D SER* 5.5 1.1 - - - +
59D GLY* 5.3 5.3 - - - -
62D SER* 4.6 15.2 + - - +
105D HIS* 5.6 1.0 + - - -
108D VAL* 4.4 22.9 - - + -
109D MET* 4.4 14.4 - - + -
112D VAL* 6.0 4.0 - - + -
428G TYR 3.0 11.6 + - - +
429G TYR* 3.5 9.9 - - - +
431G SER* 1.3 76.5 - - - +
433G PHE* 1.3 66.9 + - + +
435G MET* 3.0 12.7 + - - +
436G MET* 3.2 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 433 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D MET* 3.6 25.6 - - + -
591F TYR* 3.4 38.4 - + + -
594F TRP* 3.3 45.5 - + + -
429G TYR* 3.1 27.6 + + + -
430G ALA* 3.0 8.5 + - - +
432G ALA* 1.3 78.6 - - + +
434G SER* 1.3 66.6 + - - +
436G MET* 3.0 24.7 + - + +
437G LEU* 3.0 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 434 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TYR* 2.4 32.8 + - - -
37D THR* 5.2 3.8 + - - +
549F ILE* 4.7 14.1 + - - -
550F LEU* 5.4 8.9 - - - -
553F LEU* 4.5 13.8 - - - +
430G ALA 2.7 17.5 + - - -
431G SER* 3.2 13.9 - - - -
433G PHE* 1.3 73.2 - - - +
435G MET* 1.3 58.9 + - - +
437G LEU* 3.0 8.0 + - - +
438G GLY 2.8 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 435 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 4.5 3.0 + - - +
33D TYR* 4.1 13.2 - - + +
34D ILE* 3.9 22.9 - - + -
37D THR* 4.9 6.1 - - + -
62D SER* 3.2 39.7 - - - +
63D CYS* 3.5 34.1 - - - -
66D SER* 3.4 26.5 - - - +
105D HIS* 4.8 6.2 - - - +
431G SER* 3.1 15.5 + - - +
432G ALA 3.0 7.8 + - - +
434G SER* 1.3 75.0 - - - +
436G MET* 1.3 52.9 + - - +
438G GLY* 3.0 2.4 + - - +
439G LEU* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 436 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D HIS* 3.8 43.2 - - + +
108D VAL* 5.8 0.9 - - + -
109D MET* 3.6 37.7 - - + -
587F LEU* 4.0 26.3 - - + +
590F MET* 3.6 25.8 - - + -
432G ALA* 3.2 12.2 + - + +
433G PHE* 3.0 29.9 + - + +
435G MET* 1.3 76.6 - - - +
437G LEU* 1.3 64.6 + - - +
439G LEU* 3.0 10.8 + - - +
440G PHE* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553F LEU* 4.1 24.5 - - + -
557F PHE* 4.9 5.4 - - + -
433G PHE 3.0 9.3 + - - +
434G SER* 3.0 11.3 + - - +
436G MET* 1.3 74.4 - - - +
438G GLY* 1.3 65.7 + - - +
440G PHE* 3.0 10.7 + - + +
441G ILE* 3.0 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 438 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 4.2 13.4 - - - -
33D TYR* 4.8 10.8 - - - -
553F LEU* 5.5 2.9 - - - +
556F LEU* 5.7 4.7 - - - +
557F PHE* 6.4 1.8 - - - -
560F TRP* 5.4 0.7 - - - -
434G SER 2.8 16.7 + - - -
435G MET* 3.0 5.6 + - - -
437G LEU* 1.3 77.2 - - - +
439G LEU* 1.3 64.1 + - - +
441G ILE* 3.0 7.7 + - - +
442G PHE* 2.8 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 4.0 14.6 + - - +
97D PHE* 3.5 37.2 - - + -
98D LEU* 5.0 5.6 - - + -
101D SER* 3.2 28.3 - - - +
105D HIS* 4.1 13.9 - - + +
583F HIS* 4.2 23.8 - - + +
587F LEU* 4.8 8.7 - - + -
435G MET 2.7 15.0 + - - +
436G MET* 3.0 9.2 + - - +
438G GLY* 1.3 69.8 - - - +
440G PHE* 1.3 65.4 + - - +
442G PHE* 3.0 13.2 + - + +
443G SER* 2.9 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 440 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580F HIS* 3.8 29.8 - - + -
583F HIS* 3.8 21.8 - + - -
584F ALA* 3.8 28.0 - - + -
587F LEU* 4.0 13.0 - - + +
436G MET 3.0 9.3 + - - +
437G LEU* 3.0 13.8 + - + +
439G LEU* 1.3 75.7 - - - +
441G ILE* 1.3 75.6 + - + +
443G SER* 3.0 17.8 + - - +
444G ILE* 3.2 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 441 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556F LEU* 5.5 0.9 - - + -
557F PHE* 4.1 31.2 - - + -
560F TRP* 3.6 22.9 - - + -
437G LEU* 3.0 36.7 + - + +
438G GLY* 3.5 7.4 - - - +
440G PHE* 1.3 84.0 - - + +
442G PHE* 1.3 64.8 + - - +
444G ILE* 3.0 22.8 + - + +
445G VAL* 3.1 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 5.1 5.2 - - + -
27D LEU* 3.4 42.0 - - + -
30D TYR* 4.2 23.3 - + + -
73D LEU* 4.8 4.5 - - + -
94D PHE* 4.5 7.6 - + - -
97D PHE* 4.1 30.3 - + - -
560F TRP* 3.6 30.0 - + + -
438G GLY 2.8 12.9 + - - +
439G LEU* 3.2 13.7 - - + +
441G ILE* 1.3 77.3 - - - +
443G SER* 1.3 61.1 + - - +
445G VAL 3.0 3.1 + - - -
446G PHE* 2.8 64.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 443 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D PHE* 3.7 24.8 - - - -
98D LEU* 5.0 4.1 - - - +
579F PHE* 4.5 5.4 - - - -
580F HIS* 3.9 16.9 + - - -
583F HIS* 4.8 15.7 - - - -
439G LEU* 2.9 13.0 + - - -
440G PHE* 3.0 12.1 + - - -
442G PHE* 1.3 81.2 - - - +
444G ILE* 1.3 64.3 + - - +
446G PHE* 3.0 12.5 + - - +
447G LEU* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 444 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567F VAL* 3.6 24.7 - - + +
570F PHE* 4.6 20.0 - - + -
580F HIS* 4.2 24.2 - - + +
440G PHE* 3.4 48.7 - - + +
441G ILE* 3.0 14.2 + - + +
443G SER* 1.3 74.6 - - - +
445G VAL* 1.3 61.1 + - + +
447G LEU 4.6 0.2 - - - -
448G HIS* 3.9 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 445 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 3.7 16.2 - - + +
560F TRP* 3.6 27.6 - - + -
565F ALA* 3.6 34.5 - - + +
566F ASN 5.2 2.2 - - - +
567F VAL* 4.6 13.5 - - + -
441G ILE* 3.4 17.7 - - + +
442G PHE 3.0 6.3 + - - +
444G ILE* 1.3 82.8 - - + +
446G PHE* 1.3 60.2 + - - +
448G HIS 5.4 0.2 - - - -
449G MET* 3.3 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 446 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ARG* 3.6 65.3 + - + -
26D LEU* 4.9 6.3 - - + -
27D LEU* 5.2 4.0 - - + -
73D LEU* 3.9 15.5 - - + -
77D ILE* 3.4 34.5 - - + -
94D PHE* 3.6 38.1 - + + -
442G PHE* 2.8 45.6 + + + +
443G SER 3.0 2.6 + - - +
445G VAL* 1.3 80.0 - - - +
447G LEU* 1.3 67.4 + - + +
449G MET* 4.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ARG* 3.8 14.4 + - - +
91D GLU* 4.2 17.5 - - - +
94D PHE* 3.7 41.7 - - + -
569F ASN* 5.1 3.3 + - - +
579F PHE* 4.1 7.6 - - + -
580F HIS* 4.2 8.7 - - + +
620F MET* 3.6 32.5 - - + -
621F LEU* 4.6 1.3 - - + -
624F GLN* 3.7 25.0 - - + +
443G SER* 3.2 20.5 + - - +
446G PHE* 1.3 83.3 - - + +
448G HIS* 1.3 71.2 + - + +
449G MET 3.3 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 448 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566F ASN 3.2 5.3 - - - +
567F VAL* 3.5 18.0 - - + -
568F SER 3.2 20.8 + - - -
569F ASN* 2.3 39.9 + - - +
570F PHE* 3.7 28.0 - + - -
571F THR 5.7 0.7 - - - -
576F THR* 4.5 17.9 - - + -
580F HIS* 3.1 33.9 + + - -
620F MET* 5.0 2.9 - - - -
624F GLN* 4.5 17.2 + - - -
444G ILE* 3.9 17.2 + - - +
445G VAL 4.6 1.8 - - - -
447G LEU* 1.3 85.7 + - + +
449G MET* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il