Contacts of the helix formed by residues 455 - 471 (chain B) in PDB entry 6T2C
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 PHE 455 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLU* 4.5 14.1 - - + -
298B LEU* 4.3 9.0 - - - +
454B HIS* 1.3 92.2 + - + +
456B LYS* 1.3 66.3 + - - +
457B GLU* 3.4 19.1 - - + +
458B ASP* 3.3 20.6 + - - +
459B ILE* 3.4 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 5.4 15.4 - - - +
259A SER* 5.0 12.9 - - - -
672A ASP* 3.5 25.4 + - - +
673A PRO 5.8 0.6 + - - -
298B LEU* 4.3 11.3 - - + +
300B TYR* 4.2 26.0 - - + +
455B PHE* 1.3 74.5 - - - +
457B GLU* 1.3 60.5 + - - +
459B ILE* 3.1 11.8 + - + +
460B GLN* 3.0 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B PHE* 4.2 16.6 - - + +
456B LYS* 1.3 79.1 - - - +
458B ASP* 1.3 70.4 + - - +
460B GLN* 3.3 9.0 + - + +
461B GLN* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B THR* 3.8 42.0 + - - +
436B TYR* 3.7 13.1 - - - +
453B GLY* 4.7 0.7 - - - -
454B HIS* 3.6 16.1 + - - +
455B PHE* 3.3 37.2 + - - +
456B LYS 3.2 0.8 - - - -
457B GLU* 1.3 87.3 - - - +
459B ILE* 1.3 59.7 + - - +
461B GLN* 3.4 8.7 + - - +
462B GLY* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 5.5 2.7 - - + -
298B LEU* 4.3 7.2 - - + +
300B TYR* 3.9 40.8 - - + -
436B TYR* 5.6 0.2 - - + -
451B ILE* 3.6 30.7 - - + +
452B ASN 3.8 2.5 - - - -
453B GLY* 3.4 32.5 - - - +
455B PHE 3.4 15.0 - - - +
456B LYS* 3.1 14.5 + - + +
458B ASP* 1.3 77.0 - - - +
460B GLN* 1.3 56.0 + - - +
462B GLY* 3.3 1.6 + - - +
463B VAL* 3.0 31.0 + - + +
484B ILE* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA 3.2 12.4 + - - +
256A GLN* 2.9 26.7 - - - +
257A ILE* 3.4 30.9 + - + +
456B LYS* 3.0 12.9 + - + +
457B GLU* 3.6 12.1 - - - +
458B ASP 3.3 0.4 - - - -
459B ILE* 1.3 77.7 - - - +
461B GLN* 1.3 60.2 + - + +
463B VAL* 3.3 6.3 + - - +
464B ASN* 3.0 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ARG* 5.3 5.4 + - - -
435B THR* 5.7 0.9 + - - -
436B TYR* 4.2 17.7 + - + -
457B GLU* 2.9 31.2 + - - +
458B ASP* 3.9 9.8 + - - +
460B GLN* 1.3 78.7 - - + +
462B GLY* 1.3 59.0 + - - +
464B ASN* 3.4 11.6 + - - +
465B HIS* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B TYR* 3.7 30.2 - - - -
438B TRP* 3.4 15.1 - - - -
451B ILE* 4.9 7.0 - - - -
458B ASP 2.9 13.2 + - - -
459B ILE 3.7 3.1 - - - -
460B GLN 3.2 0.2 - - - -
461B GLN* 1.3 76.2 - - - +
463B VAL* 1.3 58.7 + - - +
465B HIS 3.3 0.3 + - - -
466B PHE* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA* 3.8 30.5 - - + +
257A ILE* 4.8 4.3 - - + -
676A PHE* 4.2 7.4 - - + -
302B ILE* 3.8 23.1 - - + -
451B ILE* 3.7 25.1 - - + -
459B ILE* 3.0 22.7 + - + +
460B GLN* 3.3 8.7 + - - +
462B GLY* 1.3 74.6 - - - +
464B ASN* 1.3 58.5 + - - +
466B PHE* 3.4 8.4 + - + +
467B TYR* 2.9 28.2 + - - +
477B MET* 5.2 2.9 - - + -
484B ILE* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 5.8 1.0 + - - -
254A ASN* 3.3 24.9 - - + +
255A ALA 3.1 24.5 + - - +
256A GLN* 4.8 2.0 - - - +
460B GLN* 3.0 40.4 + - - +
461B GLN* 3.6 14.1 - - - +
462B GLY 3.3 0.2 - - - -
463B VAL* 1.3 77.7 - - - +
465B HIS* 1.3 57.1 + - - +
467B TYR* 4.0 3.4 - - - +
468B ARG* 2.9 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 5.6 0.4 - - + -
243A GLU* 4.3 15.8 + - - -
246A LEU* 3.5 24.4 - - + +
426B LEU* 4.4 11.7 - - + -
432B LEU* 4.0 24.5 - - + +
434B ARG* 4.7 12.6 + - - +
436B TYR* 3.8 24.0 - + + +
438B TRP* 3.3 20.8 - + + -
461B GLN 2.9 17.2 + - - +
462B GLY 3.7 4.5 - - - +
463B VAL 3.3 0.4 - - - -
464B ASN* 1.3 76.9 - - - +
466B PHE* 1.3 55.5 + - - +
468B ARG* 3.9 6.3 - - - +
469B THR* 2.6 49.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ILE* 5.8 1.3 - - + -
423B VAL* 3.8 23.1 - - + -
424B LEU* 4.0 22.2 - - + -
438B TRP* 3.7 30.9 - + + -
442B GLN* 5.7 2.7 - - - -
447B PHE* 3.7 40.4 - + - -
449B LEU* 3.6 25.6 - - + -
462B GLY 3.0 17.4 + - - +
463B VAL* 3.7 6.7 - - + +
465B HIS* 1.3 77.4 - - - +
467B TYR* 1.3 61.0 + - - +
469B THR* 3.3 3.4 + - - -
470B CYS* 2.9 48.5 + - - +
477B MET* 4.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL* 4.1 9.2 - - + -
254A ASN* 3.6 20.4 - - - -
255A ALA* 3.5 28.7 - - + -
77B ASN* 3.0 39.0 + - - +
463B VAL 2.9 17.5 + - - +
464B ASN 4.0 2.2 - - - +
466B PHE* 1.3 81.2 - - + +
468B ARG* 1.3 59.3 + - - +
470B CYS* 3.3 6.1 + - + +
471B LYS* 3.0 53.6 + - + +
475B ILE 5.8 0.2 - - - -
477B MET* 3.8 50.7 + - + -
479B GLN* 4.0 10.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.1 58.1 + - + +
247A GLY 5.7 0.2 - - - -
249A MET* 3.4 52.8 + - + +
250A SER 3.6 9.3 + - - -
251A GLU* 3.2 28.6 + - - +
253A VAL* 3.3 28.8 + - + +
254A ASN* 5.1 1.5 - - - +
464B ASN* 2.9 29.2 + - - +
465B HIS* 4.1 4.9 - - - +
467B TYR* 1.3 74.8 - - - +
469B THR* 1.3 64.9 + - - +
471B LYS* 3.3 12.0 + - - -
472B LEU* 3.5 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 4.4 11.4 - - + -
246A LEU* 3.6 19.1 - - - +
91B LEU* 4.8 12.3 - - + -
423B VAL* 4.3 15.3 - - + -
426B LEU* 3.7 25.9 - - + +
438B TRP* 5.8 1.1 - - - -
465B HIS* 2.6 32.9 + - - -
466B PHE* 3.7 6.1 - - - -
468B ARG* 1.3 73.0 - - - +
470B CYS* 1.3 65.6 + - - +
472B LEU* 3.1 21.0 + - + +
473B VAL* 3.9 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B VAL* 3.8 16.6 - - - -
466B PHE* 2.9 48.8 + - - +
467B TYR* 3.6 10.1 - - + +
469B THR* 1.3 75.9 - - - +
471B LYS* 1.3 61.7 + - - +
472B LEU 3.2 1.0 + - - -
473B VAL* 3.3 11.9 + - - +
475B ILE* 2.8 59.9 + - + +
477B MET* 5.4 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A MET* 4.3 13.2 - - + -
253A VAL* 3.8 23.3 - - + -
74B PRO* 4.6 15.1 - - + +
76B ASP 4.7 3.8 - - - -
77B ASN 4.3 2.0 + - - -
78B GLU 3.2 25.4 + - - -
79B PRO* 3.9 1.8 - - - +
80B SER* 4.2 13.7 + - - +
82B TYR 4.0 11.4 - - - +
467B TYR* 3.0 49.1 + - + +
468B ARG* 3.6 10.5 - - - +
469B THR 3.2 0.4 - - - -
470B CYS* 1.3 76.0 - - - +
472B LEU* 1.3 62.3 + - - +
473B VAL 3.3 0.4 + - - -
474B GLY* 4.0 6.6 + - - +
475B ILE 4.1 4.0 - - - +
476B ASN* 2.6 34.3 + - - +
477B MET 5.9 0.2 + - - -
----------------------------------------------------------
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