Contacts of the helix formed by residues 430 - 449 (chain A) in PDB entry 6NFJ
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 THR 430 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A VAL* 5.0 0.2 - - - +
428A GLU* 2.9 15.5 + - - +
429A ASP* 1.3 70.9 - - - +
431A THR* 1.3 69.8 + - + +
432A ALA 3.2 0.2 - - - -
433A ILE* 3.2 13.8 + - - +
434A TYR* 3.3 21.1 - - + -
750A ALA* 4.2 8.5 - - + +
751A ASN* 3.8 13.7 + - + +
757A HIS* 3.2 32.8 + - + -
832A MET* 4.0 15.7 - - + +
850A LEU* 3.8 25.6 - - + -
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Residues in contact with THR 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A PHE 4.6 1.0 + - - -
421A THR* 4.2 16.3 - - - +
430A THR* 1.3 80.2 - - + +
432A ALA* 1.3 57.7 + - - +
434A TYR* 3.0 8.4 + - - +
435A MET* 2.6 47.9 + - - +
850A LEU* 5.2 3.6 - - + -
197C MET* 4.2 31.9 + - + +
198C ASP* 4.8 11.9 - - + -
202C LEU* 5.8 6.1 - - + -
203C VAL* 4.7 19.1 - - + -
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Residues in contact with ALA 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A THR* 4.7 8.5 - - + -
429A ASP* 3.9 24.1 + - + -
430A THR 3.2 0.4 - - - -
431A THR* 1.3 81.0 + - - +
433A ILE* 1.3 58.0 + - - +
435A MET* 4.1 7.1 - - - +
436A MET* 3.0 33.3 + - + +
478A LEU* 5.7 2.9 - - + -
495A SER* 4.0 19.1 - - - +
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ASP 3.9 10.8 - - - +
430A THR 3.2 7.4 + - - +
431A THR 3.1 0.6 - - - -
432A ALA* 1.3 78.5 - - - +
434A TYR* 1.3 71.1 + - + +
436A MET 3.8 0.2 - - - -
437A LYS* 2.9 28.8 + - + +
494A SER* 3.8 27.6 - - - +
495A SER* 4.4 2.5 - - - -
498A TYR* 3.8 40.8 - - + -
750A ALA 5.1 1.3 - - - +
751A ASN* 3.2 38.6 - - + +
752A PRO* 4.8 3.6 - - + -
753A TYR* 3.9 11.0 - - + -
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Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A THR* 3.3 19.1 - - + -
431A THR* 3.0 5.6 + - - +
433A ILE* 1.3 86.7 - - + +
435A MET* 1.3 64.8 + - - +
437A LYS* 3.7 8.4 - - + +
438A ASN* 3.1 31.2 + - - +
749A PRO 4.4 2.1 + - - -
750A ALA* 2.4 42.3 + - - -
752A PRO* 5.4 1.2 - - - +
830A PHE* 4.6 12.8 - + - -
850A LEU* 3.6 40.6 - - + +
852A ASP* 3.1 33.4 - - + +
853A ILE* 6.3 0.2 - - + -
855A ARG* 6.3 0.2 - - - -
202C LEU* 4.0 19.3 - - + -
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Residues in contact with MET 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 4.4 3.6 - - + -
419A TRP* 4.1 33.0 - - + +
431A THR* 2.6 35.9 + - - +
432A ALA* 4.1 7.0 - - - +
434A TYR* 1.3 74.2 - - - +
436A MET* 1.3 60.9 + - - +
437A LYS 3.5 0.2 + - - -
438A ASN* 3.5 13.4 + - - +
439A PHE* 3.3 43.8 + - + -
197C MET 4.7 3.4 - - - +
198C ASP* 5.4 1.1 - - - +
199C PRO* 4.0 20.0 - - + -
200C PHE* 3.8 37.9 - - + -
202C LEU* 4.9 8.3 - - - -
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Residues in contact with MET 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A ALA* 3.0 18.7 + - + +
433A ILE* 3.9 2.9 - - - +
435A MET* 1.3 74.3 - - - +
437A LYS* 1.3 63.9 + - - +
439A PHE* 3.5 8.6 + - - +
440A LEU* 3.2 39.5 + - + +
457A TYR* 4.1 15.0 - - - +
459A ALA* 5.1 4.3 - - + -
478A LEU* 4.1 37.0 - - + -
495A SER* 4.3 11.7 - - - +
498A TYR* 4.3 12.3 - - + -
499A TYR* 3.9 37.9 - - + -
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Residues in contact with LYS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A ILE* 2.9 19.8 + - + +
434A TYR* 3.7 13.0 - - + +
435A MET 3.2 0.4 - - - -
436A MET* 1.3 79.7 - - - +
438A ASN* 1.3 57.5 + - - +
440A LEU* 4.1 3.3 - - - +
441A SER* 3.1 28.9 + - - -
498A TYR* 3.9 22.2 - - + +
852A ASP* 5.1 2.2 - - - +
854A THR* 4.0 17.8 + - + +
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Residues in contact with ASN 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A TYR 3.1 18.0 + - - +
435A MET* 3.9 9.3 - - + +
436A MET 3.3 0.2 - - - -
437A LYS* 1.3 75.6 - - - +
439A PHE* 1.3 60.4 + - + +
441A SER* 3.1 5.3 + - - -
442A GLN* 2.7 51.5 + - - +
852A ASP* 4.7 0.5 - - - +
853A ILE* 3.3 34.1 - - - +
854A THR* 2.7 31.4 + - - -
200C PHE* 4.5 20.5 - - + -
202C LEU* 5.1 1.6 - - - +
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Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A PHE* 4.5 10.8 - + - -
394A LEU* 3.9 27.1 - - + -
396A LEU* 4.4 10.3 - - + +
417A ASN* 3.1 44.0 - - - +
418A GLY* 3.9 23.1 - - - -
419A TRP* 4.4 11.4 - + - -
435A MET* 3.3 41.9 + - + -
436A MET* 3.5 9.0 + - - +
438A ASN* 1.3 79.5 - - + +
440A LEU* 1.3 51.9 + - - +
442A GLN* 2.9 17.4 + - - +
443A VAL* 2.6 41.5 + - - +
457A TYR* 4.6 4.3 - - + +
200C PHE* 5.9 2.2 - + - -
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.4 16.4 - - + -
87A TRP* 3.6 24.2 - - + -
436A MET* 3.2 37.3 + - + +
437A LYS* 4.4 2.5 - - - +
439A PHE* 1.3 76.7 - - - +
441A SER* 1.3 57.7 + - - +
443A VAL* 4.2 5.2 - - + -
444A LEU* 2.9 30.1 + - - +
457A TYR* 3.6 34.5 - - + -
498A TYR* 5.5 1.6 - - + -
499A TYR* 4.8 2.2 - - + -
502A ILE* 3.7 39.5 - - + -
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Residues in contact with SER 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A LYS 3.1 22.5 + - - -
438A ASN* 3.3 7.9 - - - -
440A LEU* 1.3 78.9 - - - +
442A GLN* 1.3 57.7 + - - +
444A LEU* 3.9 7.2 - - - +
445A GLN* 3.0 42.4 + - - +
854A THR* 4.8 16.0 - - - +
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Residues in contact with GLN 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A LEU 3.8 5.3 + - - +
395A ASN* 3.2 31.6 - - - +
396A LEU* 2.8 33.5 + - + +
397A ARG* 3.7 23.3 - - + +
438A ASN* 2.7 30.1 + - - +
439A PHE* 3.5 13.4 - - - +
441A SER* 1.3 72.8 - - - +
443A VAL* 1.3 60.0 + - - +
445A GLN* 3.4 17.5 + - - +
446A ALA* 2.9 27.7 + - - +
200C PHE* 6.1 2.4 - - - -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.9 10.3 - - + -
85A PHE* 4.7 5.4 - - + -
396A LEU* 3.7 13.7 - - + -
400A LEU* 5.0 3.1 - - + -
414A ILE* 3.6 27.8 - - + -
439A PHE 2.6 25.9 + - - +
440A LEU* 3.9 9.4 - - + +
442A GLN* 1.3 70.1 - - - +
444A LEU* 1.3 60.4 + - - +
446A ALA* 3.1 7.3 + - - +
447A ILE* 2.9 51.9 + - + +
454A VAL* 4.5 15.7 - - + -
457A TYR* 4.6 13.5 - - + -
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASP* 3.7 35.2 - - + +
80A THR 3.5 33.7 - - - +
81A PHE* 3.6 26.9 - - + +
82A PRO* 5.4 0.7 - - + -
440A LEU 2.9 18.7 + - - +
441A SER* 3.9 6.7 - - - +
443A VAL* 1.3 76.7 - - - +
445A GLN* 1.3 64.9 + - + +
447A ILE* 3.8 3.3 - - + +
448A ARG* 2.9 43.7 + - + +
449A LEU* 5.9 1.6 - - + -
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Residues in contact with GLN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ASN* 5.9 0.2 + - - -
397A ARG* 3.9 36.5 - - - +
441A SER* 3.0 34.4 + - - +
442A GLN* 3.4 23.5 - - - +
443A VAL 3.3 0.2 - - - -
444A LEU* 1.3 76.9 - - + +
446A ALA* 1.3 62.6 + - - +
449A LEU* 3.0 31.8 + - + +
450A ASP* 3.0 18.5 + - - +
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ARG* 4.5 11.0 - - + +
400A LEU* 4.1 19.5 - - + -
442A GLN 2.9 14.5 + - - +
443A VAL 3.1 8.5 + - - +
445A GLN* 1.3 76.0 - - - +
447A ILE* 1.3 58.7 + - + +
450A ASP* 3.2 12.1 - - + -
451A GLU 2.9 12.8 + - - -
452A ILE* 2.8 44.7 + - + +
454A VAL* 5.3 0.2 - - + -
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Residues in contact with ILE 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 4.1 13.2 - - + -
82A PRO* 3.5 29.8 - - + -
85A PHE* 3.5 31.4 - - + -
443A VAL* 2.9 35.2 + - + +
444A LEU* 3.1 4.0 + - - +
446A ALA* 1.3 81.1 - - - +
448A ARG* 1.3 71.1 + - + +
451A GLU* 3.3 16.6 + - - +
452A ILE 3.8 20.7 + - - +
454A VAL* 4.1 16.2 - - + +
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASP* 6.0 1.8 - - - -
80A THR* 2.9 27.9 + - - +
81A PHE 3.4 2.8 + - - -
82A PRO* 3.3 38.4 - - - +
83A LYS 4.7 0.6 - - - +
444A LEU* 2.9 34.7 + - + +
447A ILE* 1.3 81.6 - - + +
449A LEU* 1.3 71.8 + - + +
451A GLU* 4.9 4.9 + - - +
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ARG* 4.1 22.4 - - - +
444A LEU* 5.0 2.2 - - + -
445A GLN* 3.0 39.3 + - + +
448A ARG* 1.3 93.7 - - + +
450A ASP* 1.3 63.4 + - - +
451A GLU* 3.3 8.3 + - - +
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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
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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) + - + + + + + -
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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