Contacts of the helix formed by residues 479 - 495 (chain I) in PDB entry 6GYS
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 SER 479 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428I LEU* 6.1 0.9 - - - +
432I ILE* 5.6 1.4 - - - +
473I TYR* 4.7 1.8 - - - -
474I GLN* 3.9 3.0 + - - +
477I VAL* 2.9 25.3 + - - -
478I GLU* 1.3 74.2 - - - +
480I ALA* 1.3 68.8 + - - +
481I ALA* 3.6 10.4 + - - +
482I VAL* 3.7 24.3 + - - +
483I LYS* 3.0 29.9 + - - +
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Residues in contact with ALA 480 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478I GLU 4.2 0.2 + - - -
479I SER* 1.3 75.6 + - - +
481I ALA* 1.3 60.6 + - - +
483I LYS* 3.2 7.7 + - - +
484I GLN* 2.9 28.4 + - - +
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Residues in contact with ALA 481 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429I LEU* 5.7 2.7 - - + -
432I ILE* 3.8 36.7 - - + +
436I LYS* 4.2 6.3 + - - +
479I SER* 3.5 5.5 + - - +
480I ALA* 1.3 76.0 - - - +
482I VAL* 1.3 59.9 + - - +
484I GLN* 3.4 7.0 + - - +
485I LEU* 2.9 30.8 + - - +
80K PRO* 6.2 3.8 - - + -
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Residues in contact with VAL 482 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428I LEU* 5.4 1.8 - - + -
432I ILE* 4.6 17.5 - - + -
470I ILE* 3.3 39.2 - - + +
473I TYR* 3.6 26.0 - - + -
474I GLN* 3.2 26.5 - - + +
479I SER* 3.7 21.7 + - - +
480I ALA 3.3 0.6 - - - -
481I ALA* 1.3 76.4 - - - +
483I LYS* 1.3 56.5 + - - +
485I LEU* 3.7 6.8 - - - +
486I LEU* 2.8 29.6 + - - +
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Residues in contact with LYS 483 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474I GLN* 3.1 14.0 - - - +
479I SER 3.0 19.3 + - - +
480I ALA* 3.5 6.7 - - - +
481I ALA 3.2 0.2 - - - -
482I VAL* 1.3 75.3 - - - +
484I GLN* 1.3 59.1 + - - +
486I LEU* 3.1 9.3 + - + +
487I VAL* 3.0 38.4 + - + +
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Residues in contact with GLN 484 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I LYS* 3.7 17.1 + - - +
480I ALA 2.9 16.3 + - - +
481I ALA* 3.7 8.1 - - - +
483I LYS* 1.3 77.0 - - - +
485I LEU* 1.3 61.0 + - - +
487I VAL* 3.6 20.5 + - - +
488I ASP* 3.6 11.9 + - - +
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Residues in contact with LEU 485 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432I ILE* 4.7 14.8 - - + +
435I SER* 3.7 18.6 - - - -
436I LYS* 3.6 29.3 - - + +
439I ILE* 3.8 28.7 - - + -
470I ILE* 3.7 34.8 - - + -
481I ALA 2.9 18.3 + - - +
482I VAL* 3.9 4.7 - - - +
484I GLN* 1.3 74.1 - - - +
486I LEU* 1.3 59.7 + - - +
488I ASP* 3.2 7.8 + - + +
489I LEU* 2.8 39.9 + - + +
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Residues in contact with LEU 486 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467I VAL* 6.0 0.2 - - + -
470I ILE* 4.5 1.5 - - + +
471I SER* 3.4 35.4 - - - +
474I GLN* 3.6 26.9 - - + +
482I VAL 2.8 18.9 + - - +
483I LYS* 3.1 11.2 + - + +
485I LEU* 1.3 74.8 - - - +
487I VAL* 1.3 60.0 + - - +
489I LEU* 3.3 18.5 - - + +
490I THR* 3.0 39.7 + - - +
511I THR* 6.1 2.7 - - + -
518I LYS* 5.6 3.4 - - + -
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Residues in contact with VAL 487 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483I LYS* 3.0 22.2 + - + +
484I GLN* 3.7 19.1 - - - +
485I LEU 3.2 0.2 - - - -
486I LEU* 1.3 76.3 - - + +
488I ASP* 1.3 58.4 + - - +
490I THR* 3.2 6.9 + - - -
491I GLU* 3.0 31.6 + - + +
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Residues in contact with ASP 488 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I LYS* 6.0 0.9 - - - +
439I ILE* 3.1 32.2 - - + +
443I VAL* 5.0 8.2 - - - +
484I GLN* 3.6 8.1 + - - +
485I LEU* 3.2 14.7 + - + +
487I VAL* 1.3 77.4 - - + +
489I LEU* 1.3 59.0 + - - +
491I GLU* 3.9 21.8 - - - +
492I LEU* 2.8 35.5 + - - +
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Residues in contact with LEU 489 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439I ILE* 4.2 5.8 - - + -
463I ILE* 6.3 1.3 - - + -
466I VAL* 3.8 22.4 - - + -
467I VAL* 3.7 36.1 - - + -
470I ILE* 3.7 26.7 - - + -
471I SER* 3.9 2.2 - - - +
485I LEU* 2.8 41.8 + - + +
486I LEU* 3.3 26.7 - - + +
488I ASP* 1.3 77.4 - - - +
490I THR* 1.3 53.8 + - - +
492I LEU* 3.8 2.7 - - - +
493I THR* 2.4 40.6 + - - -
511I THR* 5.9 0.7 - - + -
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Residues in contact with THR 490 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486I LEU* 3.0 23.8 + - - +
487I VAL* 3.8 5.8 - - - -
489I LEU* 1.3 75.9 - - - +
491I GLU* 1.3 62.1 + - - +
493I THR* 4.0 6.4 - - - -
494I ALA* 3.6 17.7 + - - +
511I THR* 5.0 14.2 - - + +
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Residues in contact with GLU 491 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446I PHE* 6.6 0.7 - - - -
487I VAL* 3.0 21.4 + - + +
488I ASP* 3.7 21.4 - - - +
489I LEU 3.2 0.2 - - - -
490I THR* 1.3 78.9 - - - +
492I LEU* 1.3 59.3 + - - +
494I ALA* 3.4 5.8 + - - +
495I ASN* 2.9 49.2 + - - +
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Residues in contact with LEU 492 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439I ILE* 3.7 31.4 - - + +
442I ILE* 3.8 32.3 - - + -
443I VAL* 5.0 1.1 - - + -
446I PHE* 4.1 17.7 - - + -
463I ILE* 3.9 31.0 - - + -
488I ASP* 2.8 26.0 + - - +
489I LEU* 4.3 2.0 - - - +
491I GLU* 1.3 71.5 - - - +
493I THR* 1.3 60.2 + - - +
494I ALA 3.3 0.2 - - - -
495I ASN* 3.2 9.5 - - - +
496I LEU* 3.0 52.0 + - + +
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Residues in contact with THR 493 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463I ILE* 5.1 5.5 - - - +
467I VAL* 4.0 14.9 - - - +
489I LEU 2.4 29.3 + - - -
490I THR* 4.0 7.7 - - - -
491I GLU 3.3 0.2 - - - -
492I LEU* 1.3 78.9 - - - +
494I ALA* 1.3 60.7 - - - +
496I LEU* 3.8 7.8 + - - +
504I LEU* 3.8 21.1 - - - +
507I LEU* 4.6 12.3 - - + +
508I VAL* 3.8 30.5 - - + +
511I THR* 3.8 22.5 + - + +
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Residues in contact with ALA 494 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490I THR 3.6 8.9 + - - +
491I GLU* 3.4 8.4 + - - +
493I THR* 1.3 79.7 - - - +
495I ASN* 1.3 64.7 + - - +
496I LEU 3.3 9.1 + - - +
504I LEU* 5.7 2.1 - - - +
508I VAL* 5.2 3.6 - - - +
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Residues in contact with ASN 495 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446I PHE* 3.9 34.6 - - + -
491I GLU* 2.9 46.2 + - - +
492I LEU* 3.1 13.1 + - - +
494I ALA* 1.3 82.6 - - - +
496I LEU* 1.3 63.1 + - - +
497I PRO* 4.1 2.1 - - - +
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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
------------------------------------------------------------
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