Contacts of the helix formed by residues 474 - 481 (chain I) in PDB entry 5A31
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 ARG 474 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341I TYR* 4.5 0.2 + - - -
406I VAL* 4.2 26.2 - - + +
409I SER* 3.0 23.2 + - - -
410I SER* 3.8 26.5 + - - +
413I ASN* 3.4 26.6 - - - +
414I PHE* 5.6 2.2 - - - -
451I PHE* 5.7 0.4 - - - -
455I HIS* 3.7 30.0 - - - -
471I ASN* 3.3 29.2 - - - +
472I VAL* 4.4 4.9 - - - +
473I GLU* 1.3 79.1 - - - +
475I VAL* 1.3 59.4 + - - +
476I GLY 3.2 0.7 - - - -
477I GLN* 2.9 41.9 + - - +
478I TYR* 4.3 2.6 - - - -
488I SER* 6.1 2.0 - - - +
490I PRO* 6.2 2.1 - - + +
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Residues in contact with VAL 475 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I TRP* 4.0 11.7 - - + -
341I TYR* 3.2 46.9 - - + +
344I ILE* 4.1 8.7 - - + -
403I LEU* 4.5 1.7 - - + +
406I VAL* 4.0 8.9 - - - +
407I ILE* 3.8 42.2 - - + +
410I SER* 3.9 9.6 - - - -
474I ARG* 1.3 77.1 - - - +
476I GLY* 1.3 61.7 + - - +
478I TYR* 3.3 23.3 + - - +
479I LEU* 3.5 12.7 + - + +
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Residues in contact with GLY 476 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I TRP* 2.9 40.8 - - - +
473I GLU 3.0 11.3 + - - -
475I VAL* 1.3 74.6 - - - +
477I GLN* 1.3 64.7 + - - -
478I TYR 3.1 2.0 + - - -
479I LEU 3.2 0.4 + - - -
480I LYS* 2.9 29.1 + - - +
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Residues in contact with GLN 477 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406I VAL* 6.0 0.4 - - - +
471I ASN* 5.7 5.0 + - - +
473I GLU 4.3 2.0 + - - -
474I ARG* 2.9 40.1 + - - +
476I GLY* 1.3 72.3 - - - +
478I TYR* 1.3 82.2 + - - +
480I LYS* 4.0 6.6 + - - +
481I ASP 4.2 7.3 + - - +
486I LEU* 3.0 35.1 + - - +
487I VAL* 4.3 20.0 - - + -
488I SER* 3.4 23.2 + - - +
489I PRO 5.4 0.2 - - - -
490I PRO* 4.7 13.1 - - - +
521I SER* 4.3 11.4 + - - -
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Residues in contact with TYR 478 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I LYS* 3.1 40.0 + - + -
402I GLU* 3.8 13.3 - - + +
403I LEU* 3.7 36.3 - - + -
406I VAL* 4.0 26.8 - - + +
474I ARG 4.3 8.5 - - - -
475I VAL 3.3 9.8 + - - +
476I GLY 3.1 0.8 - - - -
477I GLN* 1.3 99.5 - - - +
479I LEU* 1.3 63.4 + - + +
480I LYS 3.5 0.3 + - - -
481I ASP 3.8 5.9 + - - -
486I LEU* 5.7 1.1 - - + -
490I PRO* 3.7 21.1 - - + +
520I LYS 4.4 3.1 - - - -
521I SER* 4.3 5.0 - - - -
522I LEU* 3.8 44.9 + - + +
523I HIS* 4.1 4.9 + - - -
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Residues in contact with LEU 479 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I LEU* 4.2 14.4 - - + +
272I MET* 3.6 41.5 - - + +
273I CYS* 4.1 18.2 - - - +
276I TRP* 4.6 15.7 - - + -
344I ILE* 3.6 41.3 - - + -
403I LEU* 4.6 13.2 - - + -
475I VAL* 3.5 16.5 + - + +
476I GLY 3.2 3.3 + - - +
478I TYR* 1.3 78.6 - - + +
480I LYS* 1.3 64.0 + - - +
481I ASP 3.4 0.6 + - - -
522I LEU* 4.2 10.5 - - + -
523I HIS* 3.6 17.2 - - + -
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Residues in contact with LYS 480 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273I CYS* 6.4 0.4 - - - -
276I TRP* 4.0 26.4 - - + -
476I GLY 2.9 19.1 + - - +
477I GLN* 4.4 4.5 - - - +
478I TYR 3.4 0.2 - - - -
479I LEU* 1.3 76.6 - - - +
481I ASP* 1.3 75.9 + - - +
482I GLU* 5.2 0.2 - - - +
523I HIS* 5.0 0.3 - - - -
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Residues in contact with ASP 481 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477I GLN 4.2 5.9 + - - +
478I TYR 3.8 7.2 + - - -
479I LEU 3.4 3.4 - - - -
480I LYS* 1.3 89.9 - - - +
482I GLU* 1.3 78.1 + - - +
483I ASP* 5.1 0.2 - - - +
521I SER* 5.1 3.8 - - - -
523I HIS* 3.3 46.2 - - + +
527I ARG* 4.2 6.3 - - - +
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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