Contacts of the helix formed by residues 492 - 496 (chain D) in PDB entry 3HN3
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 GLY 492 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454D SER* 3.9 3.4 + - - -
460D GLY* 4.2 3.9 - - - -
463D LEU* 4.2 14.6 - - - -
467D ILE* 4.8 0.5 - - - +
481D PHE* 3.5 25.6 - - - -
490D ASP* 2.9 7.5 + - - -
491D LYS* 1.3 77.0 - - - +
493D ALA* 1.3 63.3 + - - +
494D PRO* 3.3 4.3 - - - -
495D TYR* 3.1 25.5 + - - +
496D VAL* 3.9 2.4 + - - +
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Residues in contact with ALA 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481D PHE* 4.5 4.3 - - - -
490D ASP* 3.1 25.4 + - + +
492D GLY* 1.3 77.6 - - - +
494D PRO* 1.3 63.3 - - - +
495D TYR 3.0 1.2 + - - -
496D VAL* 3.4 15.8 - - + +
499D ILE* 5.0 1.7 - - + +
528D TRP* 3.8 12.3 - - + -
532D TYR* 3.4 35.8 - - + +
534D LYS* 2.9 16.6 + - - -
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Residues in contact with PRO 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D ASP 3.8 1.3 - - - +
491D LYS* 3.6 16.4 - - - +
492D GLY 3.3 5.2 - - - -
493D ALA* 1.3 91.3 - - - +
495D TYR* 1.3 74.5 + - + +
496D VAL 4.2 0.2 - - - +
532D TYR* 3.5 31.4 - - + +
534D LYS* 3.1 13.6 + - - +
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Residues in contact with TYR 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D GLY 4.1 4.7 - - - -
464D LYS* 3.3 56.3 - - + +
467D ILE* 3.6 32.9 - - + +
471D LYS* 4.2 10.2 + - - -
491D LYS 3.6 20.6 - - - -
492D GLY* 3.1 19.0 + - - +
493D ALA 3.0 0.2 + - - -
494D PRO* 1.3 90.9 - - + +
496D VAL* 1.3 64.3 + - - +
497D ASP* 3.9 1.0 + - - +
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Residues in contact with VAL 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D ILE* 4.0 6.3 - - + -
479D VAL 3.7 3.8 - - - -
480D THR* 3.8 5.8 - - - +
481D PHE* 3.3 54.3 - - + +
492D GLY 4.0 1.6 - - - +
493D ALA* 3.4 15.9 - - - +
494D PRO 4.2 0.3 - - - +
495D TYR* 1.3 78.1 - - - +
497D ASP* 1.3 60.3 + - - +
498D VAL 3.4 28.3 - - - +
499D ILE* 3.9 17.0 - - + -
500D CYS 5.4 0.2 - - - +
534D LYS* 2.8 28.0 + - - +
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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
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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