Contacts of the helix formed by residues 1496 - 1505 (chain D) in PDB entry 6AH0
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 ASN1496 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1494D LEU* 4.4 0.2 - - - +
1495D SER* 1.3 74.8 - - - +
1497D ALA* 1.3 63.7 + - - +
1498D LYS 3.0 3.6 - - - -
1499D ASP* 2.8 19.5 + - - -
1500D VAL 3.7 3.3 + - - -
1722D LEU 4.3 2.6 + - - -
1723D PRO* 4.9 6.3 - - - +
1724D VAL 5.5 2.2 - - - +
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Residues in contact with ALA1497 (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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1494D LEU* 3.5 15.5 + - - +
1495D SER 3.3 5.7 + - - -
1496D ASN* 1.3 75.8 - - - +
1498D LYS* 1.3 62.6 + - - +
1500D VAL* 3.2 4.7 + - - +
1501D ALA* 2.9 21.8 + - - -
1513D ASN* 6.5 1.3 - - - +
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Residues in contact with LYS1498 (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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1495D SER 5.0 1.0 + - - -
1496D ASN 2.9 3.4 + - - -
1497D ALA* 1.3 76.8 - - - +
1499D ASP* 1.3 55.5 + - - +
1501D ALA* 3.4 1.5 + - - +
1502D HIS* 2.9 25.8 + - - -
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Residues in contact with ASP1499 (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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1496D ASN 2.8 15.8 + - - -
1498D LYS* 1.3 71.2 - - - +
1500D VAL* 1.3 62.5 + - - +
1502D HIS* 3.1 2.9 + - - +
1503D TRP* 2.9 21.5 + - - -
1762D ARG* 6.1 5.0 - - - +
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Residues in contact with VAL1500 (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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1496D ASN 3.7 4.9 + - - -
1497D ALA* 3.2 7.5 + - - +
1499D ASP* 1.3 75.0 - - - +
1501D ALA* 1.3 56.7 + - - +
1503D TRP* 3.3 1.5 + - - +
1504D LEU* 2.9 25.8 + - - -
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Residues in contact with ALA1501 (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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1347D PHE* 6.2 4.5 - - - +
1497D ALA 2.9 14.2 + - - -
1498D LYS* 3.8 2.9 - - - +
1500D VAL* 1.3 75.5 - - - +
1502D HIS* 1.3 52.0 + - - +
1504D LEU* 3.2 1.5 + - - +
1505D GLY 2.7 31.2 + - - -
1506D CYS* 2.9 22.3 + - - +
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Residues in contact with HIS1502 (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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1498D LYS 2.9 15.3 + - - -
1499D ASP* 3.1 3.8 + - - +
1501D ALA* 1.3 75.8 - - - +
1503D TRP* 1.3 62.1 + - - +
1505D GLY* 3.5 8.2 + - - -
1506D CYS 4.7 4.7 + - - -
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Residues in contact with TRP1503 (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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1499D ASP 2.9 13.2 + - - -
1500D VAL* 3.7 3.6 - - - +
1502D HIS* 1.3 79.1 - - - +
1504D LEU* 1.3 55.5 + - - +
1505D GLY* 3.2 4.0 + - - -
1757D TRP 5.3 5.2 - - - +
1758D THR 5.5 7.4 - - - -
1759D PHE* 6.0 4.3 - - - +
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Residues in contact with LEU1504 (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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1345D ASN* 5.8 1.4 - - - -
1487D ILE* 5.4 7.3 - - - +
1500D VAL 2.9 14.5 + - - -
1501D ALA* 3.5 3.1 - - - +
1503D TRP* 1.3 74.5 - - - +
1505D GLY* 1.3 63.0 + - - +
1506D CYS 3.6 0.7 - - - -
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Residues in contact with GLY1505 (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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1345D ASN* 4.6 11.9 + - - -
1501D ALA 2.7 7.5 + - - -
1502D HIS* 3.5 7.2 + - - -
1503D TRP 3.2 5.8 + - - -
1504D LEU* 1.3 81.2 - - - +
1506D CYS* 1.3 57.8 + - - -
1507D SER 4.2 0.5 + - - -
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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