Contacts of the helix formed by residues 161 - 165 (chain 1) in PDB entry 6Q8W
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 ASN 161 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1561 GLY 5.5 1.6 - - - +
1591 GLY* 4.9 0.9 - - - -
1601 LYS* 1.3 96.6 + - - +
1621 LEU* 1.3 65.9 + - - +
1631 PHE 3.5 2.9 + - - -
1641 GLY* 4.0 13.3 + - - +
1651 THR 3.2 17.3 - - - +
1661 ASP* 3.7 15.1 - - - +
1671 PHE 3.4 4.3 - - - -
1681 SER* 5.2 0.6 + - - -
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Residues in contact with LEU 162 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451 LEU* 3.9 26.9 - - + -
1191 ILE* 4.3 14.6 - - + -
1561 GLY 4.7 4.5 - - - +
1571 TYR 3.3 29.4 - - - +
1581 LEU* 3.8 1.6 - - - -
1591 GLY* 3.3 31.4 - - - +
1611 ASN* 1.3 68.1 - - - +
1631 PHE* 1.3 75.8 + - + +
1641 GLY 3.2 1.3 - - - -
1651 THR* 3.1 25.1 + - + +
1671 PHE* 3.2 26.1 + - + +
1691 PHE* 3.8 26.0 - - + +
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Residues in contact with PHE 163 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381 TYR* 5.1 4.5 - + - -
411 ALA* 3.9 9.0 - - + -
421 LYS* 3.7 49.8 - - + -
451 LEU* 3.4 37.5 - - + -
461 LYS* 3.5 37.2 + - + +
1191 ILE* 5.6 3.6 - - + -
1561 GLY 4.8 12.1 + - - -
1571 TYR* 4.3 37.2 - + - -
1611 ASN 3.5 3.0 + - - -
1621 LEU* 1.3 73.0 - - + +
1641 GLY* 1.3 55.9 + - - +
1651 THR* 3.2 5.2 + - + -
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Residues in contact with GLY 164 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1611 ASN* 4.0 14.4 + - - +
1621 LEU 3.2 1.2 - - - -
1631 PHE* 1.3 75.0 - - - +
1651 THR* 1.3 63.3 + - - +
1661 ASP* 3.9 0.3 + - - -
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Residues in contact with THR 165 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451 LEU* 4.2 30.8 + - + +
461 LYS* 5.4 7.8 - - - -
1231 TYR* 6.1 1.7 - - + -
1611 ASN* 3.2 20.6 - - - +
1621 LEU* 3.1 23.5 + - + +
1631 PHE 3.2 5.0 + - - -
1641 GLY* 1.3 81.1 - - - +
1661 ASP* 1.3 70.4 + - - +
1671 PHE* 3.1 27.2 + - + +
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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