Contacts of the helix formed by residues 1670 - 1675 (chain X) in PDB entry 3HM6
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 LYS1670 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1666X GLN* 3.3 35.1 + - - +
1667X TYR* 3.1 44.9 + - + +
1668X VAL 4.1 2.8 - - - +
1669X ALA* 1.3 82.7 - - + +
1671X ASN* 1.3 62.4 + - - +
1672X PRO* 3.6 6.9 - - - +
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Residues in contact with ASN1671 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1667X TYR* 3.4 7.7 - - - -
1670X LYS* 1.3 79.7 - - - +
1672X PRO* 1.4 62.1 - - - +
1673X LYS* 3.0 34.1 + - - +
1674X LEU* 2.9 52.6 + - + +
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Residues in contact with PRO1672 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1667X TYR* 3.0 31.1 - - + +
1668X VAL* 4.2 14.8 - - + +
1670X LYS 3.6 6.5 - - - +
1671X ASN* 1.4 86.3 - - - +
1673X LYS* 1.3 58.6 + - + +
1674X LEU 3.1 2.3 + - - -
1675X MET* 3.4 8.0 - - - +
1967X ILE* 4.8 10.5 - - + -
1972X THR* 3.9 20.4 - - + +
1976X TRP* 2.8 38.2 + - + -
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Residues in contact with LYS1673 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1671X ASN* 2.9 24.2 + - - +
1672X PRO* 1.3 76.5 - - + +
1674X LEU* 1.3 63.1 + - + +
1675X MET 3.4 2.2 - - - +
1677X ARG* 5.8 0.2 - - - +
1969X ASP* 2.7 30.4 + - - -
1971X ASP* 4.4 10.1 - - - -
1972X THR* 3.1 16.4 + - - +
1975X ILE* 3.4 51.1 - - + +
1979X ASN* 4.8 1.0 + - - -
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Residues in contact with LEU1674 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1667X TYR* 3.7 17.2 + - + -
1671X ASN* 2.9 37.7 + - + +
1673X LYS* 1.3 84.7 - - + +
1675X MET* 1.3 63.6 + - - +
1676X LEU 3.7 0.3 + - - -
1677X ARG* 3.5 24.4 + - + +
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Residues in contact with MET1675 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660X LEU* 4.5 7.0 - - + -
1663X LEU* 3.8 16.6 - - + -
1664X VAL* 3.8 39.3 - - + -
1667X TYR* 3.7 35.5 - - + -
1672X PRO 3.4 15.0 + - - +
1673X LYS 3.4 2.0 - - - -
1674X LEU* 1.3 76.8 - - - +
1676X LEU* 1.3 88.4 + - + +
1958X LEU* 4.6 1.1 - - + -
1975X ILE* 4.7 0.5 - - - +
1976X TRP* 3.6 45.9 - - + +
1979X ASN* 3.0 23.6 + - - +
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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