Contacts of the helix formed by residues 1639 - 1645 (chain A) in PDB entry 4C6P
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 ALA1639 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1614A HIS* 4.5 15.0 - - + +
1638A VAL* 1.3 87.2 - - - +
1640A PRO* 1.3 71.0 - - + +
1641A HIS* 3.3 31.9 - - + +
1642A HIS* 3.0 22.5 + - - +
1643A LEU* 3.6 4.5 + - - +
1684A ALA 3.2 13.9 - - - +
1685A SER 3.8 3.1 - - - +
1686A ASP* 4.7 1.6 - - + -
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Residues in contact with PRO1640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1638A VAL 4.5 0.9 - - - +
1639A ALA* 1.3 88.1 - - + +
1641A HIS* 1.3 63.9 + - - +
1643A LEU* 3.0 8.2 + - + +
1644A PHE* 3.0 40.8 + - + +
1683A PHE* 5.9 1.1 - - + -
1684A ALA 3.6 10.1 - - - +
1685A SER* 3.8 13.7 - - - +
1706A GLY* 5.3 3.4 - - - +
1710A MET* 3.5 37.9 - - + +
1713A LEU* 4.2 22.7 - - + -
1714A LEU* 5.3 3.1 - - + -
1774A PHE* 4.2 5.6 - - + -
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Residues in contact with HIS1641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1614A HIS* 5.7 0.4 - - - +
1639A ALA* 3.4 12.7 - - + +
1640A PRO* 1.3 80.7 - - - +
1642A HIS* 1.3 94.1 + + - +
1645A LEU* 3.1 35.2 + - + +
1660A VAL* 3.8 14.9 - - + +
1661A ARG 5.6 0.2 + - - -
1664A LEU* 3.8 5.3 - - + +
1685A SER 3.4 25.3 + - - -
1686A ASP* 4.4 14.8 + - + +
1704A PHE* 3.5 46.2 - + + +
1706A GLY* 6.3 1.0 - - - -
1774A PHE* 3.7 22.4 - - + -
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Residues in contact with HIS1642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1614A HIS* 4.6 5.3 - - + +
1615A VAL 4.3 6.1 + - - +
1616A ALA* 3.5 31.1 - - + +
1638A VAL* 4.4 0.4 - - + -
1639A ALA* 3.0 17.3 + - - +
1641A HIS* 1.3 108.3 + + - +
1643A LEU* 1.3 61.2 + - - +
1645A LEU 4.4 3.8 - - - -
1662A PRO* 2.9 41.3 + - + -
1663A GLU 3.3 13.6 + - - -
1664A LEU* 4.3 11.1 + - + +
1665A GLY 4.6 4.5 - - - +
1670A VAL* 3.5 18.7 - - - +
1673A LEU* 3.4 29.4 - - + +
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Residues in contact with LEU1643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1638A VAL* 3.7 20.0 - - + -
1639A ALA 4.0 4.3 - - - +
1640A PRO* 3.0 10.2 + - + +
1642A HIS* 1.3 79.9 - - - +
1644A PHE* 1.3 71.0 + - + +
1645A LEU 3.8 0.4 - - - -
1670A VAL* 3.4 13.0 - - - +
1673A LEU* 3.9 29.4 - - + -
1674A TRP* 3.0 55.6 + - + +
1677A MET* 4.8 4.7 - - + -
1680A ILE* 4.9 1.3 - - + -
1683A PHE* 3.7 31.2 - - + -
1714A LEU* 4.4 13.2 - - + -
1722A ARG* 4.6 2.3 + - - -
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Residues in contact with PHE1644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1640A PRO* 3.0 30.0 + - + +
1643A LEU* 1.3 88.7 - - + +
1645A LEU* 1.3 61.8 + - - +
1649A ASP* 4.3 1.6 - - - +
1670A VAL* 5.4 0.9 - - - -
1674A TRP* 3.8 25.1 - + - -
1713A LEU* 3.4 50.7 - - + -
1714A LEU* 3.9 23.1 - - + -
1716A THR* 6.0 0.9 - - - -
1717A ALA* 4.1 7.4 - - + -
1722A ARG* 3.9 15.7 - - - -
1774A PHE* 4.2 12.3 - - + -
1777A GLN* 3.2 28.2 + - - +
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Residues in contact with LEU1645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641A HIS* 3.1 33.3 + - + +
1642A HIS* 4.4 1.2 - - - -
1643A LEU 3.8 0.2 - - - -
1644A PHE* 1.3 76.9 - - - +
1646A SER* 1.3 64.3 + - - +
1649A ASP* 3.3 16.8 - - + +
1652A ARG* 3.5 22.9 - - - +
1653A LEU* 4.7 4.7 - - + -
1664A LEU* 3.9 14.2 - - + +
1665A GLY 4.9 1.9 + - - -
1670A VAL* 3.4 16.0 - - - +
1704A PHE* 4.3 6.5 - - + -
1773A PRO* 4.0 22.9 - - + +
1774A PHE* 3.6 26.9 - - + -
1777A GLN* 3.4 24.7 - - - +
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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