Contacts of the helix formed by residues 1638 - 1642 (chain A) in PDB entry 5ZCS
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 MET1638 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490A TRP* 3.6 52.3 - - + +
1518A ALA* 4.9 0.9 - - + +
1521A TRP* 3.5 39.8 - - + -
1522A GLY* 4.5 14.4 - - - -
1634A GLN* 3.0 37.3 + - + +
1635A LYS* 4.7 4.4 - - - +
1637A LEU* 1.3 76.9 - - - +
1639A VAL* 1.3 63.9 + - + +
1640A ARG 3.2 1.6 + - - -
1641A SER* 3.6 16.2 + - - -
1642A LEU* 4.7 2.3 + - - +
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Residues in contact with VAL1639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521A TRP* 3.6 25.1 - - + -
1545A PHE* 4.1 27.1 - - + -
1549A VAL* 5.9 2.0 - - + -
1595A MET* 5.6 2.0 - - + +
1598A GLU* 3.5 43.5 - - + +
1599A LEU* 5.6 9.4 - - + +
1635A LYS 4.5 10.5 - - - +
1636A ILE 4.5 5.8 - - - +
1638A MET* 1.3 77.8 - - + +
1640A ARG* 1.3 62.0 + - + +
1641A SER 3.4 0.8 + - - -
1642A LEU* 4.0 18.4 + - + +
1643A VAL* 5.3 1.0 + - - +
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Residues in contact with ARG1640 (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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1598A GLU* 2.8 31.8 + - + +
1619A TRP* 3.7 48.0 + - + +
1620A TRP* 6.3 0.2 - - - -
1622A ARG* 4.5 5.5 - - - +
1623A LEU* 3.5 32.7 - - - +
1636A ILE* 3.6 16.0 + - - +
1637A LEU* 3.8 29.5 + - + +
1638A MET 3.2 1.2 - - - -
1639A VAL* 1.3 76.5 - - + +
1641A SER* 1.3 54.5 + - - +
1642A LEU 3.2 6.3 - - - -
1643A VAL* 4.6 1.5 - - - +
1644A VAL* 2.9 42.3 + - + +
1649A ASP* 5.3 4.3 + - - -
1652A THR* 4.5 13.3 - - - +
1653A TRP* 6.4 1.1 - - + -
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Residues in contact with SER1641 (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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1637A LEU 3.7 12.1 + - - -
1638A MET* 3.6 12.0 + - - -
1639A VAL 3.4 1.4 - - - -
1640A ARG* 1.3 76.3 - - - +
1642A LEU* 1.3 64.5 + - - +
1644A VAL 3.8 11.8 - - - +
1645A SER* 5.8 0.5 - - - -
1646A PRO* 4.9 12.8 - - - +
1653A TRP* 4.9 9.9 - - - -
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Residues in contact with LEU1642 (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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1521A TRP* 3.4 51.6 - - + +
1524A GLY* 6.4 1.3 - - - -
1526A TRP* 3.7 20.0 - - + +
1549A VAL* 4.3 8.5 - - + -
1552A LEU* 4.1 30.1 - - + -
1638A MET 4.8 1.6 - - - +
1639A VAL* 4.0 15.5 - - + +
1640A ARG 3.2 1.6 - - - -
1641A SER* 1.3 81.4 - - - +
1643A VAL* 1.3 63.3 + - + +
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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