Contacts of the helix formed by residues 2176 - 2186 (chain A) in PDB entry 4YNM
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 GLU2176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2174A VAL 3.8 0.6 + - - -
2175A SER* 1.3 68.8 - - - +
2177A GLN* 1.3 60.2 + - - +
2179A PHE* 3.3 6.6 + - - +
2180A ARG* 2.9 42.8 + - - +
2197A ASN* 5.1 2.9 - - - +
2201A GLY* 3.2 40.4 + - - +
2202A MET* 4.4 0.4 + - - +
2203A VAL* 4.3 6.6 - - + +
2260A PHE* 3.8 37.3 - - + -
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Residues in contact with GLN2177 (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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2175A SER* 3.3 9.6 + - - +
2176A GLU* 1.3 77.0 - - - +
2178A GLU* 1.3 62.5 + - - +
2180A ARG* 3.2 20.4 - - - +
2181A ASN* 3.0 43.3 + - - +
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Residues in contact with GLU2178 (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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2078A VAL* 4.8 7.1 - - + +
2079A ASP* 3.6 14.3 - - - +
2174A VAL* 3.6 27.4 - - + -
2175A SER* 3.2 20.9 + - - +
2177A GLN* 1.3 77.0 - - - +
2179A PHE* 1.3 57.4 + - - +
2181A ASN* 3.1 19.3 + - - +
2182A ARG* 2.8 60.9 + - - +
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Residues in contact with PHE2179 (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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2174A VAL* 3.9 10.3 - - + +
2175A SER 3.2 10.8 + - - +
2176A GLU* 3.7 8.5 - - - +
2178A GLU* 1.3 78.8 - - - +
2180A ARG* 1.3 59.9 + - - +
2182A ARG* 3.3 5.5 + - - +
2183A MET* 2.9 53.7 + - + +
2187A TYR* 4.1 6.5 - + - -
2195A CYS* 3.4 31.4 - - + -
2203A VAL* 4.1 10.5 - - + -
2205A ASP* 3.9 25.1 - - + -
2207A TYR* 3.8 20.2 - + - -
2260A PHE* 3.4 41.3 - + - -
2262A VAL* 4.2 7.0 - - + -
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Residues in contact with ARG2180 (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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2176A GLU* 2.9 24.2 + - - +
2177A GLN* 3.2 28.0 - - - +
2179A PHE* 1.3 79.5 - - - +
2181A ASN* 1.4 61.8 + - - +
2183A MET* 3.1 17.9 + - - +
2184A ILE* 3.2 25.6 + - + +
2260A PHE* 5.0 18.3 - - + -
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Residues in contact with ASN2181 (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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2177A GLN* 3.0 39.6 + - - +
2178A GLU* 3.4 19.8 + - - +
2180A ARG* 1.4 74.5 - - - +
2182A ARG* 1.3 57.4 + - + +
2184A ILE* 3.1 10.6 + - - +
2185A GLU* 2.7 50.7 + - - +
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Residues in contact with ARG2182 (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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2078A VAL* 4.0 11.7 - - - +
2172A GLU* 2.9 46.8 + - - +
2174A VAL* 3.8 17.1 - - - +
2178A GLU* 2.8 44.0 + - - +
2179A PHE* 3.6 10.8 - - - +
2181A ASN* 1.3 76.3 - - + +
2183A MET* 1.3 57.4 + - - +
2186A GLN* 2.7 47.4 + - + +
2187A TYR* 2.9 32.4 + - + +
2205A ASP* 2.9 29.8 + - - -
2208A ARG* 5.1 1.1 - - - +
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Residues in contact with MET2183 (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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2179A PHE* 2.9 39.2 + - + +
2180A ARG* 3.1 14.1 + - - +
2182A ARG* 1.3 77.6 - - - +
2184A ILE* 1.3 59.1 + - + +
2187A TYR* 3.9 19.5 - - + +
2188A HIS* 2.9 35.7 + - - +
2193A HIS* 3.8 12.6 - - + +
2207A TYR* 3.4 22.7 - - + +
2262A VAL* 2.6 48.2 - - + +
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Residues in contact with ILE2184 (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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2180A ARG* 3.4 21.5 - - + +
2181A ASN* 3.1 11.8 + - - +
2183A MET* 1.3 80.9 - - + +
2185A GLU* 1.3 67.8 + - + +
2186A GLN 3.6 0.2 + - - -
2188A HIS* 3.4 32.0 - - + -
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Residues in contact with GLU2185 (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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2181A ASN* 2.7 32.0 + - - +
2184A ILE* 1.3 80.3 - - + +
2186A GLN* 1.3 69.2 + - + +
2188A HIS* 5.8 0.7 - - - -
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Residues in contact with GLN2186 (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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2182A ARG* 2.7 35.7 + - - +
2184A ILE 3.5 0.4 - - - -
2185A GLU* 1.3 89.3 + - + +
2187A TYR* 1.3 79.5 + - + +
2188A HIS* 3.5 4.8 + - - -
2189A ASN* 5.1 2.6 + - - +
2190A HIS* 4.0 10.0 + - - -
2208A ARG* 4.0 24.6 + - - +
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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