Contacts of the helix formed by residues 2176 - 2186 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2174B VAL 3.9 0.4 + - - -
2175B SER* 1.3 72.9 - - - +
2177B GLN* 1.3 56.6 + - - +
2179B PHE* 3.8 6.1 - - - +
2180B ARG* 2.9 42.7 + - - +
2197B ASN* 5.3 1.7 - - - +
2201B GLY* 3.2 41.4 + - - +
2202B MET* 4.3 0.9 + - - +
2203B VAL* 4.3 4.0 - - + -
2260B PHE* 3.5 42.2 - - + -
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Residues in contact with GLN2177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2175B SER* 3.2 8.5 + - - +
2176B GLU* 1.3 76.7 - - - +
2178B GLU* 1.3 57.6 + - - +
2180B ARG* 3.3 20.5 - - - +
2181B ASN* 3.0 63.5 + - - +
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Residues in contact with GLU2178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2078B VAL* 4.7 8.6 - - + +
2079B ASP* 3.6 15.2 + - - +
2174B VAL* 3.6 28.5 - - + -
2175B SER* 3.1 22.6 + - - +
2177B GLN* 1.3 76.5 - - - +
2179B PHE* 1.3 61.8 + - - +
2181B ASN* 3.1 18.2 + - - +
2182B ARG* 2.8 58.3 + - - +
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Residues in contact with PHE2179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2174B VAL* 3.7 10.7 - - + +
2175B SER 2.9 16.2 + - - +
2176B GLU* 3.9 4.0 - - - +
2178B GLU* 1.3 74.5 - - - +
2180B ARG* 1.3 57.9 - - - +
2182B ARG* 3.3 6.2 + - - +
2183B MET* 2.8 51.7 + - + +
2187B TYR* 4.0 8.1 - + - -
2195B CYS* 3.7 27.8 - - + -
2203B VAL* 4.0 17.5 - - + -
2205B ASP* 4.0 24.0 - - + -
2207B TYR* 4.0 18.2 - + - -
2260B PHE* 3.8 25.8 - + - -
2262B VAL* 3.6 26.0 - - + -
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Residues in contact with ARG2180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2176B GLU* 2.9 28.3 + - - +
2177B GLN* 3.3 24.5 - - - +
2179B PHE* 1.3 76.7 - - - +
2181B ASN* 1.3 65.1 + - - +
2183B MET* 3.3 8.8 + - + +
2184B ILE* 3.1 39.6 + - + +
2260B PHE* 5.9 6.1 - - - -
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Residues in contact with ASN2181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2177B GLN* 3.0 49.1 + - - +
2178B GLU* 3.1 17.8 + - - +
2180B ARG* 1.3 74.7 - - - +
2182B ARG* 1.3 59.4 + - + +
2184B ILE* 3.3 9.4 + - - +
2185B GLU* 2.8 42.1 + - - +
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Residues in contact with ARG2182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2078B VAL* 4.0 16.0 - - - +
2172B GLU* 3.0 44.0 + - - +
2174B VAL* 3.9 8.8 - - - +
2178B GLU* 2.8 45.8 + - - +
2179B PHE* 3.5 10.1 - - - +
2181B ASN* 1.3 73.1 - - + +
2183B MET* 1.3 60.9 + - - +
2186B GLN* 2.8 52.9 + - - +
2187B TYR* 3.0 30.4 + - + +
2205B ASP* 2.8 36.8 + - - -
2208B ARG* 5.1 1.0 - - - +
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Residues in contact with MET2183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2179B PHE* 2.8 40.0 + - + +
2180B ARG* 3.3 13.0 + - + +
2182B ARG* 1.3 73.7 - - - +
2184B ILE* 1.3 60.3 + - + +
2187B TYR* 3.9 17.2 - - - +
2188B HIS* 3.0 33.8 + - - +
2193B HIS* 4.3 14.4 - - + +
2207B TYR* 3.6 25.1 - - - +
2262B VAL* 3.2 49.1 - - + -
2264B LYS* 5.3 5.6 - - + -
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Residues in contact with ILE2184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2180B ARG* 3.1 28.4 + - + +
2181B ASN* 3.7 9.4 - - - +
2182B ARG 3.1 0.6 - - - -
2183B MET* 1.3 81.3 - - + +
2185B GLU* 1.3 66.5 - - + +
2188B HIS* 3.1 32.2 - - + -
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Residues in contact with GLU2185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2181B ASN* 2.8 23.8 + - - +
2182B ARG* 5.0 0.2 - - - -
2184B ILE* 1.3 86.6 - - + +
2186B GLN* 1.3 70.8 + - + +
2188B HIS* 5.0 4.1 - - - -
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Residues in contact with GLN2186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2182B ARG* 2.8 41.6 + - - +
2185B GLU* 1.3 88.5 + - + +
2187B TYR* 1.3 76.0 + - + +
2188B HIS* 3.5 2.9 + - - -
2189B ASN* 4.8 5.4 - - - +
2190B HIS* 3.7 13.9 + - - -
2208B ARG* 4.0 28.4 + - - +
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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