Contacts of the helix formed by residues 2199 - 2209 (chain B) in PDB entry 1V9P
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 ASN2199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2120B ASP* 5.6 2.5 - - - +
2182B PHE* 3.2 10.2 - - - -
2197B PHE* 3.2 2.5 - - - +
2198B LYS* 1.3 90.3 + - - +
2200B PRO* 1.3 77.1 - - + +
2201B ARG* 3.3 11.3 + - + +
2202B ASN* 2.5 38.2 + - - +
2203B ALA* 3.0 16.3 + - - +
2284B GLU* 5.2 4.3 - - - +
2381B ALA* 5.4 0.7 - - + -
2382B GLY 5.7 1.1 - - - +
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Residues in contact with PRO2200 (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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2120B ASP* 3.7 25.4 - - + +
2177B MET* 3.6 24.8 - - + +
2179B ILE* 5.3 3.6 - - + -
2182B PHE* 3.5 42.4 - - + -
2199B ASN* 1.3 87.1 - - + +
2201B ARG* 1.3 53.1 + - - +
2203B ALA* 3.4 1.6 - - + +
2204B ALA* 2.6 38.0 + - - +
2284B GLU* 3.9 22.7 - - + +
2382B GLY* 4.6 2.9 - - - +
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Residues in contact with ARG2201 (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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2120B ASP* 4.2 13.8 - - + +
2121B GLY* 2.8 46.8 + - - +
2122B LEU* 4.4 3.2 - - - +
2123B SER* 4.2 16.8 + - - +
2139B ARG* 6.0 3.4 - - - +
2199B ASN* 3.0 13.2 + - - +
2200B PRO* 1.3 79.5 - - - +
2202B ASN* 1.3 61.7 + - - +
2204B ALA* 3.3 3.2 - - - +
2205B ALA* 2.8 31.1 + - + +
2700B AMP 4.4 27.9 + - - -
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Residues in contact with ASN2202 (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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2197B PHE* 3.7 16.6 - - + -
2198B LYS* 4.9 4.2 + - - +
2199B ASN* 2.5 42.1 + - - +
2201B ARG* 1.3 78.7 - - - +
2203B ALA* 1.3 55.4 + - - +
2205B ALA* 3.0 6.9 + - - +
2206B GLY* 2.4 37.2 + - - -
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Residues in contact with ALA2203 (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 MET* 4.0 15.5 - - - -
2182B PHE* 3.9 19.1 - - + -
2185B LEU* 4.4 0.7 - - + -
2197B PHE* 3.4 34.5 - - + -
2199B ASN 3.0 11.6 + - - +
2200B PRO* 3.4 7.9 - - + +
2202B ASN* 1.3 76.4 - - - +
2204B ALA* 1.3 52.2 + - - +
2206B GLY 3.4 0.2 - - - -
2207B SER* 2.5 41.5 + - - -
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Residues in contact with ALA2204 (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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2120B ASP 5.4 0.2 - - - +
2121B GLY 4.6 0.7 - - - +
2122B LEU* 3.7 23.8 - - + -
2176B TYR* 4.1 6.5 - - - -
2177B MET* 4.1 20.8 - - - +
2200B PRO 2.6 21.3 + - - +
2201B ARG* 3.3 6.3 - - - +
2203B ALA* 1.3 72.6 - - - +
2205B ALA* 1.3 52.1 - - - +
2207B SER* 2.9 2.9 + - - -
2208B LEU* 2.4 38.3 + - - +
2221B LEU* 4.0 14.1 - - + +
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Residues in contact with ALA2205 (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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2122B LEU* 3.6 25.0 - - + +
2201B ARG* 2.8 19.1 + - + +
2202B ASN* 3.4 10.3 - - - +
2204B ALA* 1.3 71.0 - - - +
2206B GLY* 1.3 57.6 + - - +
2208B LEU* 3.0 1.3 + - - -
2209B ARG* 2.7 61.3 + - - +
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Residues in contact with GLY2206 (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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2197B PHE* 3.9 19.3 - - - -
2202B ASN 2.4 21.0 + - - -
2203B ALA 3.5 1.1 - - - -
2205B ALA* 1.3 72.5 - - - +
2207B SER* 1.3 56.0 + - - +
2209B ARG* 3.2 16.7 - - - +
2210B GLN* 2.9 20.0 - - - +
2219B ARG* 4.7 0.4 - - - -
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Residues in contact with SER2207 (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 MET* 3.3 18.4 - - - +
2185B LEU* 3.5 0.9 - - - +
2203B ALA 2.5 24.3 + - - -
2204B ALA* 3.4 3.1 - - - -
2206B GLY* 1.3 71.1 - - - +
2208B LEU* 1.3 62.0 + - - +
2210B GLN* 2.9 23.6 - - - +
2216B THR* 3.3 12.5 + - - -
2219B ARG* 2.6 47.8 + - - +
2221B LEU* 4.0 9.6 - - - -
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Residues in contact with LEU2208 (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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2122B LEU* 2.8 48.9 - - + -
2124B VAL* 3.9 17.5 - - + -
2138B THR* 3.9 17.7 - - + -
2148B VAL* 3.5 27.1 - - + +
2151B ASN* 2.3 42.3 - - + +
2152B LEU* 4.2 15.0 - - + +
2155B ILE* 5.9 0.7 - - + -
2175B VAL* 4.8 3.1 - - + -
2204B ALA 2.4 17.5 + - - +
2205B ALA* 3.5 3.1 - - - +
2207B SER* 1.3 73.8 - - - +
2209B ARG* 1.3 56.9 + - + +
2216B THR* 4.8 0.7 - - - -
2221B LEU* 3.9 14.5 - - + +
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Residues in contact with ARG2209 (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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2073B PHE* 3.3 26.9 - - + -
2122B LEU* 5.6 5.3 - - - +
2138B THR* 5.0 20.5 + - + +
2140B GLY* 5.7 5.5 - - - +
2146B GLU* 4.2 22.0 + - - +
2205B ALA* 2.7 40.3 + - - +
2206B GLY* 3.2 10.1 - - - +
2208B LEU* 1.3 76.0 - - + +
2210B GLN* 1.3 68.1 + - - +
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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