Contacts of the helix formed by residues 2263 - 2278 (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 GLY2263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2098B GLU* 3.0 21.5 - - - -
2109B ARG* 4.3 1.1 - - - -
2110B PRO* 4.2 7.2 - - - -
2111B PHE 2.6 21.4 + - - -
2113B TYR* 3.9 10.1 - - - -
2261B ALA 4.0 0.4 + - - -
2262B LEU* 1.3 75.8 - - - +
2264B ALA* 1.3 67.6 + - - +
2265B GLU* 3.5 4.7 - - - -
2266B GLY* 3.0 11.1 + - - -
2267B VAL* 3.4 4.0 + - - +
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Residues in contact with ALA2264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2091B TYR* 3.2 25.4 - - + +
2094B VAL* 5.1 3.8 - - + -
2095B LEU* 3.6 27.6 - - + +
2098B GLU* 2.5 24.8 + - + +
2113B TYR* 5.0 1.8 - - - -
2263B GLY* 1.3 65.6 - - - -
2265B GLU* 1.3 62.6 + - - +
2266B GLY 2.6 14.5 + - - -
2267B VAL* 2.8 29.2 + - - +
2268B GLU* 3.1 2.8 + - - +
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Residues in contact with GLU2265 (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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2091B TYR* 2.9 16.7 + - + +
2109B ARG* 2.8 37.3 + - - +
2262B LEU 4.8 1.3 - - - +
2263B GLY* 4.2 4.2 - - - -
2264B ALA* 1.3 79.0 + - - +
2266B GLY* 1.3 63.7 + - - +
2268B GLU* 3.3 12.0 + - + +
2269B GLU* 2.9 34.7 + - - +
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Residues in contact with GLY2266 (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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2261B ALA* 3.7 7.5 - - - +
2262B LEU 3.2 30.0 + - - -
2263B GLY 3.0 4.2 + - - -
2264B ALA 2.6 7.3 + - - -
2265B GLU* 1.3 78.7 - - - +
2267B VAL* 1.3 59.2 + - - -
2269B GLU* 3.5 11.0 + - - +
2270B VAL* 3.6 15.6 + - - +
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Residues in contact with VAL2267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2091B TYR* 5.9 0.4 - - + -
2094B VAL* 3.8 27.1 - - + -
2113B TYR* 3.7 27.6 - - + -
2115B VAL* 3.3 30.9 - - + +
2261B ALA* 4.0 6.3 - - + -
2263B GLY 4.0 1.6 - - - +
2264B ALA* 2.8 15.8 + - - +
2266B GLY* 1.3 69.2 - - - -
2268B GLU* 1.3 63.3 + - + +
2269B GLU 3.0 2.7 - - - -
2270B VAL* 2.9 5.9 + - - +
2271B TYR* 2.6 38.5 + - + +
2288B VAL* 5.7 0.4 - - + -
2290B VAL* 4.0 15.7 - - + -
2314B TYR* 4.7 7.6 - - + -
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Residues in contact with GLU2268 (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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2091B TYR* 3.1 46.9 - - + +
2264B ALA 3.1 0.4 + - - -
2265B GLU* 3.4 12.6 - - + +
2267B VAL* 1.3 84.2 - - - +
2269B GLU* 1.3 56.2 + - - +
2271B TYR* 3.8 3.8 - - - -
2272B ARG* 2.8 78.2 + - - +
2314B TYR* 3.1 27.8 + - - -
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Residues in contact with GLU2269 (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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2265B GLU* 2.9 29.9 + - - +
2266B GLY* 3.7 9.4 - - - +
2267B VAL 3.0 0.8 - - - -
2268B GLU* 1.3 78.9 - - - +
2270B VAL* 1.3 66.6 + - + +
2271B TYR 3.1 1.1 - - - -
2272B ARG* 2.9 29.7 + - - +
2273B ARG* 3.0 32.8 + - - +
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Residues in contact with VAL2270 (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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2115B VAL* 4.0 21.8 - - + -
2259B GLU* 3.7 32.1 - - + +
2260B LYS 4.7 1.3 - - - +
2261B ALA* 3.9 18.2 - - + -
2266B GLY 3.6 14.8 - - - +
2267B VAL* 2.9 8.2 + - - +
2269B GLU* 1.3 77.8 - - + +
2271B TYR* 1.3 57.3 + - - +
2273B ARG* 3.8 11.4 - - - +
2274B PHE* 2.9 52.8 + - + +
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Residues in contact with TYR2271 (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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2089B PHE 4.8 3.5 + - - -
2267B VAL 2.6 20.8 + - - +
2268B GLU* 3.7 4.5 - - - +
2270B VAL* 1.3 68.4 - - - +
2272B ARG* 1.3 78.6 + - + +
2273B ARG 2.9 3.1 - - - -
2274B PHE* 2.8 8.5 + - - +
2275B LEU* 2.7 48.6 + - + +
2288B VAL* 3.8 22.9 - - + +
2314B TYR* 3.3 69.7 - + + -
2315B LYS 2.7 22.5 + - - -
2316B PHE* 3.4 30.1 - + - -
2317B PRO* 3.8 8.3 - - - +
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Residues in contact with ARG2272 (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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2268B GLU* 2.8 49.8 + - - +
2269B GLU* 2.9 31.0 + - - +
2271B TYR* 1.3 92.3 - - + +
2273B ARG* 1.3 56.6 + - - +
2275B LEU* 3.9 10.8 - - + +
2276B ALA* 3.2 25.5 + - - +
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Residues in contact with ARG2273 (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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2259B GLU* 2.5 43.0 + - - -
2269B GLU* 3.0 24.1 + - - +
2270B VAL* 3.8 18.5 - - - +
2271B TYR 2.8 1.0 + - - -
2272B ARG* 1.3 74.7 - - - +
2274B PHE* 1.3 77.7 + - - +
2276B ALA* 3.4 5.2 + - + +
2277B GLN* 3.3 41.9 + - + +
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Residues in contact with PHE2274 (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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2115B VAL 4.3 8.1 - - - -
2116B GLU 4.4 2.7 - - - -
2117B HIS* 3.2 51.5 + + + +
2257B GLY* 4.1 21.8 - - - -
2258B TYR 4.3 1.3 - - - -
2259B GLU* 3.9 22.7 - - - -
2270B VAL* 2.9 29.9 + - + +
2271B TYR 2.8 3.7 + - - +
2273B ARG* 1.3 87.7 - - - +
2275B LEU* 1.3 62.3 + - - +
2277B GLN* 3.0 19.3 + - + +
2278B ARG* 2.8 28.4 + - - +
2281B LEU* 5.4 0.2 - - - +
2288B VAL* 3.7 20.9 - - + -
2316B PHE* 4.3 4.5 - - + -
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Residues in contact with LEU2275 (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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2271B TYR* 2.7 29.3 + - + +
2272B ARG* 3.9 10.5 - - + +
2274B PHE* 1.3 78.0 - - - +
2276B ALA* 1.3 63.3 + - - +
2277B GLN 3.1 0.9 + - - -
2278B ARG* 3.3 31.8 + - - +
2279B HIS* 5.1 5.4 + - - +
2316B PHE* 3.4 37.3 - - + -
2317B PRO* 3.8 27.8 - - + -
2350B GLU* 5.4 4.0 - - - +
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Residues in contact with ALA2276 (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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2272B ARG 3.2 18.4 + - - +
2273B ARG* 3.6 8.3 - - - +
2274B PHE 3.2 0.2 - - - -
2275B LEU* 1.3 80.3 - - - +
2277B GLN* 1.3 61.1 + - + +
2279B HIS* 5.4 5.1 + - - +
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Residues in contact with GLN2277 (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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2273B ARG* 3.3 32.4 + - + +
2274B PHE* 3.0 23.6 + - + +
2276B ALA* 1.3 84.8 - - + +
2278B ARG* 1.3 66.6 + - - +
2279B HIS* 3.2 3.4 - - - -
2280B ALA* 2.6 28.8 + - + +
2281B LEU* 3.7 12.3 + - + +
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Residues in contact with ARG2278 (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 ILE* 5.8 1.6 - - - +
2274B PHE 2.8 11.3 + - - +
2275B LEU* 3.3 29.1 + - - +
2277B GLN* 1.3 71.5 - - - +
2279B HIS* 1.3 71.1 + - + +
2280B ALA 2.5 14.4 + - - -
2281B LEU* 2.8 33.5 + - + +
2283B PHE 4.7 2.3 - - - +
2284B GLU* 4.8 8.6 - - - +
2285B ALA* 3.4 28.7 + - - +
2286B ASP* 3.9 19.0 + - - +
2316B PHE* 3.9 30.3 - - + +
2317B PRO* 5.1 9.3 + - - +
2318B ALA* 5.5 6.5 - - - +
2350B GLU* 3.7 22.8 + - - -
2382B GLY 5.8 0.2 - - - -
2383B GLY* 4.5 17.3 - - - -
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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