Contacts of the helix formed by residues 2188 - 2205 (chain B) in PDB entry 2H7C
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 ASN2188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2176B GLY 3.9 6.7 + - - -
2177B PHE* 3.9 13.1 + - - +
2187B GLY* 1.3 72.8 - - - +
2189B TRP* 1.3 64.6 + - - +
2190B GLY 3.1 2.7 - - - -
2191B HIS* 3.1 26.5 + - + -
2192B LEU* 3.1 14.6 + - + +
2320B GLY 4.0 1.8 + - - +
2321B THR* 3.2 14.6 - - - +
2322B VAL* 2.7 48.1 + - - +
2324B ASP* 3.3 28.0 + - - +
2327B LEU* 3.9 15.9 - - + +
2328B LEU 5.1 0.2 - - - +
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Residues in contact with TRP2189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2065B PHE* 3.1 40.7 - + - +
2066B THR* 3.5 27.8 - - - -
2067B PRO* 3.8 13.9 - - + -
2171B ARG* 3.7 20.3 + - - +
2175B TRP 3.5 20.2 - - - +
2176B GLY* 2.8 15.9 + - - +
2177B PHE* 4.1 1.6 - - - -
2178B PHE 3.2 21.7 + - - -
2184B HIS 5.6 0.2 - - - -
2185B SER* 3.4 17.1 + - - -
2186B ARG* 3.7 15.7 - - + -
2187B GLY* 3.2 33.5 - - - -
2188B ASN* 1.3 73.1 - - - +
2190B GLY* 1.3 57.4 + - - +
2192B LEU* 3.2 14.8 + - + +
2193B ASP* 2.9 35.8 + - - +
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Residues in contact with GLY2190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2170B TYR* 3.3 8.3 - - - +
2171B ARG 3.5 25.1 - - - -
2176B GLY* 2.8 10.7 + - - -
2177B PHE* 3.7 11.2 - - - -
2188B ASN 3.1 0.4 - - - -
2189B TRP* 1.3 78.0 - - - +
2191B HIS* 1.3 60.1 + - - +
2193B ASP* 3.3 7.6 + - - -
2194B GLN* 3.2 26.8 + - - +
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Residues in contact with HIS2191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2144B LEU* 4.5 2.6 - - + +
2177B PHE* 3.6 27.8 - + - -
2188B ASN* 3.1 21.9 + - - +
2190B GLY* 1.3 73.3 - - - +
2192B LEU* 1.3 66.1 + - - +
2193B ASP 3.1 1.6 - - - -
2194B GLN* 3.0 27.7 + - - +
2195B VAL* 3.0 26.8 + - - +
2225B GLU* 3.6 13.7 - - - -
2226B SER* 3.5 26.5 + - - -
2229B VAL* 4.5 7.6 - - + +
2230B LEU* 4.4 3.1 - - + +
2321B THR* 2.8 26.4 + - + +
2327B LEU* 3.3 32.8 - - + -
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Residues in contact with LEU2192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2067B PRO* 4.0 30.3 - - + -
2068B PRO* 3.5 21.1 - - + +
2187B GLY 4.6 3.8 - - - +
2188B ASN* 3.1 16.4 + - + +
2189B TRP* 3.2 28.2 + - + +
2191B HIS* 1.3 76.8 - - - +
2193B ASP* 1.3 56.7 + - - +
2195B VAL* 3.4 9.3 + - + +
2196B ALA* 3.0 21.5 + - - +
2235B LEU* 3.8 29.4 - - + -
2324B ASP* 5.3 3.6 - - - +
2326B MET* 5.6 4.7 - - + -
2327B LEU* 4.5 15.7 - - + +
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Residues in contact with ASP2193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2055B PHE* 3.2 14.2 - - + -
2068B PRO* 3.4 16.2 - - - +
2117B LEU* 3.7 15.6 - - + +
2170B TYR* 3.8 13.7 - - + -
2171B ARG* 2.7 64.6 + - - +
2189B TRP 2.9 18.5 + - - +
2190B GLY* 3.4 7.6 - - - +
2191B HIS 3.1 0.2 - - - -
2192B LEU* 1.3 76.2 - - - +
2194B GLN* 1.3 60.0 + - - +
2196B ALA* 3.2 1.6 + - - -
2197B ALA* 2.9 24.8 + - - +
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Residues in contact with GLN2194 (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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2139B ILE* 3.5 15.9 - - + +
2168B ILE* 4.1 21.1 - - + +
2170B TYR* 3.6 35.5 - - + -
2190B GLY 3.3 12.1 - - - +
2191B HIS* 3.0 31.4 + - - +
2193B ASP* 1.3 76.2 - - - +
2195B VAL* 1.3 63.7 + - - +
2197B ALA* 3.2 3.5 + - - +
2198B LEU* 3.0 28.7 + - - +
2226B SER* 3.1 33.1 + - - -
2230B LEU* 4.3 19.2 - - + +
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Residues in contact with VAL2195 (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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2191B HIS 3.0 17.4 + - - +
2192B LEU* 3.6 12.6 - - + +
2194B GLN* 1.3 77.2 - - - +
2196B ALA* 1.3 56.1 + - - +
2198B LEU* 3.1 7.9 + - - +
2199B ARG* 2.9 52.2 + - - +
2230B LEU* 3.6 23.1 - - + -
2235B LEU* 3.8 20.0 - - + +
2236B ALA* 4.6 5.4 - - + -
2239B LEU* 3.7 17.5 - - + +
2327B LEU* 4.4 13.9 - - + -
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Residues in contact with ALA2196 (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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2055B PHE* 3.9 21.1 - - + +
2056B ALA* 5.0 0.9 - - + -
2068B PRO* 3.7 22.2 - - + +
2192B LEU 3.0 14.6 + - - +
2193B ASP 3.2 8.3 + - - +
2195B VAL* 1.3 80.1 - - - +
2197B ALA* 1.3 56.3 + - - +
2199B ARG* 3.3 11.1 + - - +
2200B TRP* 3.0 26.3 + - - +
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Residues in contact with ALA2197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2055B PHE* 3.7 28.0 - - + -
2119B LEU* 4.4 3.1 - - + +
2168B ILE* 3.9 33.2 - - + -
2193B ASP 2.9 13.3 + - - +
2194B GLN 3.6 7.9 - - - +
2195B VAL 3.2 0.2 - - - -
2196B ALA* 1.3 76.5 - - - +
2198B LEU* 1.3 59.4 + - + +
2200B TRP* 3.2 4.9 + - - +
2201B VAL* 2.9 32.1 + - - +
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Residues in contact with LEU2198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137B VAL* 4.1 28.3 - - + -
2139B ILE* 5.7 1.6 - - + -
2168B ILE* 5.8 1.8 - - + -
2194B GLN* 3.0 19.9 + - + +
2195B VAL* 3.1 10.1 + - - +
2197B ALA* 1.3 77.0 - - + +
2199B ARG* 1.3 61.7 + - - +
2201B VAL* 3.3 6.2 + - + +
2202B GLN* 3.0 26.3 + - - +
2215B VAL* 4.2 3.4 - - + -
2217B ILE* 3.5 30.3 - - + -
2230B LEU* 4.0 26.5 - - + -
2236B ALA* 5.2 0.9 - - + -
2239B LEU* 3.8 37.9 - - + +
2240B PHE* 4.5 7.4 - - + -
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Residues in contact with ARG2199 (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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2195B VAL* 2.9 36.2 + - - +
2196B ALA* 3.5 13.2 - - - +
2197B ALA 3.2 0.2 - - - -
2198B LEU* 1.3 73.6 - - - +
2200B TRP* 1.3 66.0 + - - +
2202B GLN* 3.3 5.0 + - + +
2203B ASP* 3.1 41.2 + - - +
2235B LEU* 4.2 16.8 + - - +
2239B LEU* 4.1 22.8 - - - +
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Residues in contact with TRP2200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2028B THR* 4.5 11.9 + - + -
2030B HIS* 4.7 18.5 - + - +
2053B ILE* 3.6 26.7 - - + +
2054B PRO 4.0 9.4 + - - -
2055B PHE* 3.9 31.6 - - + +
2074B TRP* 5.9 2.9 - + - -
2119B LEU* 3.8 19.5 - - + -
2121B ILE* 3.8 23.8 - - + -
2196B ALA 3.0 13.8 + - - +
2197B ALA 3.3 9.0 - - - +
2199B ARG* 1.3 76.7 - - - +
2201B VAL* 1.3 70.4 + - + +
2203B ASP* 3.2 3.5 + - - -
2204B ASN* 2.9 67.7 + - + +
2205B ILE* 4.9 4.7 - - + -
2208B PHE* 3.7 24.5 - + - -
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Residues in contact with VAL2201 (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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2119B LEU* 4.8 1.8 - - + -
2135B VAL* 4.2 8.5 - - + -
2137B VAL* 4.3 20.4 - - + -
2166B VAL* 4.4 19.1 - - + -
2168B ILE* 5.7 0.2 - - + -
2197B ALA 2.9 19.7 + - - +
2198B LEU* 3.5 11.0 - - + +
2199B ARG 3.2 0.2 - - - -
2200B TRP* 1.3 90.4 - - + +
2202B GLN* 1.3 60.6 + - - +
2205B ILE* 2.9 57.2 + - + +
2215B VAL* 4.1 23.3 - - + -
2239B LEU 6.1 0.2 - - - +
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Residues in contact with GLN2202 (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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2198B LEU 3.0 17.4 + - - +
2199B ARG* 3.5 9.9 - - + +
2201B VAL* 1.3 80.0 - - - +
2203B ASP* 1.3 66.5 + - - +
2204B ASN 3.5 0.5 + - - -
2205B ILE 4.6 0.7 + - - -
2206B ALA* 5.4 1.2 + - - +
2212B PRO* 2.7 52.8 + - - +
2215B VAL* 3.5 19.2 - - - +
2238B ASN 3.9 13.3 - - - +
2239B LEU* 3.8 30.0 + - + -
2241B HIS* 4.2 5.0 - - - -
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Residues in contact with ASP2203 (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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2029B VAL* 3.5 22.6 - - + +
2199B ARG* 3.1 30.4 + - - +
2200B TRP* 3.2 1.8 + - - -
2202B GLN* 1.3 82.4 - - - +
2204B ASN* 1.3 70.2 + - - +
2206B ALA* 6.4 0.2 - - - -
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Residues in contact with ASN2204 (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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2028B THR* 3.4 7.5 - - - -
2029B VAL* 2.8 39.8 + - - +
2030B HIS* 4.6 1.7 + - - -
2200B TRP* 2.9 72.8 + - + +
2201B VAL 3.4 0.2 + - - -
2203B ASP* 1.3 90.8 - - - +
2205B ILE* 1.3 65.3 + - - +
2206B ALA* 3.1 3.8 - - - -
2207B SER* 2.9 26.5 + - - -
2208B PHE* 3.5 7.6 - - + -
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Residues in contact with ILE2205 (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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2121B ILE* 4.4 12.1 - - + -
2135B VAL* 3.7 22.9 - - + -
2164B VAL* 3.9 21.8 - - + -
2166B VAL* 4.0 18.6 - - + -
2200B TRP* 4.9 4.2 - - + -
2201B VAL* 2.9 39.9 + - + +
2202B GLN 4.6 0.4 + - - -
2204B ASN* 1.3 71.6 - - - +
2206B ALA* 1.3 60.3 + - - +
2207B SER 3.1 0.2 - - - -
2208B PHE* 2.9 28.7 + - + -
2210B GLY* 3.0 25.1 + - - +
2211B ASN 4.1 1.1 - - - -
2212B PRO* 3.7 32.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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