Contacts of the helix formed by residues 2278 - 2289 (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 THR2278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1085A PRO* 3.7 28.9 - - + -
1113A SER* 4.5 0.4 - - - +
1115A ASP* 2.7 30.9 + - + +
1118A TYR* 5.0 3.6 - - + +
2262B LYS* 4.6 2.9 - - - +
2276B THR 4.1 1.1 - - - -
2277B THR* 1.3 88.9 - - + +
2279B SER* 1.3 63.7 + - - +
2280B ALA 3.4 0.4 + - - -
2281B VAL* 3.0 23.6 + - + +
2282B MET* 3.1 31.0 + - - +
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Residues in contact with SER2279 (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 THR* 3.8 13.9 + - - -
2182B ASP* 2.8 36.9 + - - -
2184B HIS* 3.7 9.6 - - - -
2262B LYS* 3.0 22.4 + - - +
2278B THR* 1.3 71.2 - - - +
2280B ALA* 1.3 64.9 + - - +
2282B MET* 3.3 13.1 + - - +
2283B VAL* 3.0 29.1 + - - +
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Residues in contact with ALA2280 (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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1058A PRO* 3.7 28.5 - - + -
1060A LEU* 3.6 6.5 - - + +
1115A ASP* 3.4 20.6 - - - +
2184B HIS* 3.9 23.9 - - + +
2278B THR* 3.3 1.4 + - - -
2279B SER* 1.3 79.8 - - - +
2281B VAL* 1.3 57.8 + - - +
2283B VAL* 4.1 2.7 - - - +
2284B HIS* 3.0 30.8 + - - +
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Residues in contact with VAL2281 (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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1060A LEU* 4.5 9.6 - - + -
1113A SER* 3.4 24.9 - - - +
1114A GLU 5.5 0.2 - - - +
1115A ASP* 4.1 8.1 - - + +
2275B LYS* 4.1 28.0 - - + +
2277B THR* 4.4 9.2 - - - +
2278B THR* 3.0 31.6 + - - +
2280B ALA* 1.3 74.1 - - - +
2282B MET* 1.3 66.5 + - - +
2284B HIS* 3.3 4.3 + - + +
2285B CYS* 2.9 25.9 + - + +
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Residues in contact with MET2282 (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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2178B PHE* 4.9 5.8 - - + -
2180B THR* 4.2 11.9 - - + -
2262B LYS* 3.4 35.4 - - + +
2265B ALA* 4.3 7.9 - - + +
2266B GLU* 3.9 25.4 - - + -
2269B ALA* 4.0 23.1 - - + -
2274B CYS* 4.5 0.6 - - - -
2275B LYS 3.4 22.7 - - - +
2276B THR* 3.8 10.1 - - - +
2278B THR 3.1 13.3 + - - +
2279B SER* 3.3 19.5 + - - +
2281B VAL* 1.3 77.0 - - - +
2283B VAL* 1.3 60.3 + - + +
2285B CYS* 3.6 3.8 - - - +
2286B LEU* 2.9 36.2 + - - +
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Residues in contact with VAL2283 (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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2065B PHE* 4.1 13.0 - - + -
2178B PHE* 3.9 7.4 - - + -
2180B THR* 3.5 24.0 - - + -
2184B HIS* 3.8 15.9 - - + +
2185B SER* 3.5 16.8 - - - -
2279B SER 3.0 17.5 + - - +
2280B ALA* 4.1 4.5 - - - +
2282B MET* 1.3 71.7 - - - +
2284B HIS* 1.3 66.1 + - - +
2286B LEU* 3.4 5.9 + - - +
2287B ARG* 2.9 55.6 + - - +
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Residues in contact with HIS2284 (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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285A SO4 3.2 32.5 + - - -
1060A LEU* 3.7 21.8 - - + +
1061A GLY* 3.6 25.4 + - - -
284B SO4 3.0 40.6 + - - +
2280B ALA 3.0 19.7 + - - +
2281B VAL* 3.3 5.1 + - + +
2283B VAL* 1.3 76.4 - - - +
2285B CYS* 1.3 64.4 + - + +
2287B ARG* 3.3 9.5 + - - +
2288B GLN* 2.9 50.5 + - + +
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Residues in contact with CYS2285 (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 GLY 4.6 1.1 - - - -
2274B CYS* 2.0 54.1 - - + -
2275B LYS 4.6 2.5 - - - +
2281B VAL* 2.9 20.7 + - + +
2282B MET* 3.6 2.7 - - - +
2284B HIS* 1.3 77.5 - - + +
2286B LEU* 1.3 64.8 + - - +
2288B GLN* 2.9 26.4 + - - +
2289B LYS* 3.4 20.2 + - - +
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Residues in contact with LEU2286 (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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2064B ARG* 2.9 20.5 + - - -
2065B PHE* 3.7 18.8 - - + -
2174B ILE* 5.6 1.6 - - + -
2178B PHE* 3.2 49.6 - - + -
2268B ILE* 4.6 6.7 - - + +
2269B ALA* 4.4 14.8 - - + -
2272B ALA* 3.7 30.1 - - + -
2274B CYS* 3.9 9.6 - - - -
2282B MET 2.9 20.5 + - - +
2283B VAL 3.4 2.0 + - - +
2285B CYS* 1.3 75.7 - - - +
2287B ARG* 1.3 57.8 + - - +
2289B LYS* 3.2 13.9 + - + +
2294B LEU* 4.2 15.8 - - + +
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Residues in contact with ARG2287 (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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284B SO4 3.2 41.1 + - - +
2061B GLY* 4.3 13.3 - - - +
2062B PRO* 3.5 18.1 + - - -
2064B ARG* 2.7 37.7 + - + +
2065B PHE* 3.3 39.1 + - + +
2066B THR* 3.3 14.3 - - - +
2184B HIS 4.5 5.9 + - - -
2283B VAL* 2.9 48.2 + - - +
2284B HIS* 3.5 8.1 - - - +
2285B CYS 3.1 0.2 - - - -
2286B LEU* 1.3 76.7 - - - +
2288B GLN* 1.3 61.4 + - + +
2289B LYS 3.3 1.1 - - - +
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Residues in contact with GLN2288 (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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285A SO4 2.9 20.2 + - - -
1290A THR* 5.6 3.5 - - - +
384B SO4 5.5 0.9 + - - -
2284B HIS* 2.9 50.8 + - + +
2285B CYS* 2.9 15.2 + - - +
2287B ARG* 1.3 76.7 - - + +
2289B LYS* 1.3 65.2 + - + +
2290B THR* 3.7 4.9 + - - +
2293B GLU* 4.7 0.9 - - - +
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Residues in contact with LYS2289 (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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384B SO4 4.3 2.6 + - - -
2064B ARG* 2.7 28.6 + - - -
2272B ALA* 3.0 30.4 + - + +
2273B GLY* 4.3 9.5 + - - -
2274B CYS* 3.5 22.0 - - - -
2285B CYS* 3.6 12.8 - - - +
2286B LEU* 3.2 23.0 + - + +
2287B ARG 4.1 0.9 - - - +
2288B GLN* 1.3 81.2 - - - +
2290B THR* 1.3 60.5 + - - +
2293B GLU* 3.4 25.2 + - + +
2294B LEU* 3.7 22.9 - - + -
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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