Contacts of the strand formed by residues 2242 - 2246 (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 ARG2242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2214B SER* 4.1 9.6 + - - -
2215B VAL 3.4 4.4 + - - +
2216B THR* 3.3 19.8 - - + +
2217B ILE* 3.0 26.3 + - - +
2240B PHE* 3.8 4.5 - - - -
2241B HIS* 1.3 105.8 + - - +
2243B ALA* 1.3 63.5 + - - +
2344B VAL* 4.2 2.1 - - - +
2345B PRO* 3.5 23.8 - - + +
2503B PHE* 3.6 24.0 + - + +
2504B ALA 2.8 26.3 + - - -
2505B ARG 3.1 22.8 + - - -
2506B ASN* 3.5 13.1 + - - +
2507B GLY* 3.8 13.4 - - - -
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Residues in contact with ALA2243 (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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2217B ILE* 3.3 12.3 - - + -
2227B VAL* 3.7 20.4 - - + -
2231B VAL* 4.0 15.5 - - + -
2240B PHE* 4.3 5.2 - - + -
2242B ARG* 1.3 76.2 - - - +
2244B ILE* 1.3 63.3 + - - +
2344B VAL* 4.5 1.8 - - + -
2345B PRO 3.0 9.2 + - - +
2346B TYR* 3.3 17.7 - - + -
2347B MET 2.9 23.7 + - - -
2503B PHE* 3.4 5.4 - - - -
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Residues in contact with ILE2244 (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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2136B MET* 4.5 4.9 - - + -
2216B THR* 4.3 11.2 - - + -
2217B ILE 2.9 8.3 + - - +
2218B PHE* 3.2 33.2 - - + -
2219B GLY 3.2 7.1 + - - +
2227B VAL* 3.7 5.3 - - - +
2243B ALA* 1.3 80.0 - - - +
2245B SER* 1.3 64.4 + - - +
2246B GLU* 3.9 27.1 - - + +
2347B MET* 3.2 31.0 - - + +
2447B TYR* 5.1 0.9 - - + -
2500B TRP* 3.7 33.0 - - + +
2503B PHE* 3.7 26.0 - - + -
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Residues in contact with SER2245 (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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2219B GLY 3.9 3.1 - - - -
2224B GLY* 2.9 18.1 + - - -
2227B VAL* 3.4 9.4 - - - +
2244B ILE* 1.3 70.8 - - - +
2246B GLU* 1.3 62.3 + - - +
2247B SER 3.9 0.2 - - - -
2248B GLY 3.4 19.0 + - - -
2249B VAL* 4.1 7.2 - - - -
2346B TYR* 2.7 31.4 + - - -
2347B MET 2.8 9.5 + - - +
2348B VAL* 3.5 3.8 - - - +
2349B GLY 3.0 26.5 + - - +
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Residues in contact with GLU2246 (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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2138B TRP* 3.6 22.0 - - - -
2218B PHE* 3.7 6.9 - - - +
2219B GLY 2.9 14.3 + - - +
2220B GLU* 3.1 3.5 - - - +
2221B SER 2.9 25.6 + - - -
2224B GLY* 4.2 0.7 - - - -
2244B ILE* 3.9 14.8 - - + +
2245B SER* 1.3 72.5 - - - +
2247B SER* 1.3 63.8 + - - +
2248B GLY* 3.5 1.0 + - - -
2447B TYR* 3.2 21.8 - - + +
2471B GLU* 2.8 39.1 - - - +
2472B LEU* 4.0 12.5 - - - +
2475B VAL* 4.0 5.8 - - - +
2500B TRP* 3.0 28.3 + - + -
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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