Contacts of the strand formed by residues 2346 - 2351 (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 TYR2346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2227B VAL* 4.1 0.9 - - + -
2228B SER* 3.4 26.5 + - - -
2231B VAL* 4.4 15.0 - - + -
2243B ALA* 3.3 30.5 - - + -
2245B SER* 2.7 40.6 + - - -
2249B VAL* 4.2 4.3 - - - +
2344B VAL* 3.9 0.7 - - + +
2345B PRO* 1.3 75.8 - - - +
2347B MET* 1.3 60.4 - - - +
2348B VAL* 3.7 25.0 + - + -
2433B VAL* 3.8 15.3 - - + -
2437B HIS* 3.4 46.2 - + + +
2443B PRO 3.0 7.5 + - - -
2444B THR* 3.4 7.9 - - + +
2445B TYR 3.0 24.4 + - - +
2503B PHE* 3.7 4.5 - - - -
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Residues in contact with MET2347 (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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2243B ALA 2.9 11.9 + - - +
2244B ILE* 3.2 21.3 - - + +
2245B SER 2.8 26.9 + - - +
2346B TYR* 1.3 72.4 - - - +
2348B VAL* 1.3 62.6 + - - +
2445B TYR* 3.3 13.7 - - + +
2447B TYR* 4.1 13.9 - - + -
2500B TRP* 3.8 29.8 - - + -
2503B PHE* 3.7 42.7 - - + -
2509B PRO* 4.2 7.9 - - + -
2517B TRP* 3.6 37.5 - - + -
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Residues in contact with VAL2348 (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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2245B SER* 3.5 5.4 - - - +
2249B VAL* 3.9 13.9 - - + -
2346B TYR* 3.7 39.9 - - + +
2347B MET* 1.3 77.6 - - - +
2349B GLY* 1.3 61.5 + - - +
2430B SER* 3.7 39.5 - - - +
2433B VAL* 4.5 7.9 - - + -
2434B ALA* 4.4 12.3 - - + -
2444B THR* 5.4 0.7 - - + -
2445B TYR 2.8 12.0 + - - +
2446B MET* 3.0 36.3 - - + +
2447B TYR* 3.4 3.2 + - - -
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Residues in contact with GLY2349 (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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2245B SER 3.0 10.6 + - - +
2247B SER* 2.8 29.0 + - - -
2248B GLY 4.6 0.2 + - - -
2348B VAL* 1.3 77.1 - - - +
2350B ILE* 1.3 64.8 + - - +
2430B SER* 4.4 2.9 + - - -
2446B MET* 5.0 1.6 - - - -
2447B TYR* 3.3 35.4 - - - -
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Residues in contact with ILE2350 (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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2247B SER* 3.9 3.4 - - - -
2349B GLY* 1.3 79.8 - - - +
2351B ASN* 1.3 72.7 + - - +
2354B GLU* 3.3 15.7 - - + +
2426B PHE* 3.9 15.0 - - + +
2427B GLY* 3.9 20.0 - - - +
2430B SER* 3.4 28.7 - - - +
2431B VAL* 6.0 0.2 - - + -
2446B MET* 5.5 0.9 - - + -
2447B TYR* 3.2 12.9 + - - +
2448B GLU* 3.2 16.3 - - + +
2449B PHE 2.8 22.3 + - - -
2539B LEU* 4.4 20.6 - - + -
2540B LYS* 4.0 21.5 - - + -
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Residues in contact with ASN2351 (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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2247B SER* 3.8 9.3 + - - -
2350B ILE* 1.3 87.2 - - - +
2352B LYS* 1.3 65.6 + - - +
2353B GLN 3.3 0.9 + - - -
2354B GLU* 2.6 31.0 + - - +
2447B TYR* 4.4 2.8 + - - -
2448B GLU* 4.5 3.1 - - - +
2449B PHE* 3.3 26.0 - - - +
2466B GLY 3.2 17.3 - - - +
2467B ASP 2.9 21.5 + - - +
2468B HIS* 4.2 0.2 - - - +
2469B GLY 3.6 6.1 - - - +
2470B ASP* 3.5 7.7 - - - +
2471B GLU* 3.0 31.4 + - - +
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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