Contacts of the strand formed by residues 6346 - 6351 (chain F) 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 TYR6346 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6227F VAL* 4.1 2.2 - - + -
6228F SER* 3.4 26.0 + - - -
6231F VAL* 4.6 12.1 - - + -
6243F ALA* 3.2 29.8 - - + -
6245F SER* 2.5 44.4 + - - -
6249F VAL* 4.2 4.0 - - - +
6344F VAL* 3.9 0.4 - - + +
6345F PRO* 1.3 74.5 - - - +
6347F MET* 1.3 66.1 + - - +
6348F VAL* 3.8 13.9 + - + -
6433F VAL* 3.8 21.5 - - + -
6437F HIS* 3.3 48.7 - + + +
6443F PRO 2.9 8.9 + - - -
6444F THR* 3.3 7.7 - - + +
6445F TYR 2.9 24.2 + - - +
6503F PHE* 3.7 4.8 - - - -
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Residues in contact with MET6347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6243F ALA 2.9 6.9 + - - -
6244F ILE* 3.3 24.0 - - + +
6245F SER 2.9 26.5 + - - +
6346F TYR* 1.3 72.6 - - - +
6348F VAL* 1.3 62.9 + - - +
6445F TYR* 3.2 13.0 - - + +
6447F TYR* 4.0 9.9 - - + -
6499F PHE 4.7 0.2 - - - +
6500F TRP* 3.8 35.0 - - + -
6503F PHE* 3.7 40.1 - - + -
6509F PRO* 4.3 6.5 - - + -
6517F TRP* 3.5 42.4 - - + -
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Residues in contact with VAL6348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6245F SER* 3.7 5.6 - - - +
6249F VAL* 4.0 16.2 - - + -
6346F TYR* 3.8 37.5 - - + +
6347F MET* 1.3 77.0 - - - +
6349F GLY* 1.3 59.9 + - - +
6430F SER* 3.7 37.7 - - - +
6433F VAL* 4.5 7.0 - - + -
6434F ALA* 4.4 11.0 - - + -
6444F THR* 5.1 1.1 - - + -
6445F TYR 2.7 12.0 + - - +
6446F MET* 3.0 39.5 - - + +
6447F TYR* 4.3 2.0 - - - -
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Residues in contact with GLY6349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6245F SER 3.1 11.3 + - - +
6247F SER* 3.0 23.4 + - - -
6248F GLY 4.7 0.2 + - - -
6348F VAL* 1.3 76.3 - - - +
6350F ILE* 1.3 69.9 + - - +
6430F SER* 4.4 2.6 + - - -
6446F MET* 5.1 1.1 - - - -
6447F TYR* 3.3 36.5 - - - -
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Residues in contact with ILE6350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6247F SER* 4.2 3.1 - - - -
6349F GLY* 1.3 80.2 - - - +
6351F ASN* 1.3 72.1 + - - +
6354F GLU* 3.3 15.0 - - + +
6426F PHE* 4.0 13.0 - - + +
6427F GLY* 3.9 15.0 - - - +
6430F SER* 3.4 29.2 - - - +
6431F VAL* 6.0 0.4 - - + -
6446F MET* 5.5 0.9 - - + -
6447F TYR* 3.1 11.5 + - - +
6448F GLU* 3.1 15.8 - - + +
6449F PHE 2.8 23.7 + - - -
6539F LEU* 4.4 15.7 - - + -
6540F LYS* 3.9 33.2 - - + -
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Residues in contact with ASN6351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6247F SER* 3.8 10.1 + - - -
6350F ILE* 1.3 85.6 - - - +
6352F LYS* 1.3 66.2 + - - +
6353F GLN 3.3 0.6 + - - -
6354F GLU* 2.7 30.0 + - - +
6447F TYR* 4.4 2.9 - - - -
6448F GLU* 4.5 2.9 - - - +
6449F PHE* 3.3 27.5 - - - +
6466F GLY 3.1 17.0 - - - +
6467F ASP 2.8 21.7 + - - +
6468F HIS* 4.0 0.2 - - - +
6469F GLY 3.4 9.1 - - - +
6470F ASP* 3.5 3.8 - - - +
6471F GLU* 3.0 31.0 + - - +
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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