Contacts of the strand formed by residues 6242 - 6246 (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 ARG6242 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6214F SER* 4.0 8.9 + - - -
6215F VAL 3.4 2.7 + - - +
6216F THR* 3.4 19.8 - - + +
6217F ILE 3.1 21.3 + - - -
6240F PHE* 3.6 9.1 - - - -
6241F HIS* 1.3 110.1 + - - +
6243F ALA* 1.3 63.4 + - - +
6344F VAL* 4.1 4.2 - - - +
6345F PRO* 3.5 23.0 - - + +
6503F PHE* 3.6 24.9 + - + +
6504F ALA 2.6 26.7 + - - -
6505F ARG 2.9 24.5 + - - -
6506F ASN* 3.3 15.6 + - - +
6507F GLY* 3.7 12.5 - - - -
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Residues in contact with ALA6243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6217F ILE* 3.3 10.1 - - + -
6227F VAL* 3.7 16.8 - - + -
6231F VAL* 4.0 15.9 - - + -
6240F PHE* 4.4 0.9 - - + -
6242F ARG* 1.3 77.6 - - - +
6244F ILE* 1.3 67.7 + - - +
6344F VAL* 4.3 6.1 - - + -
6345F PRO 3.0 8.6 + - - +
6346F TYR* 3.2 20.5 - - + -
6347F MET 2.9 25.1 + - - -
6503F PHE* 3.4 1.9 - - - -
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Residues in contact with ILE6244 (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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6136F MET* 4.5 4.9 - - + -
6216F THR* 4.3 10.5 - - + -
6217F ILE 3.0 6.1 + - - -
6218F PHE* 3.2 33.4 - - + -
6219F GLY 3.3 7.3 + - - -
6227F VAL* 3.8 5.9 - - - +
6243F ALA* 1.3 81.7 - - - +
6245F SER* 1.3 63.6 + - - +
6246F GLU* 3.9 28.0 - - + +
6347F MET* 3.3 32.3 - - + +
6447F TYR* 5.1 0.7 - - + -
6500F TRP* 3.7 31.2 - - + +
6503F PHE* 3.7 27.8 - - + -
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Residues in contact with SER6245 (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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6219F GLY 4.0 2.2 - - - -
6224F GLY* 2.8 19.7 + - - -
6227F VAL* 3.5 5.5 - - - +
6244F ILE* 1.3 70.6 - - - +
6246F GLU* 1.3 62.7 + - - +
6247F SER 4.0 0.4 - - - -
6248F GLY 3.4 17.6 + - - -
6249F VAL* 4.1 8.1 - - - -
6346F TYR* 2.5 35.4 + - - -
6347F MET 2.9 10.1 + - - +
6348F VAL* 3.7 3.2 - - - +
6349F GLY 3.1 27.0 + - - +
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Residues in contact with GLU6246 (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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6138F TRP* 3.8 19.2 - - - -
6218F PHE* 3.7 17.8 - - - +
6219F GLY 2.9 14.8 + - - +
6220F GLU* 2.9 8.8 - - + -
6221F SER 2.7 31.7 + - - -
6224F GLY* 4.2 1.0 - - - -
6244F ILE* 3.9 12.6 - - + +
6245F SER* 1.3 71.5 - - - +
6247F SER* 1.3 60.1 + - - +
6248F GLY 3.5 0.2 + - - -
6447F TYR* 3.0 24.7 - - + +
6471F GLU* 2.8 36.0 - - - +
6472F LEU* 4.1 2.3 - - - +
6475F VAL* 4.0 6.7 - - - +
6500F TRP* 3.0 29.7 + - + -
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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