Contacts of the strand formed by residues 6133 - 6139 (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 LEU6133 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6124F PRO* 3.8 21.1 - - + -
6125F ALA* 3.7 29.4 - - + +
6131F ASN* 4.6 8.1 - - + +
6132F ARG* 1.3 77.7 - - - +
6134F PRO* 1.3 79.1 - - + +
6162F ASN* 3.0 40.6 - - + +
6163F VAL* 4.5 0.2 - - - -
6164F VAL* 4.2 6.7 - - + -
6209F GLY 2.9 16.0 + - - +
6210F GLY* 3.5 2.6 - - - -
6211F ASN* 2.6 29.6 + - - +
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Residues in contact with PRO6134 (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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6132F ARG 4.5 1.6 - - - +
6133F LEU* 1.3 90.9 - - + +
6135F VAL* 1.3 60.0 + - - +
6162F ASN 3.9 7.4 - - - +
6163F VAL* 3.4 27.2 - - + +
6164F VAL* 2.9 24.6 + - - -
6211F ASN* 4.8 0.4 - - + +
6214F SER* 3.8 24.5 - - - +
6504F ALA* 4.5 7.2 - - + +
6505F ARG* 4.3 35.9 - - + +
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Residues in contact with VAL6135 (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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6133F LEU 3.7 1.1 - - - +
6134F PRO* 1.3 77.6 - - - +
6136F MET* 1.3 59.6 + - - +
6137F VAL* 4.1 14.4 - - + -
6164F VAL* 3.4 12.6 - - + +
6166F VAL* 4.0 23.3 - - + -
6201F VAL* 4.3 5.6 - - + -
6205F ILE* 3.7 27.4 - - + -
6210F GLY* 3.9 3.6 - - - -
6211F ASN 3.7 30.7 - - - +
6214F SER 3.0 9.8 + - - +
6215F VAL* 3.5 7.9 - - + +
6216F THR* 2.7 34.7 + - - -
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Residues in contact with MET6136 (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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6135F VAL* 1.3 76.5 - - - +
6137F VAL* 1.3 62.4 + - - +
6138F TRP 3.8 0.5 + - - -
6157F LEU* 4.3 12.8 - - + -
6163F VAL* 4.1 27.4 - - + -
6164F VAL 2.8 10.6 + - - +
6165F VAL* 3.5 7.2 - - + +
6166F VAL 3.0 24.1 + - - +
6216F THR* 3.3 19.3 - - + +
6218F PHE* 3.7 24.9 - - + -
6244F ILE* 4.5 2.5 - - + -
6500F TRP* 3.7 43.5 - - + +
6501F ALA* 4.4 9.9 - - - -
6504F ALA* 3.9 23.8 - - + -
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Residues in contact with VAL6137 (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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6135F VAL* 4.1 11.7 - - + -
6136F MET* 1.3 72.8 - - - +
6138F TRP* 1.3 60.1 + - - +
6139F ILE* 3.8 3.8 + - + +
6166F VAL* 3.3 12.1 - - + +
6168F ILE* 3.6 36.8 - - + -
6198F LEU* 4.0 23.8 - - + -
6201F VAL* 4.3 10.5 - - + -
6215F VAL* 3.7 26.5 - - + -
6216F THR 2.7 12.2 + - - +
6217F ILE* 3.4 5.9 - - + +
6218F PHE* 2.9 28.8 + - - +
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Residues in contact with TRP6138 (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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6137F VAL* 1.3 71.4 - - - +
6139F ILE* 1.3 66.6 + - - +
6140F HIS* 3.5 16.7 + - + +
6149F ALA* 5.7 0.9 - - - -
6152F TYR* 3.5 39.0 - + - -
6165F VAL* 5.3 1.3 - - + -
6166F VAL 2.7 15.0 + - - +
6167F THR* 4.1 18.2 - - + -
6168F ILE* 3.2 28.3 + - - +
6218F PHE* 3.2 62.7 - + + -
6219F GLY* 3.4 12.8 - - - -
6220F GLU* 3.4 28.9 - - + -
6246F GLU* 3.8 10.5 - - - -
6472F LEU* 3.4 33.0 - - + -
6476F PHE* 3.5 17.7 - + + -
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Residues in contact with ILE6139 (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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6137F VAL* 4.4 7.0 - - + +
6138F TRP* 1.3 76.6 - - - +
6140F HIS* 1.3 64.3 + - - +
6168F ILE* 4.0 18.8 - - + -
6170F TYR* 3.9 11.7 - - + -
6194F GLN* 3.6 31.4 - - + +
6198F LEU* 5.9 1.8 - - + -
6217F ILE* 4.8 7.4 - - + -
6218F PHE 2.8 14.1 + - - +
6219F GLY* 3.1 20.8 - - - -
6220F GLU 3.7 1.2 + - - -
6223F GLY* 3.3 21.6 - - - +
6226F SER* 3.9 8.3 - - - -
6227F VAL* 4.1 17.9 - - + -
6230F LEU* 4.0 27.6 - - + -
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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