Contacts of the strand formed by residues 722 - 727 (chain I) in PDB entry 6C6U
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 GLY 722 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721I GLY* 1.3 75.2 - - - -
723I VAL* 1.3 63.9 + - - +
734I ILE* 4.5 1.6 - - - -
735I LYS 3.3 9.6 - - - -
737I ASN* 3.4 22.0 + - - +
776I PRO* 3.4 6.1 - - - +
777I VAL* 2.8 43.9 + - - +
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Residues in contact with VAL 723 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722I GLY* 1.3 77.9 - - - +
724I VAL* 1.3 72.6 + - - +
734I ILE* 4.6 2.0 - - - -
735I LYS* 2.7 52.8 + - + +
737I ASN* 4.4 12.6 - - - +
774I GLY* 4.2 18.6 - - - +
775I GLU 3.8 2.7 - - - -
776I PRO* 5.0 10.3 - - + -
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Residues in contact with VAL 724 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723I VAL* 1.3 82.9 - - - +
725I GLN* 1.3 62.1 + - - +
726I TYR 4.2 2.9 - - - +
727I VAL* 3.6 30.3 - - + -
732I ILE* 4.5 9.0 - - + -
733I VAL 3.5 11.9 - - - +
734I ILE* 3.7 23.1 - - + -
771I VAL* 4.4 10.1 - - + -
772I SER 4.0 12.6 - - - +
773I LEU* 4.9 1.3 - - - +
774I GLY* 3.5 17.9 + - - +
775I GLU* 3.2 26.3 + - + +
777I VAL* 4.4 12.3 - - + -
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Residues in contact with GLN 725 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723I VAL 3.6 4.0 + - - +
724I VAL* 1.3 74.8 - - - +
726I TYR* 1.3 65.9 + - + +
733I VAL* 2.8 32.2 + - + +
735I LYS* 4.2 25.9 - - + +
748I ILE* 3.5 20.8 - - - +
773I LEU* 3.9 19.8 - - - +
966I ILE* 6.1 0.8 - - - +
969I ALA* 5.5 8.1 - - - +
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Residues in contact with TYR 726 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G GLU* 3.6 12.9 + - - -
73G GLY* 4.2 8.0 - - - -
134G THR* 3.6 26.9 - - + -
135G ASP* 4.3 20.9 + - + -
724I VAL* 3.9 1.5 - - - +
725I GLN* 1.3 84.7 - - + +
727I VAL* 1.3 65.4 + - - +
728I ASP* 2.9 40.1 + - + -
731I ARG* 3.7 34.1 - - + -
732I ILE* 3.5 2.8 - - - -
733I VAL* 2.9 40.7 + - + +
773I LEU* 4.4 3.6 - - + -
966I ILE* 6.2 1.1 - - + -
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Residues in contact with VAL 727 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G GLN* 3.3 26.5 - - + +
134G THR* 3.2 31.7 + - - +
724I VAL* 3.6 18.4 - - + -
726I TYR* 1.3 77.5 - - - +
728I ASP* 1.3 65.4 + - - +
731I ARG 4.1 1.3 - - - -
732I ILE* 4.4 8.1 - - + -
769I PRO* 3.9 22.9 - - + -
771I VAL* 3.7 13.0 - - + +
772I SER 3.3 32.1 - - - +
773I LEU* 4.2 8.6 - - + +
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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