Contacts of the strand formed by residues 680 - 687 (chain E) in PDB entry 6C3P
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 GLN 680 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677E CYS* 4.4 7.8 + - - +
678E CYS 3.4 11.7 - - - +
679E VAL* 1.3 77.9 - - - +
681E ILE* 1.3 75.7 + - - +
682E MET* 4.6 17.5 - - + +
701E ILE 2.9 23.7 - - - +
702E ARG* 2.5 44.4 + - - +
736E ALA 3.6 0.2 - - - +
737E VAL* 3.4 1.9 - - - +
738E PHE* 3.3 55.8 + - + +
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Residues in contact with ILE 681 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679E VAL* 5.0 2.0 - - + -
680E GLN* 1.3 85.8 - - - +
682E MET* 1.3 68.2 + - - +
683E GLY 3.9 0.2 - - - -
684E GLY* 3.5 32.5 - - - +
686E PHE* 4.5 6.3 - - + -
699E ILE* 3.6 15.9 - - + -
700E THR* 3.2 11.6 - - - +
701E ILE* 3.0 50.4 + - + +
722E LEU* 5.0 4.3 - - + -
726E ALA* 4.9 16.4 - - + -
735E GLY* 4.6 0.2 - - - -
736E ALA 3.2 12.8 - - - +
737E VAL* 3.6 30.1 - - + -
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Residues in contact with MET 682 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680E GLN* 4.6 20.4 - - - +
681E ILE* 1.3 75.4 - - - +
683E GLY* 1.3 66.8 + - - +
684E GLY 3.5 0.4 - - - -
700E THR* 4.5 5.6 - - + -
702E ARG* 5.8 4.5 - - - +
735E GLY* 3.5 14.2 - - - -
736E ALA* 3.2 17.0 + - + +
738E PHE* 4.9 18.8 - - + -
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Residues in contact with GLY 683 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682E MET* 1.3 73.6 - - - +
684E GLY* 1.3 65.0 + - - +
685E TYR* 3.1 21.2 + - - -
698E ASN* 3.8 22.7 - - - -
699E ILE 3.2 11.0 + - - -
700E THR* 3.5 8.4 + - - -
734E SER* 4.6 0.3 + - - -
735E GLY* 3.6 6.1 + - - -
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Residues in contact with GLY 684 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681E ILE* 3.5 18.8 - - - -
682E MET 3.5 0.6 - - - -
683E GLY* 1.3 72.8 - - - +
685E TYR* 1.3 57.3 + - - -
686E PHE* 3.8 3.4 - - - -
697E SER* 3.3 4.0 + - - -
698E ASN 2.6 27.4 + - - -
699E ILE* 2.5 38.8 + - - +
734E SER 3.7 4.9 - - - -
735E GLY* 4.1 0.7 - - - -
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Residues in contact with TYR 685 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683E GLY* 3.1 28.9 - - - -
684E GLY* 1.3 71.8 - - - -
686E PHE* 1.3 61.9 + - - +
694E PRO* 5.3 4.3 - - + -
696E LEU 3.1 4.5 - - - +
697E SER* 3.4 27.1 - - - -
698E ASN* 3.4 28.6 + - + +
732E LYS* 3.0 8.5 - - - +
733E VAL* 2.8 27.8 + - + -
734E SER* 2.6 54.9 + - - +
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Residues in contact with PHE 686 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681E ILE* 4.6 5.6 - - + -
684E GLY* 3.8 11.4 - - - -
685E TYR* 1.3 75.2 - - - +
687E THR* 1.3 56.5 + - - +
694E PRO* 3.1 4.6 - - - +
695E THR 2.5 29.0 + - - -
696E LEU* 2.7 44.5 + - + +
699E ILE* 3.5 27.4 - - + -
722E LEU* 4.5 4.3 - - + -
725E ALA* 3.4 32.8 - - + -
726E ALA* 5.3 0.9 - - - -
730E MET* 3.3 21.5 - - - -
731E GLN 3.5 4.3 - - - -
732E LYS* 3.4 34.1 - - + -
733E VAL* 4.0 2.6 - - - +
734E SER 4.9 1.1 - - - -
735E GLY* 6.0 0.2 - - - -
737E VAL* 4.3 21.3 - - + -
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Residues in contact with THR 687 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686E PHE* 1.3 78.8 - - - +
688E TRP* 1.3 61.1 + - - +
689E THR 3.1 28.9 + - - +
690E PRO* 4.1 7.6 - - + -
692E GLY 4.4 1.4 + - - +
693E ILE 2.8 22.0 + - - -
694E PRO* 3.6 10.3 - - - +
695E THR* 3.4 7.2 - - - -
730E MET* 3.0 14.5 - - - +
731E GLN* 2.6 42.5 + - + +
733E VAL* 3.7 17.3 - - + -
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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