Contacts of the strand formed by residues 696 - 702 (chain G) 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 LEU 696 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684G GLY 3.9 1.6 - - - -
685G TYR* 3.1 4.7 - - - +
686G PHE* 2.7 72.2 + - + +
694G PRO* 4.0 1.9 - - - +
695G THR* 1.3 84.9 - - + +
697G SER* 1.3 66.7 + - - +
699G ILE* 4.3 13.0 - - + -
718G GLY* 4.3 14.4 - - - +
721G SER 4.2 4.3 - - - +
722G LEU* 3.4 40.8 - - + +
725G ALA* 4.4 0.2 - - + -
730G MET* 4.5 1.3 - - - -
902G MET* 5.6 2.0 - - - -
905G GLY* 3.4 28.3 - - - +
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Residues in contact with SER 697 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684G GLY 3.3 0.6 + - - -
685G TYR* 3.4 17.7 - - - -
694G PRO* 3.7 25.6 + - - +
695G THR 4.2 0.6 + - - -
696G LEU* 1.3 80.5 + - - +
698G ASN* 1.3 74.7 + - - +
699G ILE* 3.5 1.8 - - - +
905G GLY 3.9 6.4 + - - -
906G THR* 4.0 19.8 + - - +
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Residues in contact with ASN 698 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683G GLY* 3.8 21.8 - - - -
684G GLY 2.6 11.1 + - - -
685G TYR* 3.4 23.6 + - + +
697G SER* 1.3 77.1 - - - +
699G ILE* 1.3 57.3 + - - +
700G THR* 4.3 6.9 + - - -
906G THR* 4.4 6.3 - - + +
907G ILE* 4.2 11.3 - - - +
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Residues in contact with ILE 699 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681G ILE* 3.6 21.0 - - + +
683G GLY 3.2 5.0 + - - -
684G GLY* 2.5 41.0 + - - +
686G PHE* 3.5 28.0 - - + -
696G LEU* 4.3 14.1 - - + -
697G SER 4.2 7.4 - - - +
698G ASN* 1.3 81.7 - - - +
700G THR* 1.3 60.5 + - - +
701G ILE* 3.8 5.8 - - + -
722G LEU* 3.6 22.9 - - + -
902G MET* 6.3 1.1 - - + -
905G GLY 4.3 12.1 - - - +
906G THR* 4.4 0.2 - - - -
907G ILE* 4.1 33.4 - - + +
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Residues in contact with THR 700 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681G ILE 3.2 11.0 - - - +
682G MET* 4.5 5.1 - - + -
683G GLY* 3.5 13.5 + - - -
698G ASN* 4.2 7.2 + - - -
699G ILE* 1.3 74.6 + - - +
701G ILE* 1.3 73.6 + - - +
907G ILE* 4.1 18.9 - - - +
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Residues in contact with ILE 701 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679G VAL* 4.4 3.1 - - + +
680G GLN* 2.9 21.8 - - - +
681G ILE* 3.0 42.3 + - + +
699G ILE* 3.8 13.7 - - + -
700G THR* 1.3 91.5 - - - +
702G ARG* 1.3 69.8 + - - +
703G ILE* 3.6 24.0 - - + -
722G LEU* 3.5 29.6 - - + -
900G ILE* 4.8 15.0 - - + -
907G ILE* 3.9 16.2 - - + -
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Residues in contact with ARG 702 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677G CYS* 3.3 34.5 - - - +
678G CYS 4.2 2.9 - - - -
679G VAL 4.0 4.3 - - - -
680G GLN* 2.5 29.5 + - - +
682G MET* 5.8 4.4 - - - +
700G THR* 6.3 0.6 - - + +
701G ILE* 1.3 79.2 + - - +
703G ILE* 1.3 69.0 + - - +
704G PRO* 4.2 5.8 - - + +
898G TRP* 3.2 37.2 + - + -
900G ILE* 4.9 1.3 - - - +
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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