Contacts of the strand formed by residues 731 - 738 (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 GLN 731 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405G SER* 5.6 0.6 + - - -
687G THR* 2.6 56.4 + - + +
688G TRP 4.4 9.2 + - - +
690G PRO* 5.4 9.4 - - + -
729G GLU 3.8 2.6 + - - -
730G MET* 1.3 69.0 - - - +
732G LYS* 1.3 60.1 + - - +
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Residues in contact with LYS 732 (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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685G TYR 3.0 15.9 - - - +
686G PHE* 3.4 26.0 - - + -
730G MET 2.9 6.5 + - - +
731G GLN* 1.3 73.0 - - - +
733G VAL* 1.3 62.9 + - - +
734G SER* 4.1 9.4 - - - +
735G GLY 3.6 25.0 + - - +
736G ALA* 5.8 0.2 - - - +
737G VAL* 4.6 14.1 - - + +
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Residues in contact with VAL 733 (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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685G TYR* 2.8 21.2 + - + -
686G PHE 4.6 1.8 - - - -
687G THR* 3.7 31.9 - - + -
690G PRO* 6.2 0.4 - - + -
694G PRO* 4.3 15.5 - - + -
731G GLN 3.5 0.8 + - - -
732G LYS* 1.3 75.5 + - - +
734G SER* 1.3 64.0 + - - +
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Residues in contact with SER 734 (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 4.6 0.7 + - - -
684G GLY* 3.7 0.5 - - - -
685G TYR* 2.6 59.5 + - - +
686G PHE* 4.8 0.7 - - - -
732G LYS* 3.3 11.5 - - - +
733G VAL* 1.3 83.1 - - - +
735G GLY* 1.3 66.2 + - - +
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Residues in contact with GLY 735 (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* 4.6 2.0 - - - -
682G MET 3.5 15.9 - - - -
683G GLY 3.6 7.4 + - - -
684G GLY* 4.1 5.8 - - - -
686G PHE* 6.0 0.7 - - - -
732G LYS* 3.6 25.7 + - - +
734G SER* 1.3 85.4 + - - +
736G ALA* 1.3 60.7 + - - +
737G VAL* 4.9 1.1 - - - -
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Residues in contact with ALA 736 (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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680G GLN 3.6 0.9 - - - +
681G ILE* 3.2 24.7 - - - +
682G MET* 3.2 19.5 + - + +
732G LYS* 5.8 0.4 - - - +
735G GLY* 1.3 73.6 - - - +
737G VAL* 1.3 62.8 + - - +
738G PHE* 4.0 27.3 + - + -
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Residues in contact with VAL 737 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679G VAL* 4.7 1.1 - - + -
680G GLN 3.4 10.1 - - - +
681G ILE* 3.6 25.4 - - + -
686G PHE* 4.3 17.5 - - + -
725G ALA 5.9 1.8 - - - +
726G ALA* 5.0 7.2 - - - +
732G LYS* 4.6 15.8 - - + +
735G GLY 4.9 0.2 - - - -
736G ALA* 1.3 78.7 - - - +
738G PHE* 1.3 62.9 + - - +
739G TRP* 3.2 42.8 + - + +
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Residues in contact with PHE 738 (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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678G CYS 5.5 0.7 - - - -
679G VAL* 3.2 18.8 - - - -
680G GLN* 3.3 37.2 + - + +
682G MET* 4.9 19.5 - - + -
736G ALA* 4.0 28.9 - - + -
737G VAL* 1.3 75.7 - - - +
739G TRP* 1.3 71.2 + - - +
740G SER 5.2 2.5 - - - +
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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