Contacts of the strand formed by residues 694 - 706 (chain C) in PDB entry 6CIM
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 ILE 694 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585C ASP* 4.9 1.3 - - + -
586C TYR* 3.5 45.1 - - + +
588C ASN* 4.1 9.4 - - + +
690C GLU* 4.2 0.9 - - - -
691C MET 2.9 29.0 + - - +
692C GLY 3.1 10.3 + - - +
693C GLY* 1.3 75.7 - - - +
695C PRO* 1.3 79.4 - - + +
696C ARG* 3.0 39.1 + - - +
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Residues in contact with PRO 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588C ASN* 3.2 27.8 + - - +
688C THR* 4.5 18.2 - - + -
689C LEU 3.8 6.1 - - - +
690C GLU* 4.1 12.1 - - + -
693C GLY 3.4 10.5 - - - +
694C ILE* 1.3 86.1 - - + +
696C ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C LEU* 3.9 24.8 - - - +
578C MET* 4.2 7.1 - - - -
585C ASP* 2.9 25.7 + - - +
587C LEU 3.1 20.8 + - - -
588C ASN* 4.0 5.6 - - - -
591C PHE* 3.6 19.5 - - + -
687C LEU 3.6 0.2 - - - +
688C THR* 3.4 5.9 - - - +
689C LEU* 2.8 36.5 + - - +
691C MET* 3.0 47.5 + - + +
692C GLY* 4.3 3.4 + - - -
694C ILE* 3.0 44.0 + - - +
695C PRO* 1.3 76.7 - - - +
697C THR* 1.3 64.7 + - - +
698C PHE* 4.0 10.8 - - + -
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Residues in contact with THR 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588C ASN 3.6 13.0 + - - -
590C PRO* 3.5 16.3 - - + +
591C PHE* 2.7 36.2 + - - -
686C GLU* 3.7 33.1 + - + +
687C LEU 3.2 6.1 - - - +
688C THR* 3.8 16.8 + - - +
696C ARG* 1.3 78.4 + - - +
698C PHE* 1.3 62.0 + - - +
699C LYS* 6.0 0.7 - - + -
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Residues in contact with PHE 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567C LEU* 3.7 24.7 - - + -
574C ILE* 4.8 9.9 - - + -
591C PHE* 3.2 41.3 - + + +
593C VAL* 4.0 9.4 - - + -
629C ILE* 5.0 2.0 - - + -
686C GLU* 3.8 2.1 - - - -
687C LEU* 2.9 44.8 + - + +
689C LEU* 3.8 34.8 - - + -
691C MET* 3.8 26.5 - - + -
696C ARG* 4.0 18.8 - - + -
697C THR* 1.3 77.6 - - - +
699C LYS* 1.3 62.5 + - - +
700C PHE* 4.1 21.3 - - + -
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Residues in contact with LYS 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590C PRO* 4.0 28.8 - - + +
591C PHE 2.7 12.8 + - - +
592C THR* 3.2 32.1 - - + +
593C VAL 2.9 22.7 + - - -
685C SER 4.5 13.2 - - - +
686C GLU* 4.9 13.9 - - + +
697C THR* 6.1 0.4 - - + -
698C PHE* 1.3 75.7 - - - +
700C PHE* 1.3 66.1 - - - +
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Residues in contact with PHE 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C TRP* 3.5 35.0 - + - -
563C LEU* 3.8 31.4 - - + -
567C LEU* 3.9 14.1 - - + -
593C VAL* 3.3 37.7 - - + +
595C VAL* 4.3 4.3 - - + -
682C MET* 5.0 8.1 + - + +
683C LYS* 5.2 6.8 - - - +
685C SER 5.3 1.6 + - - -
687C LEU* 3.5 31.2 - - + -
698C PHE* 4.1 7.6 - - + -
699C LYS* 1.3 76.6 - - - +
701C ILE* 1.3 66.4 + - - +
702C PHE* 3.8 32.8 + + + -
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Residues in contact with ILE 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C THR* 3.9 25.1 - - + -
593C VAL 2.8 11.4 + - - +
594C VAL* 3.5 15.6 - - + +
595C VAL* 2.8 31.9 + - - -
700C PHE* 1.3 77.6 - - - +
702C PHE* 1.3 62.1 + - - +
703C ARG* 3.9 22.2 + - + +
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Residues in contact with PHE 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C TYR* 3.8 25.8 - + - -
563C LEU* 3.6 25.6 - - + -
595C VAL* 3.6 25.4 - - + +
597C GLU* 4.3 2.5 - - - +
679C ARG* 3.8 45.2 + - + +
682C MET* 3.6 43.7 - - + -
683C LYS* 4.2 22.0 - - + +
700C PHE* 3.8 24.0 - - + -
701C ILE* 1.3 75.2 - - - +
703C ARG* 1.3 63.9 + - - +
704C GLY 4.1 1.4 + - - -
788C VAL* 5.4 0.9 - - - +
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Residues in contact with ARG 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C VAL* 4.1 22.4 - - - -
595C VAL 2.9 12.3 + - - +
596C LYS* 3.5 1.9 - - - -
597C GLU* 2.9 19.7 + - - +
628C ARG* 5.9 1.3 - - - +
701C ILE* 4.3 15.9 - - + +
702C PHE* 1.3 78.7 - - - +
704C GLY* 1.3 61.1 + - - +
705C THR* 2.7 25.9 + - + +
788C VAL* 4.2 14.8 - - + +
949C ARG* 2.8 28.4 + - - +
950C ASP* 2.5 35.6 + - - -
956C TRP* 3.4 33.2 - - + -
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Residues in contact with GLY 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597C GLU* 3.4 22.5 - - - +
679C ARG* 4.6 6.9 - - - +
702C PHE 4.1 1.4 + - - -
703C ARG* 1.3 69.6 - - - +
705C THR* 1.3 57.2 + - - -
706C GLY 3.5 2.0 - - - -
707C TYR* 3.2 28.1 - - - +
786C GLU 4.6 7.3 + - - -
787C THR* 3.6 1.7 - - - -
788C VAL* 2.9 30.8 + - - +
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Residues in contact with THR 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C LYS* 3.5 6.5 - - + +
703C ARG* 2.7 35.7 + - + +
704C GLY* 1.3 71.0 - - - -
706C GLY* 1.3 61.6 + - - +
707C TYR* 2.9 13.4 + - - +
788C VAL* 3.5 25.7 - - + +
789C PRO* 5.4 0.7 - - - +
790C SER* 5.0 10.6 + - - -
950C ASP* 5.2 1.3 - - - +
956C TRP* 3.0 62.3 + - + +
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Residues in contact with GLY 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C LYS* 4.3 6.3 - - - +
597C GLU 3.1 12.0 + - - -
598C SER* 3.2 14.9 + - - -
599C CYS 2.8 31.9 + - - +
705C THR* 1.3 77.7 + - - +
707C TYR* 1.3 60.6 + - - -
956C TRP 5.0 4.0 - - - -
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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