Contacts of the strand formed by residues 641 - 648 (chain C) in PDB entry 3QCA
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 641 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575C LYS* 3.5 33.8 - - + +
639C PHE 3.1 2.8 - - - -
640C PRO* 1.3 93.5 - - + +
642C GLU* 1.3 69.7 + - - +
643C THR* 5.4 0.3 + - - -
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Residues in contact with GLU 642 (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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575C LYS 3.3 11.2 + - - +
576C LEU* 3.5 14.2 - - + +
577C ARG* 3.0 23.6 + - - +
617C SER* 4.7 5.9 + - - +
618C THR* 4.7 15.7 + - - +
619C PHE 5.0 3.6 - - - +
637C LYS 3.6 18.6 - - - +
638C LEU* 3.7 30.9 - - + +
639C PHE 4.5 7.8 + - - +
640C PRO 4.0 0.2 - - - -
641C GLN* 1.3 83.7 - - - +
643C THR* 1.3 73.4 + - - +
644C LEU* 4.3 3.8 - - + -
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Residues in contact with THR 643 (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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577C ARG* 3.3 31.3 + - + +
585C PHE* 4.5 15.3 - - + -
618C THR* 3.4 25.7 + - - +
641C GLN 4.3 0.5 + - - -
642C GLU* 1.3 78.0 + - - +
644C LEU* 1.3 77.1 + - - +
645C PHE* 4.0 21.1 - - + -
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Residues in contact with LEU 644 (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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576C LEU* 4.7 14.1 - - + -
577C ARG 2.6 13.1 + - - +
578C ILE* 4.1 17.3 - - + -
579C ARG* 2.9 24.9 + - - +
599C VAL* 5.1 1.8 - - + -
615C LEU* 3.4 34.3 - - + -
616C LEU 3.3 2.9 - - - +
617C SER* 3.3 29.6 - - - +
624C VAL* 4.9 2.7 - - + -
638C LEU* 3.7 35.9 - - + -
642C GLU* 4.3 6.1 - - + +
643C THR* 1.3 86.1 - - - +
645C PHE* 1.3 70.0 + - - +
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Residues in contact with PHE 645 (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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579C ARG* 3.7 26.5 - - + -
585C PHE* 5.3 3.6 - + - -
614C LYS 3.0 5.2 - - - +
615C LEU* 3.7 3.6 - - - +
616C LEU* 2.7 48.7 + - + +
618C THR* 3.6 32.8 - - + -
643C THR* 4.0 25.4 - - + -
644C LEU* 1.3 77.6 - - - +
646C LEU* 1.3 65.0 + - - +
647C GLU* 5.6 5.4 - - + +
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Residues in contact with LEU 646 (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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578C ILE* 3.8 24.4 - - + +
579C ARG 3.1 18.9 + - - +
580C THR* 4.6 4.1 - - - -
581C PRO* 4.6 16.8 - - + +
586C LEU* 4.6 3.8 - - + -
603C VAL* 4.5 10.8 - - + -
608C PHE* 3.5 47.3 - - + +
610C TRP* 6.0 0.9 - - + -
613C TYR* 3.6 31.4 - - + +
614C LYS 3.3 3.4 - - - +
615C LEU* 4.1 19.7 - - + -
645C PHE* 1.3 75.6 - - - +
647C GLU* 1.3 66.5 + - - +
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Residues in contact with GLU 647 (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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581C PRO* 5.6 1.6 - - - -
613C TYR* 3.2 9.1 - - - -
614C LYS* 2.8 41.8 + - + +
616C LEU* 5.0 16.6 - - + +
645C PHE* 4.8 7.5 - - + +
646C LEU* 1.3 79.8 - - - +
648C ALA* 1.3 66.3 + - - +
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Residues in contact with ALA 648 (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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581C PRO* 6.0 0.2 - - - +
612C GLU 3.4 8.3 - - - +
613C TYR* 3.5 18.1 - - + +
614C LYS* 5.9 0.4 - - - +
647C GLU* 1.3 78.5 - - - +
649C LYS* 1.3 63.5 + - - +
650C GLU* 5.4 2.5 - - - +
628D ASP* 6.1 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