Contacts of the strand formed by residues 641 - 648 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575D LYS* 3.6 31.4 - - + +
639D PHE* 3.5 1.8 - - - +
640D PRO* 1.3 93.5 - - + +
642D GLU* 1.3 72.2 + - - +
643D THR* 4.3 0.3 + - - -
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Residues in contact with GLU 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575D LYS* 3.1 12.8 + - - +
576D LEU* 3.4 12.5 - - + +
577D ARG* 3.1 23.4 + - - +
617D SER* 5.6 2.3 + - - +
618D THR* 4.3 14.9 + - - +
622D ARG* 5.5 2.3 + - - -
637D LYS 3.3 22.4 - - - +
638D LEU* 3.8 31.2 - - + +
639D PHE 4.7 5.3 - - - +
641D GLN* 1.3 84.9 - - - +
643D THR* 1.3 74.7 + - - +
644D LEU* 4.2 2.5 - - + -
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Residues in contact with THR 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577D ARG* 3.4 29.7 + - + +
585D PHE* 4.8 13.0 - - + -
618D THR* 2.8 32.0 + - - +
641D GLN 4.3 0.6 + - - -
642D GLU* 1.3 77.9 + - - +
644D LEU* 1.3 75.0 + - - +
645D PHE* 4.0 20.9 - - + -
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Residues in contact with LEU 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D LEU* 4.5 18.2 - - + -
577D ARG 2.6 14.0 + - - +
578D ILE* 3.9 17.3 - - + -
579D ARG* 3.0 23.1 + - - +
599D VAL* 5.0 0.7 - - + -
615D LEU* 3.3 36.3 - - + -
616D LEU 3.2 2.7 - - - +
617D SER* 3.5 27.6 - - - +
624D VAL* 4.7 2.7 - - + -
638D LEU* 3.7 37.2 - - + -
642D GLU* 4.3 3.1 - - + -
643D THR* 1.3 84.2 - - - +
645D PHE* 1.3 71.2 - - - +
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Residues in contact with PHE 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579D ARG* 3.8 25.8 - - + -
585D PHE* 5.4 2.9 - + - -
614D LYS 3.0 4.2 - - - +
615D LEU* 3.3 3.1 - - - -
616D LEU* 2.4 60.2 + - + +
617D SER 5.4 0.4 - - - -
618D THR* 3.4 32.1 - - + -
643D THR* 4.0 21.3 - - + -
644D LEU* 1.3 78.2 - - - +
646D LEU* 1.3 64.5 - - - +
647D GLU* 5.7 3.1 - - - +
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Residues in contact with LEU 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ILE* 3.5 22.8 - - + +
579D ARG 3.0 21.0 + - - +
580D THR* 4.4 15.2 - - + +
581D PRO* 4.6 11.6 - - + +
586D LEU* 4.4 5.6 - - + -
603D VAL* 4.5 10.3 - - + -
608D PHE* 3.7 38.1 - - + +
613D TYR* 3.6 32.8 - - + +
614D LYS 3.2 8.7 - - - +
615D LEU* 4.3 15.5 - - + -
645D PHE* 1.3 76.5 - - - +
647D GLU* 1.3 67.4 + - - +
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Residues in contact with GLU 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D PRO* 5.5 2.5 - - - -
613D TYR* 3.4 9.6 - - - -
614D LYS* 2.7 45.4 + - + +
616D LEU* 4.5 25.4 - - + +
621D ARG* 5.7 2.6 + - - -
645D PHE* 4.8 3.0 - - - +
646D LEU* 1.3 78.6 - - - +
648D ALA* 1.3 67.2 + - - +
649D LYS 3.4 0.2 + - - -
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Residues in contact with ALA 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D PRO* 5.7 2.3 - - + +
612D GLU 4.0 8.1 - - - +
613D TYR* 4.2 11.7 - - + -
647D GLU* 1.3 75.9 - - - +
649D LYS* 1.3 58.9 + - - +
650D GLU* 3.4 13.7 + - + +
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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