Contacts of the strand formed by residues 573 - 579 (chain A) 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 VAL 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572A PRO* 1.3 75.2 - - + +
574A SER* 1.3 63.5 + - - +
575A LYS* 3.6 5.3 + - + +
589A ARG* 5.2 13.2 - - + +
590A PHE 3.8 5.4 - - - +
592A ALA* 4.8 1.6 - - - -
639A PHE* 6.0 0.4 - - - -
640A PRO* 3.8 21.0 - - - +
571C GLU* 5.1 18.4 - - + +
591C LEU* 5.1 9.4 - - + -
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Residues in contact with SER 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A PRO 3.7 0.8 + - - -
573A VAL* 1.3 70.3 - - - +
575A LYS* 1.3 58.8 - - - +
576A LEU* 3.9 6.6 + - - -
588A ARG 3.9 0.2 - - - +
589A ARG* 3.0 6.1 - - - -
590A PHE* 2.8 38.1 + - - -
592A ALA* 2.9 30.7 - - - +
633A LEU* 3.5 27.0 - - - +
638A LEU 3.5 17.1 + - - -
639A PHE* 4.4 1.1 - - - +
640A PRO* 4.5 5.4 - - - -
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Residues in contact with LYS 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A VAL* 3.6 3.1 + - + +
574A SER* 1.3 70.8 - - - +
576A LEU* 1.3 62.6 + - - +
577A ARG* 3.5 29.3 - - + +
587A GLU* 3.6 24.8 + - + -
588A ARG 4.8 1.3 - - - +
589A ARG* 3.7 28.5 - - + +
640A PRO 3.4 19.5 + - - +
641A GLN* 3.7 27.1 - - + +
642A GLU 3.5 22.7 + - - +
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Residues in contact with LEU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A SER* 4.6 5.4 - - - +
575A LYS* 1.3 81.2 - - - +
577A ARG* 1.3 63.2 + - - +
578A ILE* 4.1 16.3 + - + +
587A GLU* 3.5 5.7 - - - +
588A ARG 3.0 32.6 + - - +
590A PHE* 3.7 28.9 - - + -
599A VAL* 3.8 31.6 - - + -
602A PHE* 6.0 0.8 - - + -
633A LEU* 4.4 5.2 - - + -
638A LEU* 4.2 40.6 - - + +
639A PHE* 6.0 0.2 - - - -
640A PRO 6.4 0.4 - - - -
642A GLU* 3.7 12.3 - - + +
644A LEU* 4.8 7.2 - - + -
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Residues in contact with ARG 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A LYS* 3.5 28.3 - - + +
576A LEU* 1.3 78.1 - - - +
578A ILE* 1.3 56.5 + - - +
579A ARG 3.9 0.4 - - - -
585A PHE* 3.3 56.3 - - + +
586A LEU 3.4 7.6 - - - +
587A GLU* 3.3 27.8 + - - +
642A GLU 3.1 15.3 + - - +
643A THR* 3.3 21.9 + - + +
644A LEU 2.7 32.4 + - - +
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Residues in contact with ILE 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A LEU* 4.1 25.1 - - + +
577A ARG* 1.3 75.2 - - - +
579A ARG* 1.3 64.1 + - - +
580A THR 3.6 0.5 + - - -
585A PHE* 3.5 2.6 - - - -
586A LEU* 2.7 55.1 + - + +
599A VAL* 4.8 4.5 - - + -
602A PHE* 4.1 11.7 - - + -
603A VAL* 3.9 21.8 - - + -
615A LEU* 3.7 24.7 - - + -
644A LEU* 3.6 24.5 - - + +
646A LEU* 3.7 26.0 - - + -
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Residues in contact with ARG 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A ARG 3.8 1.4 + - - -
578A ILE* 1.3 71.8 - - - +
580A THR* 1.3 66.5 + - - +
583A GLY* 5.2 4.3 - - - +
584A GLU 3.4 6.3 - - - +
585A PHE* 3.5 26.6 - - + -
644A LEU 2.9 9.0 + - - +
645A PHE* 3.7 30.5 - - + -
646A LEU* 3.1 28.6 + - - +
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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