Contacts of the strand formed by residues 573 - 579 (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 VAL 573 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571D GLU 4.2 1.0 + - - -
572D PRO* 1.3 71.7 - - - +
574D SER* 1.3 61.9 + - - +
575D LYS* 3.5 2.1 + - + +
589D ARG* 5.3 17.3 - - + +
590D PHE 3.8 4.5 - - - +
592D ALA* 4.9 0.9 - - - -
640D PRO* 3.2 29.4 - - - +
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Residues in contact with SER 574 (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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572D PRO 3.8 0.8 + - - -
573D VAL* 1.3 70.9 - - - +
575D LYS* 1.3 58.8 + - - +
576D LEU* 3.8 5.4 + - - -
588D ARG 3.9 0.2 - - - +
589D ARG* 3.0 6.7 - - - +
590D PHE* 2.8 39.8 + - - -
592D ALA* 2.8 32.4 - - - +
633D LEU* 3.5 20.0 - - - +
638D LEU 3.5 23.5 + - - -
639D PHE* 4.1 1.0 - - - +
640D PRO* 4.2 7.2 - - - -
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Residues in contact with LYS 575 (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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573D VAL* 4.6 2.5 - - + +
574D SER* 1.3 70.3 - - - +
576D LEU* 1.3 62.4 + - - +
577D ARG* 3.5 28.5 - - + +
587D GLU* 3.5 26.1 + - + -
588D ARG 4.7 0.7 - - - +
589D ARG* 3.7 28.9 - - + +
640D PRO 3.2 21.0 + - - +
641D GLN* 3.6 25.0 - - + +
642D GLU 3.1 25.3 + - - +
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Residues in contact with LEU 576 (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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574D SER* 4.5 3.1 - - - +
575D LYS* 1.3 79.6 - - - +
577D ARG* 1.3 63.6 + - - +
578D ILE* 4.1 14.4 + - + +
587D GLU* 3.5 4.7 - - - +
588D ARG 3.0 33.1 + - - +
590D PHE* 3.7 30.3 - - + -
599D VAL* 3.8 31.6 - - + -
602D PHE* 5.8 0.7 - - + -
633D LEU* 4.6 6.7 - - + -
638D LEU* 3.9 32.5 - - + +
642D GLU* 3.4 22.4 - - + +
644D LEU* 4.5 10.1 - - + -
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Residues in contact with ARG 577 (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* 3.5 28.3 - - + +
576D LEU* 1.3 77.3 - - - +
578D ILE* 1.3 58.1 + - - +
585D PHE* 3.3 57.3 - - + +
586D LEU 3.4 7.2 - - - +
587D GLU* 3.3 28.0 + - - +
642D GLU 3.1 14.0 + - - +
643D THR* 3.4 22.6 + - + +
644D LEU 2.6 34.0 + - - +
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Residues in contact with ILE 578 (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* 4.1 16.2 - - + +
577D ARG* 1.3 76.8 - - - +
579D ARG* 1.3 62.8 + - - +
580D THR 3.7 0.3 + - - -
585D PHE* 3.5 3.2 - - - -
586D LEU* 2.8 46.4 + - + +
599D VAL* 4.7 6.3 - - + -
602D PHE* 4.1 17.0 - - + -
603D VAL* 3.9 22.7 - - + -
615D LEU* 3.4 28.3 - - + -
644D LEU* 3.5 28.9 - - + +
646D LEU* 3.5 28.3 - - + +
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Residues in contact with ARG 579 (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 3.8 0.8 + - - -
578D ILE* 1.3 71.2 - - - +
580D THR* 1.3 66.4 + - - +
583D GLY* 5.2 4.7 - - - +
584D GLU 3.4 5.6 - - - +
585D PHE* 3.6 25.7 - - + -
644D LEU 3.0 9.2 + - - +
645D PHE* 3.8 28.9 - - + -
646D LEU* 3.0 31.2 + - - +
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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