Contacts of the strand formed by residues 585 - 591 (chain B) 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 PHE 585 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B ARG* 3.4 50.5 - - + +
578B ILE 3.6 1.8 - - - -
579B ARG* 3.5 35.0 - - + -
583B GLY 4.5 11.4 - - - -
584B GLU* 1.3 85.7 + - - +
586B LEU* 1.3 67.5 + - - +
587B GLU* 3.6 6.3 + - - +
643B THR* 5.0 12.6 - - + -
645B PHE* 5.4 3.6 - + - -
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B ARG* 3.4 4.2 - - - +
578B ILE* 2.8 46.7 + - + +
580B THR* 3.8 24.9 - - + +
584B GLU 3.8 2.0 + - - -
585B PHE* 1.3 75.8 - - - +
587B GLU* 1.3 59.6 + - - +
602B PHE* 4.2 8.1 - - + -
603B VAL* 4.5 8.3 - - + -
606B LYS* 3.7 48.7 - - + +
608B PHE* 4.1 12.3 - - + -
646B LEU* 4.3 10.8 - - + -
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Residues in contact with GLU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LYS* 3.4 22.9 + - + -
576B LEU 3.5 12.3 - - - +
577B ARG* 3.3 36.2 + - + -
585B PHE* 3.6 6.3 + - - +
586B LEU* 1.3 78.3 - - - +
588B ARG* 1.3 78.2 + - - +
589B ARG* 5.8 3.0 - - - -
602B PHE* 4.2 9.2 - - - -
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Residues in contact with ARG 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B LYS* 4.8 0.4 - - - +
576B LEU 2.9 30.8 + - - +
587B GLU* 1.3 82.4 - - - +
589B ARG* 1.3 82.0 + - - +
590B PHE* 3.6 31.5 - - + -
598B ILE* 5.6 1.4 - - - +
602B PHE* 3.2 48.6 - - + +
606B LYS* 4.9 6.2 - - - +
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Residues in contact with ARG 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B VAL* 5.3 15.0 - - + +
574B SER 3.0 9.4 - - - +
575B LYS* 3.7 33.7 - - + +
587B GLU* 5.8 3.8 - - - -
588B ARG* 1.3 93.6 + - - +
590B PHE* 1.3 70.8 + - - +
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Residues in contact with PHE 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B PRO 3.6 2.3 - - - +
573B VAL* 3.8 2.9 - - - -
574B SER 2.8 28.4 + - - +
576B LEU* 3.8 24.5 - - + -
588B ARG* 3.6 37.0 - - + -
589B ARG* 1.3 80.3 - - - +
591B LEU* 1.3 74.4 + - - +
592B ALA 3.3 0.2 + - - -
594B ASN* 3.9 6.7 - - + +
598B ILE* 3.4 33.2 - - + -
599B VAL* 4.0 20.0 - - + -
602B PHE* 3.8 37.0 - + + -
633B LEU* 3.8 12.3 - - + -
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Residues in contact with LEU 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571B GLU* 5.2 13.5 - - + -
572B PRO* 3.7 6.1 - - + +
574B SER* 3.9 0.2 - - - -
590B PHE* 1.3 74.3 - - - +
592B ALA* 1.3 57.8 + - - +
593B SER* 2.9 24.9 - - - +
594B ASN* 2.9 57.9 + - - +
633B LEU* 3.4 8.7 - - - +
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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