Contacts of the strand formed by residues 518 - 522 (chain A) in PDB entry 4P6Q
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 CYS 518 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A THR* 3.2 6.8 + - - +
517A ASN* 1.3 80.7 - - - +
519A VAL* 1.3 66.3 - - - +
556A LEU* 3.8 29.6 - - - -
557A VAL 3.6 6.1 - - - -
558A LEU* 3.7 20.0 - - + -
565A ALA* 4.6 0.7 - - - -
586A PHE* 3.4 5.5 - - - +
587A ALA* 2.8 43.5 + - - +
592A GLN* 3.6 27.4 - - - +
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Residues in contact with VAL 519 (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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518A CYS* 1.3 79.4 - - - +
520A TRP* 1.3 62.3 + - - +
521A LEU* 4.0 13.7 - - + -
537A PHE* 5.0 4.5 - - + -
556A LEU* 3.3 6.2 - - - -
557A VAL* 2.8 42.6 + - + +
559A TYR* 3.7 26.9 - - + -
565A ALA* 3.9 24.7 - - + +
568A ALA* 3.9 10.8 - - + -
569A VAL* 4.1 4.9 - - + -
584A VAL* 3.7 26.7 - - + -
585A ASP 3.6 5.4 - - - +
586A PHE* 4.7 0.2 - - - +
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Residues in contact with TRP 520 (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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438A ARG* 3.1 60.3 - - + +
484A CYS 3.4 15.4 + - - -
485A ASP* 4.0 10.3 - - + -
486A ILE* 4.0 22.2 - - + -
518A CYS 4.1 0.2 + - - -
519A VAL* 1.3 73.9 - - - +
521A LEU* 1.3 64.7 + - - +
522A ASP* 3.3 40.8 - - + -
554A MET* 3.7 23.0 - - + +
555A ALA 3.4 6.5 - - - -
556A LEU* 4.1 16.6 - - + -
583A LYS* 4.2 8.1 - - + -
584A VAL* 3.3 9.9 - - - +
585A ASP* 2.7 43.2 + - + +
587A ALA* 4.1 7.2 - - + -
595A PHE* 4.4 9.3 - + - -
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Residues in contact with LEU 521 (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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519A VAL* 4.0 11.0 - - + -
520A TRP* 1.3 85.9 - - - +
522A ASP* 1.3 59.1 + - - +
524A LEU* 4.3 19.1 - - + -
533A LEU* 4.4 13.5 - - + -
537A PHE* 3.6 38.8 - - + -
553A GLY 4.7 0.4 - - - -
554A MET* 3.1 10.3 - - - +
555A ALA* 2.9 35.7 + - + +
557A VAL* 3.9 15.9 - - + -
572A THR* 4.4 7.6 - - + -
577A ILE* 5.0 1.1 - - + -
582A ILE* 4.5 10.1 - - + -
583A LYS 3.4 4.5 - - - +
584A VAL* 3.8 22.7 - - + -
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Residues in contact with ASP 522 (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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431A GLU* 4.9 3.1 - - - +
485A ASP* 4.1 9.5 - - - +
486A ILE 5.2 0.2 + - - -
520A TRP* 3.3 34.2 - - + -
521A LEU* 1.3 74.1 - - - +
523A GLY* 1.3 69.1 + - - +
524A LEU 3.7 1.3 - - - -
552A LYS 4.1 5.4 - - - +
553A GLY 3.7 4.6 - - - +
554A MET* 3.4 26.9 - - - +
582A ILE* 3.4 8.6 - - - +
583A LYS* 2.9 55.6 + - + +
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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