Contacts of the strand formed by residues 531 - 535 (chain A) in PDB entry 5FWP
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 LYS 531 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A VAL* 4.8 9.8 + - + +
476A MET* 3.4 40.0 + - + +
477A LYS 4.4 3.8 + - - -
480A GLN 2.9 22.1 + - - -
481A LYS* 3.5 30.7 - - - +
482A SER* 4.4 1.8 - - - -
483A ILE* 3.9 7.9 - - + +
527A GLU* 4.1 1.8 - - - -
528A PHE 2.8 35.8 + - - +
529A ASP 3.3 6.3 - - - +
530A GLY* 1.3 83.0 - - - +
532A SER* 1.3 68.1 + - - +
533A LEU* 3.8 2.4 - - - +
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Residues in contact with SER 532 (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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481A LYS 4.4 2.7 + - - -
482A SER* 3.4 16.1 - - - -
483A ILE* 2.8 24.4 + - - +
526A LYS 3.4 11.2 - - - -
527A GLU* 3.8 16.1 - - - +
530A GLY 4.1 1.0 + - - -
531A LYS* 1.3 76.4 - - - +
533A LEU* 1.3 63.2 + - - +
534A VAL* 4.2 6.6 - - - +
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Residues in contact with LEU 533 (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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469A LEU* 5.4 4.9 - - + -
483A ILE* 3.4 29.4 - - + -
485A TYR* 3.7 25.6 + - + -
513A MET* 4.8 13.0 - - + -
522A VAL* 5.2 5.4 - - + -
525A LEU* 3.9 32.8 - - + +
526A LYS* 2.9 26.3 + - - +
527A GLU* 3.7 3.6 - - - -
528A PHE* 3.7 27.1 - - + +
531A LYS 3.8 1.1 - - - +
532A SER* 1.3 77.7 - - - +
534A VAL* 1.3 64.2 + - - +
535A SER 4.2 0.3 + - - -
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER* 3.4 27.1 - - - +
483A ILE 2.7 12.7 + - - +
484A TYR* 3.5 13.8 - - + -
485A TYR* 3.1 26.8 + - - -
532A SER* 4.2 7.0 - - - +
533A LEU* 1.3 76.5 - - - +
535A SER* 1.3 66.4 + - - +
536A VAL 3.5 0.9 + - - -
540A GLY 5.7 0.9 - - - +
541A LEU* 3.6 31.0 - - + -
542A GLU 5.8 0.7 - - - +
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Residues in contact with SER 535 (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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485A TYR* 3.4 37.9 + - - -
486A ILE* 4.8 0.9 - - - -
487A THR* 5.0 2.3 + - - -
533A LEU 4.2 0.2 + - - -
534A VAL* 1.3 80.3 - - - +
536A VAL* 1.3 63.1 + - - +
537A THR* 2.6 35.6 + - - +
538A LYS* 3.4 31.9 + - - +
541A LEU* 4.2 2.4 - - - +
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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