Contacts of the strand formed by residues 515 - 520 (chain B) in PDB entry 4RS6
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 GLY 515 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B TYR* 2.8 34.7 + - - -
511B SER* 3.1 12.6 + - - -
514B TYR* 1.3 79.9 - - - +
516B PHE* 1.3 59.7 + - - -
527B VAL* 5.2 0.9 - - - -
528B LEU 3.7 10.1 - - - -
530B ASN* 4.1 8.1 - - - -
575B PHE* 3.7 8.8 - - - -
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Residues in contact with PHE 516 (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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507B TRP* 3.9 39.3 - + + -
508B VAL 3.7 2.7 - - - -
509B ASP* 3.8 20.0 - - + -
511B SER* 4.8 0.2 - - - +
515B GLY* 1.3 73.9 - - - -
517B GLY* 1.3 67.2 + - - +
518B TYR* 4.1 9.3 - + + -
527B VAL* 3.3 5.6 - - - +
528B LEU* 2.9 36.2 + - + +
575B PHE* 4.3 0.6 - - - -
602B LEU* 3.7 28.3 - - + -
605B TRP* 3.4 38.4 - + + +
607B LYS* 5.8 0.2 - - + -
612B LEU* 4.0 27.6 - - + -
614B MET* 4.0 15.0 - - + -
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Residues in contact with GLY 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B TRP* 3.3 2.9 - - - +
508B VAL* 2.8 37.1 + - - +
516B PHE* 1.3 76.4 - - - +
518B TYR* 1.3 64.7 + - - +
526B GLY 3.2 10.8 - - - -
527B VAL* 4.3 1.8 - - - -
575B PHE* 3.7 21.6 - - - -
579B MET* 4.2 4.7 - - - -
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Residues in contact with TYR 518 (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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504B VAL* 3.9 15.3 - - + -
506B LYS 3.3 12.8 - - - +
507B TRP* 4.3 0.7 - - + -
516B PHE* 4.1 21.5 - + + -
517B GLY* 1.3 78.8 - - - +
519B GLN* 1.3 59.5 + - - +
520B LEU* 3.7 39.3 - - + -
524B THR* 6.1 0.2 - - + -
525B VAL* 3.3 3.3 - - - -
526B GLY* 2.8 55.7 + - - -
527B VAL* 3.9 2.9 - - - -
528B LEU 4.7 0.2 - - - -
534B HIS* 2.6 35.3 + - - -
536B SER* 4.8 0.3 + - - -
579B MET* 3.4 14.1 - - - +
600B LEU 4.3 1.7 + - - -
601B TYR* 3.7 4.7 - - - -
602B LEU* 3.4 24.8 + - + -
614B MET* 5.0 0.7 - - - -
616B PHE* 3.8 11.9 - + - -
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Residues in contact with GLN 519 (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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504B VAL* 3.5 5.7 - - - +
505B THR* 3.0 38.2 + - - +
506B LYS* 3.0 43.5 + - + +
518B TYR* 1.3 74.3 - - - +
520B LEU* 1.3 70.7 + - - +
523B HIS* 4.1 27.5 + - - +
524B THR 3.6 9.2 - - - +
525B VAL* 4.2 12.1 - - + +
541B LYS* 6.1 1.1 - - - -
579B MET* 3.7 18.6 - - + +
580B GLU* 5.5 1.0 - - - -
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Residues in contact with LEU 520 (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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502B GLN* 4.4 11.2 - - - +
503B TRP* 3.5 8.7 - - - +
504B VAL* 3.6 27.6 - - + -
505B THR* 4.0 3.8 + - - -
518B TYR* 3.7 26.7 - - + -
519B GLN* 1.3 80.9 + - - +
521B SER* 1.3 55.1 + - - +
522B ASP* 3.0 22.4 - - - +
523B HIS* 2.7 28.8 + - - -
524B THR* 2.9 23.4 + - + +
599B ARG* 5.5 1.1 - - + -
600B LEU* 4.1 36.3 - - + +
616B PHE* 4.0 9.2 - - + -
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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