Contacts of the strand formed by residues 535 - 537 (chain J) in PDB entry 4XLR
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 535 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716I LYS* 4.3 5.4 - - - -
32J ILE* 6.1 0.9 - - + -
37J LEU* 3.4 35.9 - - + -
527J MET* 3.6 38.8 - - + -
528J VAL* 3.3 29.4 - - + -
529J GLN* 3.3 45.3 - - + -
533J GLY 4.3 3.4 - - - -
534J ARG* 1.3 79.2 - - - +
536J ALA* 1.3 58.6 + - - +
273L ILE* 6.2 0.4 - - + -
328L GLU 4.3 2.3 - - - +
329L PRO* 3.2 25.4 - - + +
330L VAL* 3.3 7.4 + - - +
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Residues in contact with ALA 536 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527J MET* 3.1 28.9 - - - +
528J VAL 3.1 15.8 + - - +
530J VAL* 6.1 2.9 - - + -
534J ARG 4.2 0.2 + - - -
535J PHE* 1.3 74.7 - - - +
537J THR* 1.3 63.4 + - - +
329L PRO* 4.3 0.7 - - - -
330L VAL* 3.4 20.2 - - + +
332L LEU* 4.2 6.7 - - + -
344L TYR* 4.1 26.7 - - + +
348L ILE* 4.6 6.3 - - + -
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Residues in contact with THR 537 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J PHE* 4.4 0.9 - - - -
526J PRO 3.2 15.7 + - - -
527J MET* 3.7 13.9 - - - +
536J ALA* 1.3 79.2 - - - +
538J SER* 1.3 61.7 + - - +
541J ASN* 2.7 32.4 + - + +
542J ASP* 4.5 11.7 - - - +
272L THR* 5.1 5.4 - - + -
329L PRO* 3.6 25.4 - - + +
330L VAL 3.0 11.0 + - - +
331L SER* 3.2 1.9 - - - -
332L LEU* 2.5 39.7 + - - +
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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