Contacts of the strand formed by residues 514 - 517 (chain B) in PDB entry 2R5N
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 THR 514 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455B GLN 3.0 9.1 + - - -
456B VAL* 3.5 6.1 - - - +
457B MET* 2.8 28.2 + - - +
488B MET* 4.7 0.4 - - - -
489B SER* 3.3 7.4 - - - +
491B TRP* 3.6 31.4 - - + +
502B ALA 4.4 0.2 - - - +
505B TYR* 4.6 0.4 - - + -
506B GLY* 3.3 35.3 + - - +
509B ARG* 3.2 22.9 - - - +
512B GLY 4.4 0.2 + - - -
513B PRO* 1.3 76.3 - - - +
515B ALA* 1.3 61.3 + - - +
516B LEU* 3.9 12.9 + - + -
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Residues in contact with ALA 515 (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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457B MET* 3.4 9.0 - - + -
459B TYR* 4.1 16.4 - - + -
482B LEU* 4.0 27.1 - - + -
488B MET* 4.2 12.8 - - - -
489B SER 2.7 14.3 + - - +
490B THR* 3.4 4.6 - - - +
491B TRP* 2.9 28.6 + - - +
514B THR* 1.3 72.6 - - - +
516B LEU* 1.3 63.3 + - - +
517B ILE* 4.5 3.4 - - + -
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Residues in contact with LEU 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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361B SER* 4.7 2.0 - - - +
456B VAL* 3.8 19.3 - - + -
457B MET 2.8 12.5 + - - +
458B VAL* 4.5 5.4 - - + -
459B TYR* 2.8 34.0 + - - +
491B TRP* 3.6 4.9 - - + +
493B PRO* 5.6 0.7 - - + -
499B SER 5.3 0.2 - - - +
502B ALA* 3.8 37.7 - - + +
503B TRP* 3.3 47.8 - - + +
506B GLY* 5.7 0.2 - - - -
514B THR* 4.0 12.8 - - + -
515B ALA* 1.3 78.4 - - - +
517B ILE* 1.3 61.0 + - - +
518B LEU* 3.8 20.8 - - + +
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Residues in contact with ILE 517 (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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357B SER* 4.4 1.0 + - - -
435B LEU* 4.0 27.4 - - + -
459B TYR* 3.6 6.3 - - + -
462B ASP* 3.5 25.8 - - + +
479B VAL* 3.8 24.5 - - + -
482B LEU* 4.1 17.7 - - + -
490B THR* 3.7 19.5 - - + -
491B TRP 2.7 21.4 + - - +
492B ARG* 3.6 27.3 - - + +
493B PRO* 3.3 21.0 - - - +
515B ALA* 4.5 2.7 - - + +
516B LEU* 1.3 75.5 - - - +
518B LEU* 1.3 60.0 - - - +
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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