Contacts of the strand formed by residues 499 - 504 (chain B) in PDB entry 3H44
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 GLN 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B ARG* 4.3 4.8 - - - +
304B ILE* 3.7 2.1 - - - +
305B VAL* 3.0 45.0 + - + +
486B GLU* 5.9 2.9 - - - +
489B THR* 3.5 27.2 + - - +
491B ARG 3.5 8.3 + - - +
492B THR* 3.3 22.9 + - - +
497B GLY 3.3 14.4 + - - +
498B THR* 1.3 68.7 - - - +
500B TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.5 32.7 - - + +
207B ALA* 4.8 5.7 + - - +
208B THR* 4.0 25.3 - - + +
302B TYR* 4.3 12.6 - + + -
303B LYS 3.3 12.8 - - - +
304B ILE* 4.0 14.8 - - + -
489B THR* 3.4 8.7 - - - -
490B ASP 3.3 3.5 + - - -
491B ARG* 2.8 83.3 + - + +
492B THR 4.1 2.1 + - - -
493B GLU* 3.9 15.9 - - - -
498B THR* 3.5 11.0 - - + +
499B GLN* 1.3 75.7 - - - +
501B LYS* 1.3 82.3 + - - +
502B GLN* 4.6 5.5 + - + -
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Residues in contact with LYS 501 (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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301B LEU 3.7 0.3 - - - +
302B TYR* 3.4 5.5 - - - -
303B LYS* 2.9 47.1 + - + +
488B LYS 3.4 21.1 - - - +
489B THR* 4.0 11.2 - - + -
490B ASP* 4.0 27.9 + - - +
491B ARG* 4.9 0.2 - - - -
500B TYR* 1.3 82.3 - - - +
502B GLN* 1.3 67.4 + - - +
503B GLU* 3.2 36.3 + - + +
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Residues in contact with GLN 502 (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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208B THR* 5.2 4.0 - - - +
300B GLN* 3.0 28.1 + - - +
301B LEU 3.5 3.6 - - - +
302B TYR* 3.6 32.8 + - + -
490B ASP* 5.7 0.2 - - - +
491B ARG* 3.6 45.2 + - - +
500B TYR* 4.6 6.6 + - + -
501B LYS* 1.3 84.2 + - - +
503B GLU* 1.3 72.1 + - - +
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Residues in contact with GLU 503 (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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300B GLN* 3.5 8.7 + - - -
301B LEU* 2.7 54.4 + - + +
303B LYS* 3.2 37.7 + - - -
501B LYS* 3.2 26.5 + - + +
502B GLN* 1.3 83.2 - - - +
504B ALA* 1.3 66.9 + - - +
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Residues in contact with ALA 504 (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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299B LYS* 4.5 0.9 - - + +
300B GLN* 3.6 18.7 + - - +
301B LEU* 5.2 0.9 - - - +
503B GLU* 1.3 80.6 - - - +
505B ILE* 1.3 65.6 + - - +
506B PRO* 3.5 8.4 - - + +
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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