Contacts of the strand formed by residues 302 - 305 (chain A) in PDB entry 4OQB
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 LEU 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU* 3.2 23.5 - - + +
293A LEU 4.0 11.2 - - - +
294A PRO 4.6 0.4 - - - +
295A CYS* 3.8 41.1 - - + +
301A GLN* 1.3 99.4 - - - +
303A VAL* 1.3 60.2 + - - +
309A TYR* 4.1 15.0 - - + +
310A TYR 3.5 5.6 - - - +
311A CYS* 4.1 12.6 - - + +
323A VAL* 4.8 9.2 - - + -
325A THR* 3.9 28.7 - - + -
328A PRO* 3.9 15.7 - - + -
329A ASN 5.7 0.2 - - - +
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Residues in contact with VAL 303 (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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282A ARG* 3.4 55.0 - - + +
292A LEU* 4.8 1.3 - - - -
301A GLN* 3.8 4.9 - - - +
302A LEU* 1.3 80.9 - - - +
304A PHE* 1.3 75.9 + - - +
305A LYS* 3.4 4.1 + - + +
309A TYR* 4.0 4.5 - - - -
310A TYR* 2.8 35.2 + - - +
312A THR* 3.4 29.2 - - + +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 4.6 4.9 - - - -
76A GLU* 3.5 29.1 - - + +
281A ASP* 5.5 6.7 - - - -
285A ASP* 4.9 4.9 + - + +
292A LEU* 5.3 0.6 - - - +
303A VAL* 1.3 82.3 - - - +
305A LYS* 1.3 61.6 + - - +
306A SER 3.2 28.7 - - - -
308A ALA 3.6 9.6 - - - -
309A TYR* 3.6 27.6 - + + -
355A ARG* 3.4 58.3 - - - +
356A ILE 5.7 0.7 - - - -
357A PHE* 4.1 13.5 - + - -
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Residues in contact with LYS 305 (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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10A ARG* 4.1 8.1 - - - +
72A ASP* 3.1 39.7 + - - -
73A GLY* 5.7 0.4 - - - -
76A GLU* 4.2 5.7 - - - +
303A VAL* 3.4 4.7 + - + +
304A PHE* 1.3 75.3 - - - +
306A SER* 1.3 64.1 + - - +
307A ASP* 2.7 22.1 + - - +
308A ALA 2.8 17.0 + - - +
310A TYR* 3.5 28.8 - - + -
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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