Contacts of the strand formed by residues 303 - 307 (chain B) in PDB entry 2B7O
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 VAL 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B THR* 4.2 2.9 - - - -
279B VAL* 3.2 15.7 - - + +
280B TRP* 5.5 0.2 - - - -
281B ILE* 5.6 2.9 - - + -
296B ALA* 4.2 15.0 - - + -
299B ILE* 4.2 20.4 - - + -
301B ASN 3.7 9.2 - - - +
302B PRO* 1.3 79.6 - - - +
304B GLY* 1.3 61.8 + - - +
305B VAL* 5.7 0.2 - - + -
323B LEU* 4.7 14.6 - - + -
330B GLY 5.3 0.2 - - - +
331B ARG* 2.9 41.9 + - - +
332B LEU* 3.4 16.2 - - + +
333B THR* 2.9 26.6 + - - -
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Residues in contact with GLY 304 (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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278B THR* 4.8 0.6 + - - -
279B VAL 3.0 9.3 + - - -
280B TRP* 3.3 14.6 - - - +
281B ILE* 3.0 23.7 + - - +
303B VAL* 1.3 76.9 - - - +
305B VAL* 1.3 69.9 + - - +
332B LEU* 4.6 0.2 - - - -
333B THR* 3.1 19.3 - - - -
335B VAL* 4.7 3.8 - - - -
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TRP* 5.6 0.2 - - - -
281B ILE* 3.6 9.9 - - + +
286B ARG* 4.0 26.2 - - + -
293B ILE* 4.3 8.5 - - + -
303B VAL* 5.7 0.9 - - + -
304B GLY* 1.3 79.1 - - - +
306B LYS* 1.3 72.3 + - - +
307B LEU* 3.6 11.9 + - + +
319B TYR* 4.5 12.8 - - + -
323B LEU* 3.5 31.9 - - + -
332B LEU* 4.2 6.5 - - + -
333B THR 3.0 7.3 + - - +
334B LEU* 3.8 12.5 - - + -
335B VAL* 2.9 26.3 + - - +
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TRP* 3.5 26.5 - - + +
281B ILE 3.0 17.4 + - - +
282B GLY* 4.0 4.3 - - - -
283B GLU* 3.5 11.2 - - - +
286B ARG* 3.3 26.3 - - - -
305B VAL* 1.3 72.2 - - - +
307B LEU* 1.3 61.2 + - - +
308B GLY 4.1 0.4 - - - -
335B VAL* 3.4 29.8 - - + -
337B ARG* 3.9 7.4 - - + -
366B ASP* 2.7 24.1 + - - +
369B HIS* 3.4 1.0 + - - -
409B HIS* 4.2 10.2 + - - -
703B PEP 2.5 61.6 + - - +
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Residues in contact with LEU 307 (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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283B GLU* 4.1 0.2 - - - -
305B VAL* 4.0 23.1 - - + +
306B LYS* 1.3 78.3 - - - +
308B GLY* 1.3 60.9 + - - +
311B MSE 3.5 41.5 - - + -
316B ALA* 4.5 3.8 - - + -
319B TYR* 4.3 8.3 - - + -
334B LEU* 3.8 37.7 - - + -
335B VAL 2.7 16.5 + - - +
336B SER* 4.7 2.0 - - - +
337B ARG* 3.1 24.8 + - - -
338B MSE 3.3 19.5 - - + +
347B LEU* 6.2 1.6 - - + -
350B ILE* 4.5 14.1 - - + -
363B TRP* 4.9 2.0 - - + -
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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