Contacts of the strand formed by residues 301 - 306 (chain B) in PDB entry 2C31
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 LYS 301 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B LEU* 3.2 38.6 - - + +
274B ASP 3.1 15.5 + - - +
275B VAL* 3.4 15.0 - - + +
276B CYS 3.1 22.5 + - - -
299B LEU 4.2 0.4 + - - +
300B LYS* 1.3 71.9 - - - +
302B TYR* 1.3 61.4 + - - +
319B ALA* 4.4 10.5 - - + -
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Residues in contact with TYR 302 (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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209B LEU* 4.6 0.2 - - - -
276B CYS* 3.5 34.5 - - + -
278B LEU* 3.9 15.5 - - + -
283B LEU* 4.1 21.5 - - + -
290B GLY* 3.6 15.1 + - - -
295B TRP* 3.3 36.2 - + - -
299B LEU* 4.1 13.2 - - + -
300B LYS* 3.3 37.0 + - + +
301B LYS* 1.3 73.0 - - - +
303B VAL* 1.3 58.6 + - - +
316B GLN* 4.2 5.4 - - + -
317B PRO 3.9 13.4 + - - -
318B ILE* 3.5 28.5 - - + +
319B ALA* 3.0 14.0 + - - +
320B ALA 2.9 29.1 + - - -
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA* 3.9 29.4 - - + +
209B LEU* 4.1 14.1 - - + -
210B ILE* 4.5 5.8 - - + -
275B VAL* 4.6 4.9 - - + -
276B CYS 3.0 5.7 + - - +
277B VAL* 4.0 35.2 - - + -
278B LEU* 2.7 28.6 + - - +
301B LYS 3.9 0.2 + - - -
302B TYR* 1.3 75.6 - - - +
304B GLN* 1.3 66.3 - - - +
305B ILE* 4.8 4.9 - - + -
320B ALA* 3.5 23.8 - - + +
322B VAL* 4.6 5.2 - - + -
333B LEU* 5.8 1.8 - - + -
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Residues in contact with GLN 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 LEU* 3.3 23.5 - - + +
281B ALA 3.3 25.3 + - - -
282B ARG* 4.4 4.2 - - - +
283B LEU* 4.7 4.2 - - - +
303B VAL* 1.3 79.0 - - - +
305B ILE* 1.3 71.7 + - - +
306B ASP* 4.5 6.9 + - + -
311B GLU* 4.3 22.6 + - - +
312B MET* 3.4 30.5 - - + +
313B ASP 5.0 0.2 + - - -
318B ILE* 3.5 30.8 - - + +
320B ALA 3.2 6.1 + - - -
321B PRO 3.8 0.2 - - - -
322B VAL* 2.8 30.0 + - - +
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Residues in contact with ILE 305 (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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203B ILE* 6.5 0.2 - - + -
277B VAL* 5.1 3.1 - - + -
278B LEU 2.8 14.5 + - - +
279B ILE* 4.3 23.8 - - + -
280B GLY* 3.1 24.8 + - - -
281B ALA 4.9 0.2 + - - -
303B VAL* 4.8 6.1 - - + -
304B GLN* 1.3 78.4 - - - +
306B ASP* 1.3 65.2 + - - +
322B VAL* 3.3 20.9 - - + +
324B GLY 4.6 3.6 - - - +
326B ILE* 4.3 21.3 - - + +
329B ALA* 3.6 31.2 - - + -
330B VAL* 4.4 16.4 - - + +
333B LEU* 4.4 21.1 - - + -
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Residues in contact with ASP 306 (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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280B GLY* 4.4 2.1 - - - -
281B ALA 4.6 1.0 + - - -
282B ARG* 4.9 0.7 - - - +
304B GLN* 4.5 13.1 + - + +
305B ILE* 1.3 78.2 - - - +
307B ILE* 1.3 63.5 + - - +
308B GLN* 3.0 28.1 + - - +
311B GLU* 4.4 12.2 - - + +
312B MET* 4.0 15.9 - - + +
322B VAL 3.2 5.1 + - - +
323B VAL* 3.3 10.0 - - - +
324B GLY 3.1 20.0 + - - -
1555B ADP 2.5 61.3 + - - +
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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