Contacts of the strand formed by residues 265 - 272 (chain A) in PDB entry 3F2B
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 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A VAL* 3.8 19.5 - - + -
258A SER 3.4 13.3 + - - +
259A GLU* 4.3 15.1 + - + +
260A LEU* 4.8 1.6 - - - -
263A GLY 3.6 2.8 + - - -
264A ARG* 1.3 73.8 + - - +
266A LEU* 1.3 72.6 + - - +
282A MET 3.8 0.3 - - - +
283A PHE* 3.7 2.6 - - - -
284A SER* 2.9 41.2 + - - -
290A ALA* 3.6 25.4 - - + +
293A MET* 3.9 13.0 - - - +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLU 4.1 0.3 - - - +
257A VAL* 3.4 4.2 - - - -
258A SER* 2.9 45.6 + - - +
260A LEU* 3.8 28.2 - - + +
264A ARG 4.3 0.4 + - - -
265A THR* 1.3 76.9 - - - +
267A LEU* 1.3 77.6 + - - +
268A THR* 3.7 18.2 - - - +
281A LYS* 4.0 24.0 - - + -
282A MET 3.4 16.4 - - - +
283A PHE* 4.0 20.9 - - + +
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Residues in contact with LEU 267 (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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255A ALA* 4.5 8.1 - - + -
256A GLU 3.7 11.9 - - - +
257A VAL* 3.9 14.4 - - + -
266A LEU* 1.3 75.3 - - - +
268A THR* 1.3 65.2 + - - +
269A MET* 3.8 31.0 - - + -
280A VAL* 3.6 1.4 - - + +
281A LYS* 3.4 5.7 - - - -
282A MET* 2.9 42.2 + - + +
293A MET* 3.8 42.1 - - + +
296A VAL* 4.3 13.9 - - + +
324A LEU* 4.0 22.0 - - + -
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Residues in contact with THR 268 (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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254A ASP* 4.1 3.1 - - - +
255A ALA* 3.4 1.6 - - - -
256A GLU* 2.8 46.9 + - - +
258A SER* 5.1 1.7 + - - -
266A LEU* 3.7 22.5 + - - +
267A LEU* 1.3 74.3 + - - +
269A MET* 1.3 62.6 + - - +
279A LEU* 3.9 27.4 - - + -
280A VAL 3.5 4.5 - - - +
281A LYS* 4.7 8.6 - - + +
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Residues in contact with MET 269 (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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252A VAL* 4.5 7.6 - - + -
254A ASP 3.1 11.0 - - - +
255A ALA* 4.4 0.9 - - + -
267A LEU* 3.8 24.5 - - + -
268A THR* 1.3 73.8 - - - +
270A LYS* 1.3 66.9 + - - +
271A ILE* 4.1 13.0 - - + -
279A LEU* 3.2 7.9 - - - +
280A VAL* 2.7 66.6 + - + +
296A VAL* 3.8 25.4 - - + -
302A VAL* 4.2 5.4 - - + -
304A VAL* 3.8 13.7 - - + -
324A LEU* 3.6 27.6 - - + -
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Residues in contact with LYS 270 (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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252A VAL* 3.4 2.4 - - - +
253A PHE* 3.2 53.5 + - + -
254A ASP* 2.9 33.2 + - + +
269A MET* 1.3 71.4 - - - +
271A ILE* 1.3 67.5 + - - +
278A ILE 3.5 5.2 - - - +
279A LEU* 3.7 25.1 - - + -
1031A ALA* 4.3 12.1 - - + +
1034A ASP* 2.8 30.4 + - - +
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Residues in contact with ILE 271 (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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236A LEU* 3.5 4.1 - - + +
248A VAL* 3.8 29.6 - - + -
249A GLN* 4.4 10.3 - - - +
250A GLY 4.3 9.0 - - - +
251A TYR 3.1 11.9 - - - +
252A VAL* 4.2 9.4 - - + -
253A PHE* 3.8 3.4 - - - -
269A MET* 4.1 26.0 - - + -
270A LYS* 1.3 80.3 - - - +
272A THR* 1.3 60.6 + - - +
277A SER* 3.1 3.6 - - - -
278A ILE* 2.9 50.4 + - + +
280A VAL* 3.8 17.0 - - + -
302A VAL* 5.0 4.3 - - + +
304A VAL* 4.8 10.8 - - + -
319A ILE* 5.2 0.2 - - + -
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Residues in contact with THR 272 (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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236A LEU* 3.8 1.1 - - - -
250A GLY* 3.9 2.5 - - - -
251A TYR* 2.9 35.1 + - + +
253A PHE* 4.0 14.8 - - + -
271A ILE* 1.3 73.8 - - - +
273A ASP* 1.3 59.8 + - - +
274A TYR* 3.0 44.2 + - + +
276A ASN 2.7 18.1 + - - -
277A SER* 2.8 17.8 + - - -
301A TRP* 4.8 0.3 - - - -
1035A ARG* 3.6 12.1 + - + -
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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