Contacts of the strand formed by residues 274 - 282 (chain A) in PDB entry 1B4V
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 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A GLU* 3.7 35.7 - - + +
267A GLN 3.6 15.7 - - - +
268A LYS* 3.9 14.1 - - + -
272A GLY 3.6 3.2 + - - -
273A LYS* 1.3 81.7 + - - +
275A LEU* 1.3 60.8 + - - +
276A ALA* 3.6 18.4 - - - +
277A THR* 4.0 13.5 - - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLN* 2.7 39.4 + - + +
268A LYS 3.9 17.9 - - - +
269A ASP* 3.8 15.7 - - + +
273A LYS* 3.5 46.2 - - - +
274A LEU* 1.3 74.1 - - - +
276A ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 276 (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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266A GLU* 3.6 2.3 - - - -
267A GLN* 2.8 35.3 + - - +
274A LEU* 3.6 7.2 - - - +
275A LEU* 1.3 83.1 - - - +
277A THR* 1.3 63.0 + - - +
278A LYS* 3.7 22.2 - - + +
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Residues in contact with THR 277 (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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264A THR* 4.7 12.1 - - + -
265A VAL 3.3 14.1 - - - +
266A GLU* 4.0 16.0 + - + +
274A LEU* 4.0 18.5 - - - +
276A ALA* 1.3 77.8 + - - +
278A LYS* 1.3 67.7 + - - +
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Residues in contact with LYS 278 (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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245A GLN* 5.1 2.2 - - - +
248A HIS* 3.2 30.3 - - + -
263A LEU 3.5 2.1 - - - +
264A THR* 3.5 3.1 - - - -
265A VAL* 2.8 51.0 + - + +
267A GLN* 2.8 34.2 + - - +
276A ALA* 3.7 15.7 - - + +
277A THR* 1.3 75.4 - - - +
279A GLU* 1.3 66.5 + - - +
280A ILE* 4.9 10.8 - - + -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLY* 3.9 14.9 - - - +
254A ARG* 3.5 27.5 + - - -
262A ALA* 4.2 8.5 - - - +
263A LEU 3.3 10.2 - - - +
264A THR* 3.1 31.2 - - + +
278A LYS* 1.3 77.0 - - - +
280A ILE* 1.3 65.1 + - - +
281A SER 4.2 0.2 - - - -
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Residues in contact with ILE 280 (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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9A GLY* 3.3 11.2 - - - +
11A VAL* 4.7 4.9 - - + -
14A VAL* 4.0 21.3 - - + -
37A LEU* 4.0 16.2 - - + -
39A LEU* 4.0 22.9 - - + -
245A GLN* 4.3 7.6 - - - +
248A HIS* 5.3 0.2 - - + -
262A ALA* 3.5 1.6 - - - -
263A LEU* 2.8 46.5 + - + +
265A VAL* 3.9 29.4 - - + -
278A LYS* 4.9 13.7 - - + -
279A GLU* 1.3 80.8 - - - +
281A SER* 1.3 65.4 + - - +
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Residues in contact with SER 281 (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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9A GLY 2.8 15.0 + - - +
10A TYR* 3.3 19.7 - - - +
11A VAL* 3.0 23.4 + - - -
256A THR* 4.9 7.6 - - - -
261A TYR 3.1 11.9 - - - -
262A ALA* 4.1 10.5 - - - +
279A GLU 4.2 0.6 - - - -
280A ILE* 1.3 79.7 - - - +
282A CYS* 1.3 64.5 + - - +
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Residues in contact with CYS 282 (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 TYR* 3.7 10.3 - - - -
11A VAL 3.0 20.6 - - - +
12A PRO 3.7 4.0 - - - +
14A VAL* 3.7 23.8 - - + +
260A GLY* 3.6 4.3 - - - -
261A TYR* 2.8 42.3 + - - +
263A LEU* 5.4 3.4 - - - -
281A SER* 1.3 76.4 - - - +
283A ARG* 1.3 58.1 + - - +
284A TYR 3.4 23.1 - - - +
285A LEU* 4.0 17.7 - - - -
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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