Contacts of the strand formed by residues 259 - 266 (chain A) in PDB entry 3V50
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 ARG 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLU* 2.8 44.6 + - + -
49A MET 3.1 11.0 - - - +
50A ASP* 4.3 5.3 + - - -
51A LEU* 4.0 3.6 - - - +
55A ARG* 5.7 0.2 - - - +
57A LEU* 3.5 31.6 - - - +
249A LEU* 3.2 7.1 - - - +
250A LEU* 2.9 34.8 + - - +
257A ALA 3.5 0.4 - - - -
258A GLU* 1.3 106.1 + - + +
260A ILE* 1.3 67.1 + - - +
261A VAL* 3.9 5.3 + - + -
290A TRP* 2.9 68.3 + - + +
291A GLN* 4.5 5.7 + - - -
292A ARG* 3.7 5.9 + - - +
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Residues in contact with ILE 260 (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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47A ILE 3.8 0.7 - - - +
48A GLU* 3.4 4.3 - - - -
49A MET* 2.7 45.3 + - + +
51A LEU* 3.7 21.0 - - + +
187A ALA* 3.7 23.8 - - + +
190A LEU* 4.5 12.8 - - + -
191A ARG* 3.6 36.8 - - + +
194A LEU* 5.4 0.2 - - + -
248A ALA 3.3 7.4 - - - +
249A LEU* 3.5 20.9 - - + -
259A ARG* 1.3 71.8 - - - +
261A VAL* 1.3 64.3 + - - +
262A VAL* 3.9 24.0 - - + +
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Residues in contact with VAL 261 (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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46A MET* 4.7 3.8 - - + -
47A ILE 3.4 8.3 - - - +
48A GLU* 4.4 13.5 - - + -
246A ILE 3.7 1.7 - - - +
247A VAL* 3.7 1.7 - - - -
248A ALA* 2.8 36.8 + - - +
250A LEU* 4.4 22.7 - - + -
259A ARG* 4.6 5.8 - - + -
260A ILE* 1.3 79.7 - - - +
262A VAL* 1.3 63.3 + - - +
263A ILE* 4.0 13.9 - - + -
286A LEU* 4.0 24.7 - - + -
290A TRP* 5.4 1.3 - - + -
302A MA4 3.5 33.4 - - + +
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Residues in contact with VAL 262 (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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46A MET* 3.2 5.7 - - - -
47A ILE* 3.0 33.3 + - + +
183A PRO* 4.0 19.3 - - + +
186A MET* 4.2 3.8 - - + -
187A ALA* 4.0 21.3 - - + +
190A LEU* 4.4 1.1 - - + -
246A ILE 3.4 2.7 - - - -
247A VAL* 4.0 20.0 - - + -
260A ILE* 3.9 18.8 - - + -
261A VAL* 1.3 77.2 - - - +
263A ILE* 1.3 64.4 - - - +
264A TYR* 3.4 37.9 - - + -
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Residues in contact with ILE 263 (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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44A VAL* 4.3 8.5 - - + -
45A GLY 3.3 7.0 - - - +
46A MET* 3.7 13.9 - - + -
245A GLY* 3.1 3.3 - - - -
246A ILE* 2.9 44.6 + - + +
261A VAL* 4.0 8.5 - - + -
262A VAL* 1.3 79.9 - - - +
264A TYR* 1.3 66.5 + - - +
265A LEU* 4.1 22.2 - - + -
279A ILE* 4.1 18.8 - - + -
282A ILE* 3.7 32.8 - - + -
302A MA4 3.5 30.7 - - + -
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Residues in contact with TYR 264 (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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44A VAL* 3.3 4.3 - - - +
45A GLY 2.8 33.7 + - - +
66A PHE* 3.6 32.9 - + + -
67A PRO 3.6 21.8 - - - -
68A MET* 3.9 4.0 - - - -
69A MET* 3.7 14.4 - - + -
71A THR* 2.8 37.1 + - + -
181A THR* 3.5 31.6 - - + +
183A PRO* 4.6 11.7 - - + -
186A MET* 3.6 16.2 - - + +
244A ARG 3.5 2.2 - - - -
245A GLY* 3.9 1.6 - - - -
246A ILE 4.8 0.7 - - - -
247A VAL* 3.7 3.5 - - + +
262A VAL* 3.4 28.9 - - + -
263A ILE* 1.3 76.9 - - - +
265A LEU* 1.3 66.4 + - - +
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Residues in contact with LEU 265 (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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40A LEU* 3.8 24.2 - - + -
43A ARG 3.3 6.1 - - - +
44A VAL* 3.5 29.4 - - + -
66A PHE* 4.3 2.2 - - - -
67A PRO* 5.1 1.7 - - - +
69A MET* 5.3 1.0 - - - +
242A GLY 4.3 4.3 - - - +
243A ALA* 3.3 5.8 - - - +
244A ARG* 2.8 34.4 + - + +
263A ILE* 4.1 7.2 - - + -
264A TYR* 1.3 82.9 - - - +
266A ARG* 1.3 63.8 + - - +
268A THR* 4.9 4.5 - - + -
275A ARG* 3.9 28.3 - - + +
278A GLN* 5.3 1.3 - - + -
279A ILE* 3.9 37.5 - - + +
282A ILE* 5.2 2.5 - - + -
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Residues in contact with ARG 266 (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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42A GLY* 3.6 1.7 - - - -
43A ARG* 2.9 47.3 + - + +
65A ARG* 2.9 38.6 + - - +
66A PHE* 3.7 22.4 - - + +
67A PRO* 3.7 30.4 - - + +
172A ALA* 4.7 3.6 + - + +
173A LEU 3.5 23.4 + - - -
174A PRO* 4.2 1.6 - - - +
175A GLY* 4.0 11.9 - - - +
176A ASP 4.7 6.9 + - - -
180A THR* 4.8 4.8 - - - +
241A ARG 4.1 0.2 - - - -
242A GLY 4.8 0.2 - - - -
243A ALA* 4.3 8.7 - - + +
265A LEU* 1.3 77.3 - - - +
267A ASP* 1.3 90.2 + - - +
268A THR* 3.4 4.7 + - - +
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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