Contacts of the strand formed by residues 262 - 269 (chain B) in PDB entry 3V4P
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 SER 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TYR* 3.5 19.2 - - - -
132B PRO 3.5 15.7 - - - -
133B VAL* 3.6 8.5 - - - +
134B ASP 3.0 24.8 + - - +
261B VAL* 1.3 72.6 - - - +
263B ARG* 1.3 59.7 + - - +
264B LEU* 4.0 2.0 + - - +
324B GLN* 3.3 11.1 + - - -
367B TYR* 4.3 17.5 + - - -
442B GLY 3.3 26.3 + - - -
443B PHE* 5.0 1.7 - - - +
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Residues in contact with ARG 263 (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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134B ASP* 3.7 5.8 - - + -
253B GLN* 3.1 32.2 + - - +
258B TRP* 3.4 41.5 + - + +
259B ARG 3.0 30.6 + - - +
260B ASN* 4.2 7.8 - - - +
261B VAL 3.0 15.2 + - - +
262B SER* 1.3 73.0 + - - +
264B LEU* 1.3 62.6 + - - +
321B ALA 3.0 27.7 + - - -
322B ASN* 3.9 16.6 + - - +
323B ILE* 3.9 10.9 - - + +
324B GLN* 2.9 35.2 + - - +
442B GLY 4.6 0.2 + - - -
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Residues in contact with LEU 264 (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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133B VAL* 4.3 15.5 - - + -
134B ASP 2.7 15.6 + - - +
135B LEU* 3.4 22.7 - - + -
136B TYR 2.8 30.5 + - - -
163B LEU* 6.4 1.1 - - + -
258B TRP* 3.5 8.2 - - - -
262B SER* 5.1 2.0 - - - +
263B ARG* 1.3 82.1 - - - +
265B LEU* 1.3 55.4 + - - +
266B VAL 4.1 0.4 - - - -
323B ILE* 4.3 0.4 - - - -
324B GLN* 3.5 31.0 - - + +
326B ILE* 3.9 17.9 - - + -
363B ILE* 5.3 3.4 - - + -
367B TYR* 3.7 33.0 - - + -
370B LEU* 3.6 17.5 - - + -
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Residues in contact with LEU 265 (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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136B TYR* 3.4 40.8 - - + +
138B LEU* 4.0 18.8 - - + -
246B ILE* 4.6 11.7 - - + -
249B ALA* 4.4 14.4 - - + -
258B TRP* 4.4 9.2 - - + -
264B LEU* 1.3 73.1 - - - +
266B VAL* 1.3 78.2 + - - +
267B PHE* 3.5 13.2 + - + +
318B LEU* 5.4 7.4 - - + -
323B ILE* 3.7 18.8 - - + -
324B GLN 2.9 11.3 + - - +
325B PRO* 3.8 6.9 - - + +
326B ILE* 2.9 28.1 + - - -
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Residues in contact with VAL 266 (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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135B LEU* 3.5 29.2 - - + -
136B TYR 2.6 14.4 + - - +
137B TYR* 3.8 33.0 - - + -
138B LEU* 2.6 35.5 + - - +
264B LEU 4.1 0.2 - - - -
265B LEU* 1.3 72.6 - - - +
267B PHE* 1.3 65.2 + - - +
268B THR* 4.5 5.4 - - - +
326B ILE* 3.6 15.3 - - + +
328B ALA* 4.8 9.0 - - + -
359B VAL* 5.2 1.6 - - + -
363B ILE* 3.8 27.4 - - + -
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Residues in contact with PHE 267 (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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138B LEU* 3.5 11.9 - - + -
177B PHE* 3.4 37.5 - + - -
240B GLU* 6.4 0.2 - - + -
242B GLY* 3.8 21.3 - - - -
243B PHE* 6.1 1.8 - + - -
246B ILE* 3.6 29.4 - - + -
265B LEU* 3.5 12.0 + - + +
266B VAL* 1.3 71.4 - - - +
268B THR* 1.3 59.4 + - - +
269B SER* 4.0 10.8 - - - -
272B THR 5.9 0.2 - - - -
273B PHE* 5.5 4.0 - - + -
325B PRO* 6.4 0.4 - - + -
326B ILE 2.9 9.8 + - - +
327B PHE* 3.6 21.1 - + + -
328B ALA 2.9 25.0 + - - +
329B VAL* 4.7 0.8 - - + +
337B TYR* 3.4 43.3 - + - -
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Residues in contact with THR 268 (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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137B TYR* 3.7 30.4 + - + +
138B LEU 3.1 6.2 + - - +
139B MET* 3.6 30.3 - - + -
140B ASP* 3.2 23.6 + - - +
145B MET* 4.3 8.4 - - + +
177B PHE* 4.2 3.8 - - - -
266B VAL* 3.9 3.1 + - + -
267B PHE* 1.3 74.3 - - - +
269B SER* 1.3 67.6 + - - +
328B ALA* 3.0 19.7 + - - -
352B LEU* 3.2 19.6 - - - +
356B SER* 5.3 0.7 - - - -
359B VAL* 6.1 0.4 - - - -
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Residues in contact with SER 269 (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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140B ASP* 3.4 22.1 + - - +
145B MET* 4.4 6.1 - - - -
177B PHE* 4.9 0.7 - - - -
240B GLU* 4.5 2.9 - - - +
267B PHE* 4.0 22.1 + - - -
268B THR* 1.3 79.5 + - - +
270B ASP* 1.3 68.8 + - - +
271B ASP* 3.3 22.9 + - - -
272B THR 4.5 2.6 + - - -
328B ALA 3.0 7.3 + - - +
329B VAL* 3.1 11.1 - - - +
330B THR* 3.0 24.9 + - - +
337B TYR* 4.0 2.7 + - - -
352B LEU* 5.2 1.1 - - - +
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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