Contacts of the strand formed by residues 256 - 264 (chain B) in PDB entry 7UUT
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 VAL 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B VAL* 3.5 12.1 - - + +
237B ASP 4.3 1.3 - - - +
238B ALA 4.2 0.2 - - - -
239B ALA* 3.5 36.1 - - + +
252B ALA 3.2 17.1 + - - +
253B VAL 3.6 1.7 + - - +
254B LYS 3.5 2.0 - - - +
255B ILE* 1.3 78.6 - - - +
257B LYS* 1.3 73.2 + - - +
258B PRO* 4.4 0.2 - - - +
260B GLY* 3.6 28.3 - - - +
261B THR 3.7 2.7 - - - +
262B ILE* 3.8 21.3 - - + -
288B LYS* 3.0 31.3 + - + -
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Residues in contact with LYS 257 (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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97A ARG* 3.7 28.1 - - - +
169B THR* 6.0 1.0 - - - -
234B LYS* 3.5 39.0 + - - +
235B GLY* 3.8 7.3 + - - -
236B VAL 2.9 27.0 + - - +
237B ASP* 3.1 36.2 + - - +
255B ILE 3.7 1.4 + - - -
256B VAL* 1.3 79.8 - - - +
258B PRO* 1.3 84.3 - - + +
259B GLY 3.3 0.2 + - - -
260B GLY* 2.9 18.4 + - - +
288B LYS* 3.9 3.7 - - - +
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Residues in contact with PRO 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 6.2 0.9 - - + -
97A ARG* 2.9 33.9 + - - +
99A TYR* 4.9 0.7 - - - +
102A HIS* 3.6 29.2 - - + +
105A GLY* 4.8 1.1 - - - -
106A MET* 3.6 46.4 - - + +
256B VAL 4.4 0.4 - - - +
257B LYS* 1.3 88.0 - - + +
259B GLY* 1.3 58.9 + - - +
286B ALA 3.3 15.0 - - - +
288B LYS* 4.0 4.2 - - - -
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Residues in contact with GLY 259 (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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97A ARG* 4.2 4.5 + - - -
99A TYR* 3.5 41.7 + - - -
257B LYS 3.3 0.4 + - - -
258B PRO* 1.3 71.0 - - - +
260B GLY* 1.3 64.6 + - - +
261B THR* 4.7 2.1 + - - -
286B ALA 3.0 12.3 + - - -
287B HIS* 3.1 20.5 + - - +
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Residues in contact with GLY 260 (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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97A ARG* 4.6 1.7 - - - +
237B ASP 3.3 17.3 - - - -
256B VAL* 3.6 14.8 - - - -
257B LYS* 2.9 13.1 + - - -
258B PRO 3.3 1.4 + - - -
259B GLY* 1.3 81.0 - - - +
261B THR* 1.3 64.3 + - - -
287B HIS 3.3 1.6 + - - +
288B LYS* 3.5 1.6 - - - -
289B THR* 3.1 22.5 + - - -
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Residues in contact with THR 261 (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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161B LEU 3.5 23.8 - - - +
162B ALA* 3.4 22.0 + - - +
163B ASP* 4.0 12.6 + - - +
237B ASP 3.4 5.9 + - - -
238B ALA* 3.3 4.9 - - - +
239B ALA 3.0 25.1 + - - +
256B VAL* 3.7 3.0 - - - +
259B GLY 4.7 1.7 + - - -
260B GLY* 1.3 76.1 + - - -
262B ILE* 1.3 74.7 + - - +
263B ALA* 4.0 0.6 + - + +
289B THR* 3.4 21.9 + - - +
291B LYS* 4.4 11.0 - - + -
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Residues in contact with ILE 262 (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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239B ALA* 3.5 4.3 - - + +
241B ILE* 3.7 32.1 - - + -
249B MET* 4.2 11.9 - - + -
252B ALA* 3.8 19.5 - - + +
253B VAL* 4.1 20.2 - - + +
256B VAL* 3.8 32.5 - - + -
261B THR* 1.3 75.5 - - - +
263B ALA* 1.3 57.4 + - - +
264B ASN 4.9 0.7 - - - +
288B LYS* 4.1 19.1 - - + -
289B THR 2.6 18.2 + - - +
290B ILE* 4.4 11.7 - - + -
291B LYS 2.7 32.6 + - - +
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Residues in contact with ALA 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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158B GLY* 3.3 28.7 - - - +
161B LEU* 3.7 13.7 - - + +
162B ALA* 3.6 24.7 - - + +
239B ALA 2.8 10.5 + - - +
240B ILE* 3.2 7.9 - - + +
241B ILE 2.8 30.5 + - - -
261B THR 3.9 0.8 - - - -
262B ILE* 1.3 71.5 - - - +
264B ASN* 1.3 56.2 + - - +
291B LYS* 3.5 6.1 - - - -
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Residues in contact with ASN 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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281A TRP* 4.0 9.2 - - + -
284A GLY* 2.8 36.8 + - - -
161B LEU* 4.3 1.7 - - - +
241B ILE* 3.3 28.4 - - + +
249B MET* 4.6 3.4 - - + -
262B ILE* 4.0 1.3 + - + -
263B ALA* 1.3 72.4 - - - +
265B VAL* 1.3 64.5 + - - +
266B ASN 3.1 27.5 + - - -
268B PHE* 3.2 23.5 - - - -
291B LYS 2.7 17.4 + - - +
292B GLY* 3.2 20.1 - - - -
293B GLY 3.3 6.8 + - - -
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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