Contacts of the strand formed by residues 263 - 269 (chain B) in PDB entry 5GT8
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 TRP 263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ASP* 6.2 4.7 - - + -
182B ASN 3.7 0.2 - - - +
183B ARG* 3.4 3.6 - - - -
184B PHE* 2.5 60.2 + - + +
185B CYS* 4.6 1.1 - - - -
186B VAL* 3.9 26.1 - - + +
257B SER 5.1 10.2 + - - -
258B SER* 6.3 1.2 - - - +
261B GLU 4.7 5.5 + - - -
262B LEU* 1.3 80.8 - - + +
264B ARG* 1.3 58.7 + - - +
294B SER* 4.1 20.0 - - - -
295B ALA 5.0 0.4 - - - -
296B TYR* 3.3 36.1 - + - -
307B LEU* 3.3 32.8 - - + -
308B VAL 3.2 24.9 - - - +
309B PRO* 3.6 28.7 - - + -
310B GLU* 4.6 0.7 - - - -
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Residues in contact with ARG 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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179B SER* 4.0 7.4 + - - +
180B PRO 3.5 22.8 + - - +
181B GLN* 3.7 33.5 + - - +
182B ASN 3.4 18.6 - - - -
183B ARG* 5.2 6.6 - - - +
263B TRP* 1.3 73.7 - - - +
265B MET* 1.3 62.2 + - - +
307B LEU* 3.5 3.3 - - - -
308B VAL* 2.9 36.0 + - - +
310B GLU* 4.0 25.2 + - + +
313B ILE* 3.4 45.0 - - + +
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Residues in contact with MET 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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179B SER* 2.6 36.6 + - - -
180B PRO* 4.0 8.8 + - + +
182B ASN 4.5 0.2 + - - -
184B PHE* 3.4 36.0 - - + -
225B ILE* 3.6 21.8 - - + -
227B PHE* 4.2 12.8 - - + -
264B ARG* 1.3 78.1 - - - +
266B VAL* 1.3 71.5 + - - +
267B ARG* 3.5 24.2 - - + -
305B HIS* 3.2 34.3 - - + +
306B ALA 3.8 3.1 - - - -
307B LEU* 3.5 19.7 - - + -
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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
----------------------------------------------------------
177B ILE* 3.8 34.3 - - + -
178B GLN 4.1 3.8 - - - -
179B SER* 4.3 4.0 - - - -
265B MET* 1.3 80.2 - - - +
267B ARG* 1.3 71.4 + - - +
268B ILE* 5.1 2.9 - - + -
284B ILE* 5.8 7.2 - - + -
288B LEU* 6.4 0.4 - - + -
305B HIS* 3.3 2.1 - - - -
306B ALA* 2.9 46.7 + - + +
308B VAL* 4.7 3.1 - - + -
313B ILE* 4.1 18.6 - - + -
316B VAL* 4.2 21.8 - - + -
317B ILE* 5.4 6.3 - - + -
320B LEU* 5.9 2.9 - - + -
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Residues in contact with ARG 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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47B THR* 3.7 23.2 - - - +
48B PRO* 4.7 4.9 - - - +
49B GLU* 5.9 0.6 - - - +
176B PRO 4.1 0.2 - - - +
178B GLN* 3.3 63.9 + - + +
180B PRO* 4.8 3.1 - - - -
225B ILE* 3.5 19.0 - - - +
265B MET* 3.5 16.2 - - + -
266B VAL* 1.3 81.9 - - - +
268B ILE* 1.3 65.8 + - - +
303B PHE* 3.1 58.8 - - + +
304B ASP 3.2 6.3 - - - +
305B HIS* 3.4 28.5 - - + +
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Residues in contact with ILE 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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176B PRO* 4.0 15.3 - - + +
177B ILE* 3.9 34.3 - - + -
178B GLN* 5.3 0.7 - - - +
266B VAL* 5.1 2.9 - - + -
267B ARG* 1.3 80.5 - - - +
269B GLY* 1.3 62.7 + - - +
280B ILE* 4.2 20.9 - - + +
283B GLN* 4.5 8.5 - - + +
284B ILE* 3.7 36.8 - - + -
303B PHE* 3.3 10.2 - - - -
304B ASP* 2.9 40.3 + - + +
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Residues in contact with GLY 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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176B PRO* 4.9 16.4 + - - +
268B ILE* 1.3 83.2 - - - +
270B GLY* 1.3 60.1 + - - -
271B GLN* 5.6 2.0 - - - -
302B ASN 3.8 6.3 - - - -
303B PHE* 3.4 16.4 - - - -
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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