Contacts of the strand formed by residues 282 - 286 (chain B) in PDB entry 3GUC
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 TYR 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLY 5.1 0.3 + - - -
215B HIS* 3.8 31.9 - + + +
216B ILE 3.5 10.3 - - - -
217B GLN* 4.2 15.3 - - + +
232B PRO* 6.5 1.3 - - + -
234B VAL* 3.8 38.7 + - + +
280B SER* 4.4 2.6 - - - -
281B PHE* 1.3 76.8 - - - +
283B LEU* 1.3 59.4 + - - +
284B GLY* 3.5 24.9 - - - -
293B PRO* 3.7 11.6 - - - +
294B THR* 2.8 23.7 + - - -
295B MET* 3.0 56.5 + - + +
296B SER* 5.2 0.2 - - - -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASP* 3.7 35.9 - - + +
292A PHE* 4.1 16.4 - - + -
215B HIS* 3.2 2.8 - - - -
216B ILE* 2.8 47.3 + - + +
264B ILE* 3.1 39.2 - - + +
268B ASN* 4.5 0.7 - - - +
280B SER* 4.0 10.3 - - - -
282B TYR* 1.3 76.1 - - - +
284B GLY* 1.3 67.6 + - - +
285B TYR* 6.4 0.2 - - + -
292B PHE* 4.0 30.1 - - + +
293B PRO 3.7 1.8 - - - +
294B THR* 4.4 7.4 - - - +
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Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLY 3.6 6.5 - - - -
215B HIS* 4.0 0.4 - - - -
282B TYR* 3.5 20.2 - - - -
283B LEU* 1.3 76.8 - - - +
285B TYR* 1.3 62.0 + - - +
292B PHE* 3.0 28.9 - - - +
293B PRO* 2.8 27.0 + - - -
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 4.8 4.4 - - + +
267A GLN* 2.9 38.2 + - - +
213B SER* 3.1 11.1 - - - -
214B GLY 2.8 37.1 + - - +
215B HIS* 5.4 0.4 - - - -
257B THR* 3.8 30.3 - - + -
260B VAL* 3.7 35.1 - - + +
261B VAL* 4.2 10.5 - - + -
264B ILE* 5.3 4.0 - - + -
284B GLY* 1.3 73.9 - - - +
286B ASN* 1.3 66.1 + - - +
287B ALA* 3.7 19.8 - - + +
290B ASP* 4.0 9.1 + - - -
291B PHE 3.5 1.8 - - - -
292B PHE* 3.3 39.3 - + + -
293B PRO* 4.4 0.8 - - - +
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Residues in contact with ASN 286 (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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212B VAL 3.8 6.0 - - - +
213B SER* 4.7 2.7 - - - +
236B ALA* 4.0 10.7 - - - +
237B ALA* 2.9 45.3 + - - +
238B ASN* 6.0 0.2 - - - +
285B TYR* 1.3 72.4 - - - +
287B ALA* 1.3 54.1 + - - +
288B MET* 2.9 22.5 + - - +
289B GLN* 3.0 16.3 + - - +
290B ASP* 2.8 34.0 + - - -
291B PHE* 2.8 31.5 + - + +
293B PRO* 4.8 3.3 - - + +
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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