Contacts of the strand formed by residues 334 - 340 (chain B) in PDB entry 4G85
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 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B MET* 3.5 15.7 - - + -
188B ASP* 3.3 31.6 - - + +
192B LEU* 5.4 0.2 - - + -
211B VAL* 4.1 6.5 - - + -
212B ASN 3.7 6.5 - - - +
213B ASP* 2.9 9.8 + - - +
301B ASP* 5.8 0.4 - - - +
302B LEU* 3.7 26.5 - - + -
305B LEU* 3.8 15.7 - - + -
331B TYR* 4.5 0.2 - - - +
333B GLY* 1.3 74.6 - - - +
335B ILE* 1.3 65.5 + - - +
336B TYR* 4.4 16.4 - - + -
361B GLY* 3.4 2.2 - - - -
362B ARG* 3.0 34.0 + - + +
380B VAL* 5.7 0.7 - - + -
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Residues in contact with ILE 335 (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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211B VAL* 3.4 2.8 - - - +
212B ASN* 3.0 33.6 + - + +
213B ASP 4.3 1.6 - - - -
214B ARG* 3.7 25.1 - - + +
217B LEU* 5.0 10.3 - - + -
324B LEU* 3.7 31.0 - - + +
325B ALA* 5.9 0.2 - - - -
326B ARG* 4.7 20.0 - - + +
327B GLY 5.4 0.2 - - - +
328B LEU* 6.0 0.9 - - - -
331B TYR* 3.6 37.2 - - + -
333B GLY 3.6 16.4 + - - +
334B VAL* 1.3 77.6 - - - +
336B TYR* 1.3 74.5 + - - +
360B GLY 3.8 4.5 - - - +
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Residues in contact with TYR 336 (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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188B ASP 4.1 2.0 + - - -
191B CYS* 3.3 27.0 - - + +
192B LEU* 3.6 41.5 - - + -
195B MET* 4.2 19.7 - - + -
209B VAL* 4.3 4.7 - - + -
210B LYS 2.8 22.2 - - - +
211B VAL* 3.9 8.1 - - + -
324B LEU* 3.6 5.6 - - - -
331B TYR* 5.8 0.9 - - - -
334B VAL* 4.4 17.0 - - + -
335B ILE* 1.3 81.9 - - - +
337B GLU* 1.3 58.1 - - - +
359B ALA* 3.3 3.3 - - - +
360B GLY* 2.8 67.4 + - - +
361B GLY* 3.8 8.5 - - - -
380B VAL* 3.8 9.1 - - + +
381B GLY 3.3 11.5 + - - -
382B LEU* 4.6 2.0 - - + -
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B MET* 4.9 0.4 - - - -
209B VAL* 4.5 3.4 - - - -
210B LYS* 2.8 52.3 + - + +
239B ASP* 5.3 1.6 - - - +
242B ASP* 4.4 6.3 - - - +
324B LEU* 3.6 28.9 - - + +
326B ARG* 3.9 15.2 - - + +
336B TYR* 1.3 75.8 - - - +
338B ALA* 1.3 66.3 + - - +
339B VAL* 4.4 3.6 - - + +
355B GLY 4.6 8.1 - - - +
356B SER* 4.7 15.5 - - - -
358B ALA 3.5 5.6 - - - +
359B ALA* 4.0 16.3 - - + +
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Residues in contact with ALA 338 (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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195B MET* 3.7 23.6 - - + +
199B LEU* 3.8 18.2 - - + -
207B PHE* 5.7 1.1 - - + -
208B LEU 3.6 8.3 - - - +
209B VAL* 4.3 1.6 - - + +
337B GLU* 1.3 76.8 - - - +
339B VAL* 1.3 58.4 + - - +
355B GLY 2.6 26.9 - - - +
357B VAL* 4.2 4.8 + - + -
358B ALA 2.5 32.7 + - - +
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Residues in contact with VAL 339 (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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207B PHE* 3.1 7.4 - - - +
208B LEU* 2.8 50.0 + - + +
210B LYS* 3.8 32.5 - - + +
337B GLU* 4.4 9.9 - - - +
338B ALA* 1.3 82.1 - - - +
340B LEU* 1.3 73.8 + - - +
341B LEU* 4.3 9.3 - - + +
355B GLY* 4.0 11.9 - - - +
357B VAL* 5.2 1.1 - - - -
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Residues in contact with LEU 340 (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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199B LEU* 5.9 1.1 - - + -
204B ILE* 2.9 53.4 - - + +
205B GLY* 4.7 2.2 - - - -
206B ASP 3.7 10.5 - - - +
207B PHE* 4.4 4.9 - - + +
339B VAL* 1.3 86.4 - - - +
341B LEU* 1.3 74.4 + - - +
342B GLN 4.0 1.9 + - - -
355B GLY 4.4 12.4 + - - +
357B VAL* 3.7 30.4 - - + +
392B ILE* 4.5 16.6 - - + -
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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