Contacts of the strand formed by residues 309 - 319 (chain B) in PDB entry 2GB0
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 LEU 309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B GLY* 4.2 4.3 - - - -
227B PHE 3.6 11.7 - - - +
228B PHE* 3.8 24.0 - - + -
284B PHE* 3.5 33.4 - - + -
291B GLU* 3.8 19.7 - - - +
295B ARG* 3.5 17.7 - - - +
308B GLU* 1.3 78.3 - - - +
310B LYS* 1.3 60.6 + - - +
311B ARG* 3.4 29.4 - - - +
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Residues in contact with LYS 310 (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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227B PHE* 2.8 12.2 + - + +
228B PHE 3.8 2.7 - - - -
229B GLU* 2.9 51.3 + - + +
261B GLY 3.5 18.1 + - - -
262B CYS* 3.2 29.8 - - - +
263B GLY* 4.2 0.2 - - - -
308B GLU* 3.7 13.0 - - + +
309B LEU* 1.3 75.0 - - - +
311B ARG* 1.3 66.2 + - + +
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Residues in contact with ARG 311 (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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46B GLY* 4.0 28.5 - - - +
47B ASP* 4.2 15.6 + - - +
150B GLU* 4.6 3.8 + - - -
226B GLY* 3.5 0.3 - - - -
227B PHE* 2.8 71.6 + - + -
262B CYS* 6.3 0.6 - - - +
309B LEU* 3.4 13.6 - - - +
310B LYS* 1.3 83.0 - - + +
312B GLY* 1.3 71.8 + - - +
313B ALA* 5.2 3.4 - - - +
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Residues in contact with GLY 312 (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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225B VAL* 3.4 11.2 - - - -
227B PHE* 5.1 1.3 - - - -
284B PHE* 3.8 28.9 - - - +
309B LEU* 5.2 0.6 - - - +
311B ARG* 1.3 85.5 + - - +
313B ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 313 (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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45B HIS* 4.4 12.8 - - + -
46B GLY* 4.3 19.5 - - - -
224B VAL* 3.3 8.1 - - - +
225B VAL* 3.1 47.2 + - + +
227B PHE* 5.4 1.1 - - + -
282B ARG 5.9 0.2 - - - -
284B PHE* 3.9 2.0 - - - -
311B ARG* 5.2 7.4 - - - +
312B GLY* 1.3 75.3 - - - +
314B VAL* 1.3 66.2 + - - +
315B CYS* 5.3 1.6 - - + -
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Residues in contact with VAL 314 (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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40B THR 4.5 2.3 - - - +
45B HIS* 2.7 23.2 + - - -
222B ARG* 3.6 44.0 - - + +
223B GLN 3.9 2.5 - - - -
224B VAL* 3.9 7.6 - - + -
280B ILE* 4.0 9.6 - - + +
281B ASN 3.7 8.3 - - - +
282B ARG* 3.4 42.6 + - + +
283B GLU 3.7 2.5 - - - -
284B PHE* 3.6 17.9 - - - +
313B ALA* 1.3 80.0 - - - +
315B CYS* 1.3 65.8 + - - +
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Residues in contact with CYS 315 (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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42B GLY 4.1 1.1 - - - -
43B SER* 3.7 14.8 - - - -
45B HIS* 3.6 18.8 - - + +
49B ARG* 3.7 15.7 - - - +
222B ARG* 3.7 2.3 - - - -
223B GLN 2.8 31.8 + - - -
225B VAL* 6.2 0.4 - - + -
313B ALA* 5.3 2.2 - - + -
314B VAL* 1.3 80.7 - - - +
316B MET* 1.3 69.2 + - - +
400B FAD 1.8 60.6 - - + -
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Residues in contact with MET 316 (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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41B ASN 3.2 27.6 - - - +
42B GLY* 3.8 14.1 + - - +
43B SER* 2.8 29.9 + - - +
203B ALA* 3.6 24.9 - - + -
204B TRP* 3.9 11.4 - - + -
220B PRO* 5.3 0.2 - - + -
221B TYR 3.3 9.4 - - - +
275B ILE* 3.8 12.3 - - + -
277B PRO* 3.8 27.1 - - - -
280B ILE* 3.5 25.1 - - + -
282B ARG* 3.9 8.7 - - - +
315B CYS* 1.3 82.9 - - - +
317B TYR* 1.3 68.7 + - - +
400B FAD 3.4 5.6 - - - +
806B CL 4.0 2.1 - - - +
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Residues in contact with TYR 317 (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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219B GLN 4.4 0.2 - - - -
220B PRO* 3.2 4.7 - - - +
221B TYR* 2.8 35.5 + - + +
223B GLN* 3.4 35.0 + - + -
254B TYR* 3.3 23.7 + - - -
269B HIS* 2.8 55.2 + + - -
316B MET* 1.3 75.0 - - - +
318B THR* 1.3 62.9 + - - +
319B LYS* 4.0 21.1 - - + -
343B SER 4.4 2.7 - - - -
344B GLY* 3.4 24.9 + - - +
400B FAD 3.4 39.2 - + - -
806B CL 3.6 5.2 - - - -
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Residues in contact with THR 318 (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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43B SER* 5.1 2.6 + - - -
202B GLY 3.9 9.0 - - - +
203B ALA* 3.0 37.8 + - - +
206B SER* 4.6 2.7 - - - -
218B LEU* 4.0 33.4 - - + -
219B GLN 3.6 5.4 - - - +
220B PRO* 4.2 9.1 - - + +
317B TYR* 1.3 77.6 + - - +
319B LYS* 1.3 58.8 + - - +
341B GLY* 3.3 17.8 - - - +
342B PHE 5.1 0.4 - - - -
343B SER* 2.9 23.6 + - - +
806B CL 3.4 10.5 - - - +
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Residues in contact with LYS 319 (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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217B PRO 3.9 0.7 - - - +
218B LEU* 3.3 7.9 - - - -
219B GLN* 3.0 37.7 + - + +
221B TYR* 3.5 46.8 + - + +
223B GLN* 4.8 3.8 + - - -
269B HIS 4.9 5.5 + - - -
270B THR* 4.7 13.1 + - - +
272B GLY 5.8 0.8 - - - +
317B TYR* 4.1 22.4 - - + -
318B THR* 1.3 74.3 - - - +
320B THR* 1.3 69.0 + - - +
323B GLU* 4.1 23.4 + - + +
343B SER* 3.4 22.0 - - - +
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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