Contacts of the strand formed by residues 264 - 268 (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 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLY 3.7 1.0 - - - +
227B PHE* 3.4 0.9 - - - -
228B PHE* 2.8 33.1 + - + -
230B SER* 3.2 18.8 + - - +
235B TYR* 3.8 32.1 - - + -
241B PHE* 3.9 17.5 - - + -
244B PHE* 4.3 7.2 - - + -
256B PHE 3.4 15.0 - - - +
258B SER* 3.9 6.4 - - - +
263B GLY* 1.3 71.1 - - - -
265B LYS* 1.3 76.3 + - - +
266B LEU* 4.0 7.0 - - + -
298B LEU* 3.8 25.8 - - + -
302B MET* 4.0 11.2 - - - -
305B ALA* 3.9 10.5 - - + +
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Residues in contact with LYS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY* 2.9 24.8 + - - -
48B THR* 3.0 39.8 + - - +
49B ARG* 4.1 4.4 - - - +
225B VAL* 3.8 33.7 - - + +
226B GLY 3.2 10.3 - - - +
227B PHE* 3.5 34.5 - - + +
254B TYR* 5.2 0.8 - - - -
255B GLY* 3.0 5.6 - - - -
256B PHE* 2.9 56.9 + - + +
257B PRO 5.8 0.2 - - - +
262B CYS* 6.1 0.2 - - - -
263B GLY 3.4 1.5 + - - +
264B LEU* 1.3 76.6 - - - +
266B LEU* 1.3 65.3 + - - +
400B FAD 5.7 1.2 - - - +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B VAL* 3.3 7.3 - - - -
226B GLY 2.9 32.9 + - - +
228B PHE* 4.6 6.7 - - + -
244B PHE* 3.6 27.8 - - + -
253B TYR* 4.2 6.7 - - + -
254B TYR* 3.3 17.7 - - - +
264B LEU* 4.0 8.5 - - + +
265B LYS* 1.3 77.3 - - - +
267B GLY* 1.3 64.8 + - - +
294B LEU* 3.4 48.8 - - + +
297B PHE* 3.6 29.4 - - + -
298B LEU* 3.7 11.0 - - + -
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Residues in contact with GLY 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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224B VAL 3.9 10.1 - - - -
225B VAL* 4.0 1.6 - - - -
253B TYR* 3.4 7.7 - - - +
254B TYR* 2.9 58.0 + - - -
266B LEU* 1.3 75.0 - - - +
268B TYR* 1.3 62.1 + - - -
294B LEU* 4.0 6.1 - - - -
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Residues in contact with TYR 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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250A ASN* 3.8 15.2 - - - +
268A TYR* 5.1 0.9 + - - -
223B GLN* 3.3 20.8 + - - -
224B VAL* 4.4 6.7 + - + +
250B ASN* 2.5 37.1 + - - +
251B GLY* 4.2 0.7 - - - -
252B ILE 3.5 8.3 - - - -
253B TYR* 3.5 36.3 - + + -
254B TYR* 4.2 2.1 + - - -
267B GLY* 1.3 70.1 - - - -
269B HIS* 1.3 58.3 + - - +
270B THR* 3.5 19.3 - - - -
271B PHE* 3.4 35.8 - + + +
293B ASN* 3.6 39.3 - - + -
294B LEU* 3.9 11.4 - - + +
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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