Contacts of the strand formed by residues 251 - 258 (chain B) in PDB entry 3G65
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 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B PHE* 3.9 1.2 - - - -
167B PHE* 6.5 0.4 - - + -
179B ILE* 3.9 21.3 - - + -
181B MET* 6.3 0.9 - - - -
223B TYR* 3.6 25.8 - - + +
228B LEU* 3.9 37.9 - - + -
243B ILE* 4.0 21.8 - - + -
244B ARG 3.2 18.8 - - - +
245B THR* 4.9 3.8 - - - -
249B GLY 3.6 0.2 + - - -
250B PHE* 1.3 73.9 - - - +
252B SER* 1.3 62.8 + - - +
253B LEU* 4.1 19.5 - - + -
269B TYR 4.1 1.1 - - - +
270B TYR* 3.2 30.0 - - - +
271B CYS* 2.8 16.4 + - + +
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Residues in contact with SER 252 (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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147B PHE* 3.3 33.9 - - - -
242B SER 3.0 7.4 + - - +
243B ILE* 3.6 1.2 - - - -
244B ARG* 2.8 57.8 + - - -
251B LEU* 1.3 74.1 - - - +
253B LEU* 1.3 63.8 + - - +
254B GLN* 4.8 2.8 + - - +
268B GLU* 5.3 4.9 + - - +
269B TYR 3.3 4.4 + - - -
270B TYR* 4.0 13.2 + - - -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 5.0 12.3 - - + -
228B LEU* 4.1 16.4 - - + -
231B SER* 3.6 21.1 - - - +
241B VAL* 4.7 4.5 - - + -
242B SER 4.0 1.6 - - - -
243B ILE* 4.0 38.1 - - + -
251B LEU* 4.1 15.7 - - + -
252B SER* 1.3 73.9 + - - +
254B GLN* 1.3 60.4 + - - +
255B TYR* 3.3 34.8 - - + +
267B VAL 3.3 2.3 - - - +
268B GLU* 3.1 5.5 - - - -
269B TYR* 2.7 47.5 + - + +
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Residues in contact with GLN 254 (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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240B LYS 3.8 0.5 - - - +
241B VAL* 3.2 6.4 - - - +
242B SER* 2.8 55.1 + - - +
244B ARG* 3.1 27.4 + - - +
252B SER* 3.8 2.7 + - - +
253B LEU* 1.3 72.8 - - - +
255B TYR* 1.3 63.2 + - - +
256B MET* 4.3 1.4 + - + +
266B PHE* 3.3 38.0 - - + -
267B VAL 3.5 2.7 - - - +
268B GLU* 3.7 30.0 + - + +
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Residues in contact with TYR 255 (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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167B PHE* 5.7 1.7 - - - -
231B SER* 3.4 20.7 + - - -
234B ALA* 3.7 18.6 - - + +
235B LEU* 3.7 24.5 - - + +
238B SER* 3.3 26.9 - - - -
240B LYS 3.6 2.0 - - - -
241B VAL* 3.8 24.1 - - + +
253B LEU* 3.3 41.8 - - + +
254B GLN* 1.3 73.6 - - - +
256B MET* 1.3 64.2 + - - +
257B ILE* 3.7 3.3 + - + -
265B CYS 3.6 0.3 - - - +
266B PHE* 3.5 12.4 - - - -
267B VAL* 2.7 56.4 + - + +
269B TYR* 3.5 23.3 - + - -
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Residues in contact with MET 256 (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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238B SER* 3.2 2.5 - - - -
239B CYS* 2.9 31.9 + - + +
240B LYS* 3.1 57.9 + - + +
242B SER* 5.9 2.7 - - - +
254B GLN* 5.7 1.6 - - + +
255B TYR* 1.3 72.7 - - - +
257B ILE* 1.3 61.7 + - - +
258B ARG* 4.0 2.8 + - + -
264B ILE* 3.7 28.5 - - + -
265B CYS 3.7 2.9 - - - -
266B PHE* 4.2 21.5 - - + -
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Residues in contact with ILE 257 (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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29B THR* 5.2 2.9 - - + -
30B ILE* 4.3 17.3 - - + +
33B ALA* 4.2 15.3 - - + -
234B ALA* 4.7 4.7 - - + +
237B LEU* 3.5 48.7 - - + +
238B SER* 4.1 8.5 - - - -
255B TYR* 4.6 5.4 - - + +
256B MET* 1.3 74.3 - - - +
258B ARG* 1.3 68.7 + - - +
259B ASN* 4.2 3.1 - - - +
265B CYS* 2.7 49.2 + - + +
267B VAL* 3.8 28.3 - - + -
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Residues in contact with ARG 258 (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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237B LEU 5.2 0.6 + - - -
239B CYS* 4.6 24.1 - - + -
256B MET* 4.0 2.6 + - + +
257B ILE* 1.3 80.8 - - - +
259B ASN* 1.3 70.5 + - - +
260B GLU* 5.5 0.5 - - - +
262B GLY* 3.3 33.3 + - - +
263B GLN 3.6 4.0 - - - -
264B ILE* 4.1 20.6 - - + +
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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