Contacts of the strand formed by residues 262 - 266 (chain B) in PDB entry 4J1O
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 GLY 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B TYR* 3.2 17.6 - - - -
241B LEU 3.1 19.8 + - - -
260B CYS* 3.5 8.1 - - - -
261B ASP* 1.3 78.9 - - - +
263B PHE* 1.3 73.9 + - - -
288B LEU* 4.0 6.7 - - - +
289B PRO 3.1 14.1 - - - -
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Residues in contact with PHE 263 (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 TYR* 3.7 13.2 - - - -
241B LEU* 3.3 30.5 - - + +
245B GLY* 5.3 3.6 - - - -
251B VAL* 4.0 33.2 - - + -
254B ALA* 4.2 9.6 - - + -
255B ALA 5.0 0.4 - - - -
260B CYS* 3.6 27.4 - - - -
262B GLY* 1.3 79.5 - - - -
264B GLY* 1.3 64.6 + - - +
265B MET* 4.4 9.0 - - + -
279B PHE* 3.8 23.1 - + + -
283B CYS* 3.6 31.4 - - - -
288B LEU* 4.0 17.3 - - + -
289B PRO 3.1 6.9 + - - +
290B HIS* 3.1 25.8 - - + -
291B SER* 3.1 4.7 + - - -
318B GLU* 5.4 0.2 - - - +
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Residues in contact with GLY 264 (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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135B TYR* 5.7 0.4 - - - -
219B GLU* 4.4 17.4 + - - -
240B TYR* 4.5 4.8 - - - +
241B LEU 2.8 12.0 + - - +
242B ASP* 3.1 17.7 - - - +
263B PHE* 1.3 72.3 - - - +
265B MET* 1.3 58.7 + - - +
266B LYS* 5.4 0.7 - - - -
269B ARG* 2.9 17.2 + - - -
291B SER* 3.2 14.4 - - - -
293B ASP* 4.5 4.7 - - - -
407B PBE 5.9 0.2 - - - -
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Residues in contact with MET 265 (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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242B ASP 5.4 0.2 - - - +
245B GLY* 3.6 27.8 - - - +
251B VAL* 3.8 18.2 - - + -
263B PHE* 3.7 7.8 - - + -
264B GLY* 1.3 73.9 - - - +
266B LYS* 1.3 74.7 - - - +
269B ARG* 3.7 10.1 - - - +
270B ILE* 4.0 14.1 - - + -
276B MET* 3.6 26.5 - - + +
279B PHE* 3.5 46.9 - - + -
291B SER* 3.6 17.2 + - - +
292B CYS* 3.7 1.9 - - - -
293B ASP* 2.9 26.1 + - - +
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Residues in contact with LYS 266 (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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56B TYR* 2.7 34.6 + - + -
242B ASP* 3.0 20.8 + - - +
264B GLY 5.1 0.4 - - - +
265B MET* 1.3 83.0 - - - +
267B LEU* 1.3 66.7 + - - +
268B THR* 4.9 0.9 - - - +
269B ARG* 3.2 45.4 + - + +
270B ILE* 3.2 11.1 + - - +
293B ASP* 3.3 10.2 + - + +
294B ASP* 3.8 17.0 - - - +
295B ALA* 3.6 33.7 - - + +
407B PBE 3.1 27.3 + - - -
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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