Contacts of the strand formed by residues 261 - 266 (chain B) in PDB entry 1I2M
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 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B PHE* 4.1 19.7 - - + -
254B ALA 3.6 5.6 - - - +
255B ILE* 4.7 5.4 - - + -
259B GLY 4.3 6.3 - - - +
260B HIS* 1.3 73.5 - - - +
262B TYR* 1.3 63.4 + - - +
285B ASN* 3.4 8.6 + - - +
286B LEU* 3.0 33.7 + - + +
289B PHE* 3.8 23.4 + - + +
296B TRP* 3.8 34.3 - - + -
299B PHE* 3.8 28.0 - - + -
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Residues in contact with TYR 262 (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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231B LEU* 3.7 26.2 - - + -
240B VAL* 4.0 21.8 - - + +
242B PHE* 4.2 21.5 - + + -
253B PHE* 3.3 6.6 - - - +
254B ALA* 2.7 41.5 + - + +
256B SER* 4.1 12.1 - - - -
260B HIS* 3.8 33.1 + - + -
261B VAL* 1.3 79.2 - - - +
263B GLY* 1.3 59.2 + - - +
264B PHE* 4.9 3.8 - - + -
283B PRO* 4.6 4.5 - - + -
284B GLN* 3.3 11.4 - - - +
285B ASN* 3.7 38.1 + - + +
286B LEU* 4.1 2.9 - - - -
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Residues in contact with GLY 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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252B THR 3.2 11.2 - - - -
253B PHE* 4.5 0.7 - - - -
262B TYR* 1.3 76.3 - - - +
264B PHE* 1.3 64.6 + - - +
272B LEU* 4.2 10.1 - - - -
280B CYS* 4.1 5.4 - - - -
283B PRO* 3.6 0.2 - - - +
284B GLN* 3.0 32.9 + - - +
286B LEU* 3.7 19.0 - - - +
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Residues in contact with PHE 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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193B LEU* 4.0 21.5 - - + -
195B THR* 4.8 2.7 - - + -
202B GLY 3.5 5.2 - - - +
203B GLN* 3.2 24.8 - - - -
204B LEU 3.7 4.7 - - - -
205B GLY* 3.3 28.9 - - - -
229B VAL* 4.3 11.9 - - + -
231B LEU* 6.2 0.2 - - + -
242B PHE* 6.1 1.8 - + - -
251B PHE* 3.4 2.6 - - - +
252B THR* 2.8 57.7 + - + -
254B ALA* 4.9 9.9 - - + -
262B TYR* 5.1 2.5 - - + -
263B GLY* 1.3 83.5 - - - +
265B GLY* 1.3 61.7 + - - +
272B LEU* 3.6 9.4 - - - +
280B CYS* 3.4 14.6 - - - +
282B ILE 4.6 0.2 - - - -
283B PRO* 3.8 31.9 - - + -
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Residues in contact with GLY 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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201B GLN 3.0 18.4 - - - -
202B GLY 3.5 0.8 + - - -
203B GLN 3.5 14.4 - - - -
250B TYR 3.6 5.8 - - - -
251B PHE* 4.0 0.4 - - - -
264B PHE* 1.3 75.1 - - - +
266B LEU* 1.3 66.1 + - - -
267B SER 3.6 0.3 + - - -
272B LEU* 3.7 2.1 - - - +
280B CYS* 2.8 37.4 + - - +
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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
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71A LYS 3.9 7.4 - - - +
72A PHE* 3.8 26.7 - - + +
201B GLN* 3.5 20.8 + - + -
250B TYR* 2.9 49.7 + - + +
251B PHE* 3.7 9.8 - - + +
265B GLY* 1.3 72.8 - - - -
267B SER* 1.3 59.0 - - - +
268B ASN* 3.3 31.9 - - - +
271B GLN* 2.9 29.6 - - - +
272B LEU* 3.7 2.8 - - - +
278B GLU 3.5 17.7 - - - +
279B SER* 4.6 3.4 - - - +
303B GLN 4.0 3.6 - - - +
304B HIS* 4.5 0.4 - - + -
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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