Contacts of the strand formed by residues 264 - 269 (chain B) in PDB entry 3IH9
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 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 3.5 29.3 - - - -
62B ILE 6.0 0.7 - - - -
65B ALA* 5.3 3.4 - - - -
204B LEU* 4.3 3.1 - - - -
258B LYS 4.2 0.6 - - - +
259B SER* 3.4 1.7 + - - -
260B GLY* 2.9 28.7 + - - -
262B ALA* 3.6 3.2 - - - +
263B GLY* 1.3 79.4 - - - +
265B VAL* 1.3 64.5 + - - +
277B VAL 3.2 9.9 - - - -
278B PHE* 4.4 0.2 - - - -
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Residues in contact with VAL 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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204B LEU* 3.5 8.4 - - - +
242B MET* 5.8 2.2 - - + -
249B TRP* 5.8 1.3 - - + -
257B ALA* 4.3 6.5 - - + -
258B LYS 3.5 13.0 - - - +
259B SER* 3.8 12.3 - - - +
263B GLY 4.3 0.9 - - - +
264B GLY* 1.3 78.6 - - - +
266B LEU* 1.3 71.0 + - - +
275B ILE* 3.6 1.3 - - + +
276B GLY* 3.5 4.5 - - - -
277B VAL* 2.9 38.8 + - + +
288B SER* 3.8 25.1 - - - +
291B GLY* 4.1 16.6 - - - +
292B VAL* 4.6 5.8 - - + +
295B CYS* 4.2 21.8 - - - -
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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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65B ALA* 4.2 13.0 - - + +
68B PRO* 3.8 15.9 - - + -
69B PHE* 3.7 30.1 - - + -
204B LEU* 3.5 34.9 - - + +
208B GLY* 3.6 11.2 - - - +
211B LEU* 4.5 3.4 - - + -
237B MET* 3.5 26.0 - - + -
257B ALA* 2.9 28.9 - - - +
258B LYS* 2.8 22.2 + - + +
265B VAL* 1.3 73.2 - - - +
267B GLY* 1.3 79.8 + - - +
275B ILE* 3.7 2.9 - - - +
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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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208B GLY* 3.6 0.9 - - - -
237B MET* 5.1 0.2 - - - -
255B ILE* 4.5 4.7 - - - -
256B PRO 3.5 7.2 - - - -
257B ALA* 4.2 4.0 - - - -
266B LEU* 1.3 82.8 - - - +
268B ALA* 1.3 64.3 + - - +
274B GLY* 3.6 3.1 - - - -
275B ILE* 2.8 51.7 + - - +
295B CYS* 5.9 1.1 - - - -
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Residues in contact with ALA 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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208B GLY* 3.5 23.8 - - - +
211B LEU* 4.2 20.6 - - + -
212B ALA* 4.4 3.6 - - - +
234B VAL* 4.0 8.0 - - + +
237B MET* 4.7 7.6 - - + -
255B ILE* 4.3 2.6 - - - +
256B PRO* 3.0 36.5 + - - +
267B GLY* 1.3 75.7 - - - +
269B LEU* 1.3 60.7 + - - +
270B PRO* 3.5 4.6 - - - +
273B VAL 3.7 5.2 - - - -
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Residues in contact with LEU 269 (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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212B ALA* 3.2 6.8 - - - +
254B GLY 3.8 8.3 - - - +
255B ILE* 4.8 12.5 - - + +
256B PRO* 4.1 4.0 - - + -
268B ALA* 1.3 72.3 - - - +
270B PRO* 1.3 69.9 - - + +
272B ARG* 3.0 35.1 + - - +
273B VAL* 3.0 26.9 + - + +
275B ILE* 6.1 0.2 - - - +
304B LEU* 3.6 35.7 - - + +
305B HIS 3.7 18.2 - - - +
306B LEU* 3.5 45.8 - - + +
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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