Contacts of the strand formed by residues 290 - 294 (chain B) in PDB entry 2IHU
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 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ALA 4.6 2.2 - - - +
212B LEU* 3.8 17.9 - - + +
213B LEU* 3.5 41.5 - - + +
216B ALA* 4.0 15.5 - - + -
218B HIS 3.9 0.2 + - - -
219B PRO* 3.3 7.0 - - + +
220B VAL 3.0 27.4 + - - +
288B VAL* 3.4 4.2 - - - +
289B ASP* 1.3 83.3 + - - +
291B VAL* 1.3 63.6 + - - +
292B LEU* 4.0 20.9 - - + -
314B LYS* 3.4 25.1 - - + +
316B VAL* 3.9 25.1 - - + -
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 3.9 6.3 - - + -
222B VAL* 3.9 27.1 - - + -
285B PHE* 4.9 1.3 - - + -
288B VAL* 3.9 17.7 - - + -
290B LEU* 1.3 75.0 - - - +
292B LEU* 1.3 62.1 + - - +
293B THR* 3.7 17.7 + - + +
307B TRP* 4.1 28.9 - - + -
313B LYS* 3.9 20.9 - - + -
314B LYS 2.9 13.2 + - - +
315B THR* 3.3 10.2 - - + -
316B VAL 2.8 26.0 + - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ALA* 4.7 3.4 - - + +
213B LEU* 5.1 4.5 - - + -
219B PRO* 4.5 9.2 - - + -
220B VAL 3.0 23.2 + - - +
221B LEU* 3.6 23.3 - - + -
222B VAL 2.8 25.3 + - - -
245B ILE* 5.5 1.3 - - + -
290B LEU* 4.0 26.2 - - + -
291B VAL* 1.3 72.6 - - - +
293B THR* 1.3 62.6 + - - +
294B VAL* 3.2 12.6 + - + +
316B VAL* 3.5 35.2 - - + +
318B ILE* 4.3 7.0 - - + -
342B PHE* 4.6 7.0 - - + -
346B PHE* 4.3 23.3 - - + -
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Residues in contact with THR 293 (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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222B VAL* 3.4 14.4 - - + -
291B VAL* 3.9 17.0 - - + +
292B LEU* 1.3 68.4 - - - +
294B VAL* 1.3 61.8 + - - +
295B GLY 3.4 1.7 + - - -
296B TYR* 3.6 27.5 + - + +
307B TRP* 3.7 30.1 - - + -
316B VAL 2.9 12.1 + - - -
317B ARG* 3.4 5.9 - - - -
318B ILE* 3.1 22.6 + - - +
329B TYR* 2.8 29.3 + - - +
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Residues in contact with VAL 294 (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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221B LEU* 4.0 28.3 - - + -
222B VAL 2.7 11.7 + - - +
223B VAL* 3.5 8.2 - - + -
224B GLY 3.0 26.0 + - - -
227B ALA* 4.0 5.0 - - + +
236B ILE* 3.9 21.3 - - + -
292B LEU* 3.4 17.0 - - + +
293B THR* 1.3 68.4 - - - +
295B GLY* 1.3 60.3 + - - +
318B ILE* 4.2 18.2 - - + -
339B VAL* 3.6 26.5 - - + -
342B PHE* 5.1 5.8 - - + -
343B VAL* 4.9 5.4 - - + -
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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