Contacts of the helix formed by residues 254 - 258 (chain B) in PDB entry 2I91
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 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B LYS* 3.8 28.3 - - + +
252B ARG* 4.1 9.0 - - - +
253B LEU* 1.3 78.1 - - - +
255B ARG* 1.3 56.3 + - - +
256B GLU* 3.4 16.8 - - + +
257B HIS* 2.7 53.9 + - + +
258B LEU* 3.9 3.2 + - - +
272B LEU* 4.3 8.5 - - - -
275B ASP 5.9 0.2 - - - +
277B PRO* 4.1 31.2 - - + -
14F A 6.5 0.2 - - - -
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Residues in contact with ARG 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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254B VAL* 1.3 74.8 - - + +
256B GLU* 1.3 82.8 + - - +
258B LEU* 2.8 31.2 + - - +
263B LEU* 4.1 28.5 - - + +
269B TRP* 3.7 28.9 - - + -
272B LEU* 4.1 22.3 - - + +
276B MET* 6.2 1.7 - - + -
280B ALA* 4.3 7.7 - - + +
284B ASN* 3.9 13.5 + - - +
12F U 3.1 64.7 + - - +
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Residues in contact with GLU 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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169B THR 4.6 4.9 - - - +
170B LYS* 3.2 54.1 - - + +
171B TYR* 5.1 0.5 - - - -
174B ARG* 4.2 15.1 + - - +
236B LYS* 5.3 3.6 + - - -
254B VAL* 3.1 17.3 + - + +
255B ARG* 1.3 99.4 + - - +
257B HIS* 1.3 61.4 - - - +
258B LEU 3.3 5.3 + - - +
4E U 5.5 9.4 - - - +
5E A 4.5 18.4 - - - +
12F U 3.7 19.8 - - - +
13F C 4.2 0.2 + - - -
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Residues in contact with HIS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 4.6 1.0 + - - +
169B THR* 3.0 49.6 + - - -
170B LYS* 3.8 7.1 + - - +
228B TYR* 3.4 14.2 + - - -
232B THR* 3.5 22.0 - - + +
235B VAL* 3.7 15.9 - - + +
236B LYS* 4.1 20.2 - - - +
252B ARG 4.8 1.0 + - - -
253B LEU* 3.4 21.9 - - + +
254B VAL* 2.7 57.2 + - + +
256B GLU* 1.3 71.5 - - - +
258B LEU* 1.3 64.7 + - + +
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Residues in contact with LEU 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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235B VAL* 3.7 22.9 - - + -
236B LYS* 5.6 0.7 - - - -
244B ILE* 4.3 8.1 - - + -
248B ILE* 3.8 26.7 - - + -
253B LEU* 4.9 2.0 - - + -
254B VAL 3.9 7.0 - - - +
255B ARG 2.8 15.4 + - - +
256B GLU 4.1 4.9 - - - +
257B HIS* 1.3 95.2 - - + +
259B LEU* 1.3 70.1 + - - +
260B THR* 3.4 2.8 + - - -
262B HIS* 4.4 6.7 - - + +
263B LEU* 4.3 12.3 - - + +
268B ILE* 3.3 34.3 - - + -
272B LEU* 3.9 15.0 - - + -
5E A 4.2 8.5 + - - +
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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