Contacts of the helix formed by residues 297 - 306 (chain B) in PDB entry 2R9R
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 ILE 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ILE* 4.8 17.5 - - + -
180B PHE* 3.7 35.9 - - + -
181B CYS* 5.4 3.4 - - - -
294B ILE* 3.1 23.1 + - + +
295B MET 3.0 2.0 + - - -
296B ARG* 1.3 73.1 - - - +
298B LEU* 1.3 68.2 + - + +
299B ARG* 2.9 10.8 - - + -
300B ILE* 2.9 37.6 + - + +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ILE* 4.8 4.4 - - - +
261B VAL* 3.7 31.9 - - + +
262B ALA* 5.7 1.1 - - - -
295B MET* 3.0 29.9 + - + +
297B ILE* 1.3 80.5 - - + +
299B ARG* 1.3 58.2 + - - +
300B ILE* 2.8 12.6 + - - -
301B PHE* 2.9 48.6 + - + +
302B LYS 4.2 0.5 + - - -
503B PGW 3.9 17.7 - - + -
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ILE* 3.7 8.7 - - - +
176B SER* 2.8 63.0 + - - +
177B ILE* 4.3 11.4 - - + +
179B SER* 5.8 0.4 - - - -
180B PHE* 4.0 5.6 - - - +
226B GLU* 2.8 43.2 + - - -
230B ILE* 4.2 8.6 - - - +
233B PHE* 4.5 16.2 - - + -
262B ALA* 4.4 28.8 + - + +
295B MET 4.5 0.4 + - - -
296B ARG* 2.9 49.9 + - - +
297B ILE* 2.9 6.6 - - + +
298B LEU* 1.3 77.3 - - - +
300B ILE* 1.3 63.6 + - - +
301B PHE 3.2 0.2 - - - -
302B LYS* 3.1 21.0 + - - +
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Residues in contact with ILE 300 (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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177B ILE* 3.3 41.3 - - + -
297B ILE* 2.9 28.6 + - + +
298B LEU 2.8 1.0 + - - -
299B ARG* 1.3 79.6 - - - +
301B PHE* 1.3 99.1 + - + +
302B LYS 2.8 6.9 + - - -
303B LEU* 3.0 32.7 + - + +
310B LEU* 5.2 1.4 - - - +
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ILE* 3.5 26.6 - - + +
298B LEU* 2.9 41.9 + - + +
300B ILE* 1.3 93.1 - - + +
302B LYS* 1.3 54.3 + - - +
303B LEU 3.0 6.1 - - - -
304B SER* 2.7 30.6 + - - +
310B LEU* 5.3 14.6 - - + -
511B PGW 4.7 23.6 - - + -
512B PGW 3.8 41.1 - - + -
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Residues in contact with LYS 302 (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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173B ILE* 3.5 28.1 - - + +
233B PHE* 3.4 39.7 + - + +
236B GLU* 2.7 29.2 + - - +
258B ILE* 3.8 18.3 - - + +
259B ASP* 3.1 29.9 + - - +
262B ALA* 3.8 27.8 - - + -
299B ARG* 3.1 17.8 + - + +
300B ILE 2.8 1.0 + - - -
301B PHE* 1.3 75.9 - - - +
303B LEU* 1.3 63.8 + - - +
304B SER 3.1 1.6 + - - -
305B ARG* 3.4 19.4 + - - +
306B HIS* 3.9 2.8 + - - -
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Residues in contact with LEU 303 (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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170B VAL* 4.2 26.7 - - + -
173B ILE* 3.8 32.5 - - + -
174B LEU* 4.2 21.1 - - + -
177B ILE* 4.7 7.2 - - + -
300B ILE* 3.0 24.2 + - + +
302B LYS* 1.3 76.0 - - - +
304B SER* 1.3 55.6 + - - +
305B ARG 3.0 6.3 - - - -
306B HIS* 2.9 23.6 + - + +
307B SER* 3.1 13.9 + - - -
310B LEU* 4.1 11.2 - - + -
510B PGW 5.0 19.7 - - + +
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Residues in contact with SER 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B MET* 3.4 8.6 - - - +
258B ILE* 3.6 15.6 - - - +
301B PHE* 2.7 23.5 + - - -
303B LEU* 1.3 79.4 - - - +
305B ARG* 1.3 57.8 + - - +
306B HIS 3.1 0.4 + - - -
307B SER 3.5 2.6 - - - +
310B LEU* 3.6 34.2 - - - +
311B GLN* 3.0 30.8 + - - +
512B PGW 4.3 19.1 - - - +
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Residues in contact with ARG 305 (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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153B PHE 5.0 0.2 + - - -
154B GLU* 4.5 22.1 + - - +
236B GLU* 5.3 0.9 - - - -
240B ARG* 3.2 44.7 - - - +
253B ASN* 5.7 0.6 - - - +
255B MET* 3.2 50.3 + - + +
256B ASN* 3.9 8.1 + - - -
259B ASP* 2.8 28.9 + - - -
302B LYS* 3.4 12.9 + - - +
303B LEU 3.0 0.6 - - - -
304B SER* 1.3 80.3 + - - +
306B HIS* 1.3 79.1 + - + +
307B SER 3.6 0.2 - - - -
311B GLN* 3.8 8.3 + - - -
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Residues in contact with HIS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PRO* 5.4 6.7 - - + +
166B ALA* 3.9 34.2 - - + +
169B SER* 3.8 18.5 - - - -
170B VAL* 3.8 27.3 - - + +
173B ILE* 4.4 8.9 - - + +
236B GLU* 5.1 1.7 + - - -
240B ARG* 5.5 0.9 - - - -
302B LYS 3.9 17.2 + - - -
303B LEU* 2.9 10.3 + - + +
305B ARG* 1.3 104.5 + - + +
307B SER* 1.3 57.0 + - - +
308B LYS 4.1 1.4 + - - -
311B GLN* 4.7 1.1 - - - -
510B PGW 3.8 19.9 + - - +
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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
------------------------------------------------------------
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