Contacts of the helix formed by residues 235 - 245 (chain A) in PDB entry 4F5G
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 ALA 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.7 9.2 - - - +
222A ILE* 4.8 4.3 - - + -
225A GLN* 3.5 25.4 - - - +
231A LEU 3.4 2.4 + - - -
232A GLU 3.1 8.0 + - - +
233A GLU 3.1 1.2 - - - -
234A ASP* 1.3 74.2 - - - +
236A GLU* 1.3 65.4 + - - +
237A GLY 3.2 2.9 - - - -
238A LEU* 3.3 9.7 + - + +
239A ARG* 2.8 49.4 + - - +
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Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 3.8 42.8 - - + +
204A TRP* 5.5 1.6 - - + -
229A ARG* 2.8 32.0 + - - +
232A GLU 3.4 10.1 + - - +
233A GLU* 3.1 26.2 + - - +
234A ASP 3.3 0.2 - - - -
235A ALA* 1.3 78.0 - - - +
237A GLY* 1.3 57.8 + - - +
239A ARG* 3.2 7.1 + - - +
240A ALA* 2.8 30.7 + - - +
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLY 4.9 2.0 + - - -
204A TRP* 3.4 49.8 - - - +
233A GLU 4.8 0.2 + - - -
234A ASP 4.6 3.2 + - - -
235A ALA 3.2 0.4 - - - -
236A GLU* 1.3 75.5 - - - +
238A LEU* 1.3 66.1 + - - +
240A ALA* 3.1 4.7 + - - +
241A PHE* 3.1 26.0 + - - -
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.5 50.3 - - + +
93A PHE* 3.5 31.4 - - + -
189A GLY* 5.1 5.4 + - - -
204A TRP* 5.5 0.2 - - - -
220A ILE* 4.3 31.9 - - + +
222A ILE* 4.4 10.8 - - + -
234A ASP 5.5 0.2 - - - +
235A ALA* 3.3 13.0 + - + +
237A GLY* 1.3 73.6 - - - +
239A ARG* 1.3 62.2 + - - +
241A PHE* 3.1 6.4 + - - +
242A ALA* 2.8 23.1 + - + -
248A LEU* 4.4 2.6 - - + +
250A VAL* 4.0 22.0 - - + -
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Residues in contact with ARG 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU 2.9 24.5 + - - -
92A LEU 2.8 20.1 + - - +
93A PHE* 3.4 17.0 + - + +
94A GLY* 3.4 20.8 - - - +
225A GLN* 4.5 0.6 - - - +
232A GLU* 2.7 49.8 + - - +
235A ALA* 2.8 31.7 + - - +
236A GLU* 3.8 6.5 - - - +
238A LEU* 1.3 77.6 - - + +
240A ALA* 1.3 61.5 + - - +
242A ALA* 3.6 5.9 - - + +
243A ALA* 2.8 30.1 + - - +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 4.6 4.5 - - + -
204A TRP* 4.2 22.7 - - + +
205A GLN* 4.3 21.3 - - + +
208A ALA* 3.7 3.5 - - - +
236A GLU 2.8 14.0 + - - +
237A GLY 3.1 10.5 + - - +
239A ARG* 1.3 76.2 - - - +
241A PHE* 1.3 62.3 + - - +
243A ALA* 3.5 8.4 + - - +
244A MET* 3.5 24.1 - - - +
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Residues in contact with PHE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 3.5 24.7 - + - -
204A TRP* 3.5 33.9 - + - -
207A LEU* 3.9 7.6 - - + -
208A ALA* 3.8 24.9 - - + -
211A SER* 3.7 24.0 - - - -
218A PRO* 3.6 23.6 - - + -
220A ILE* 4.3 11.2 - - + -
237A GLY 3.1 21.0 + - - +
238A LEU* 3.4 9.4 - - - +
240A ALA* 1.3 75.7 - - - +
242A ALA* 1.3 64.7 + - - +
244A MET 3.1 1.6 + - - -
245A HIS* 2.9 51.9 + + - +
248A LEU* 3.9 12.8 - - + -
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 4.0 14.8 - - + -
99A LEU* 3.8 26.4 - - + +
104A ARG* 4.9 4.5 + - - -
238A LEU 2.8 19.0 + - - +
239A ARG* 3.2 8.9 + - + +
241A PHE* 1.3 75.5 - - - +
243A ALA* 1.3 61.6 + - - +
244A MET 3.2 0.5 + - - -
245A HIS 3.7 14.3 - - - +
248A LEU* 3.5 21.7 - - + +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ARG 2.8 17.0 + - - +
240A ALA* 3.7 9.2 - - - +
241A PHE 3.2 0.2 - - - -
242A ALA* 1.3 77.7 - - - +
244A MET* 1.3 74.9 + - + +
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Residues in contact with MET 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLN 5.7 0.7 - - - +
208A ALA* 4.1 15.3 - - + -
209A GLN* 4.4 17.9 - - - +
212A VAL* 3.1 32.0 - - + +
240A ALA 3.5 16.4 - - - +
241A PHE 3.1 1.0 + - - -
243A ALA* 1.3 95.2 - - + +
245A HIS* 1.3 65.2 + - - +
246A LYS 4.2 0.7 + - - -
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Residues in contact with HIS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 5.7 0.2 - - - +
104A ARG* 2.9 17.7 + - - -
208A ALA* 3.2 26.9 - - + -
211A SER* 2.6 24.8 + - - -
212A VAL* 3.6 16.0 + - + -
216A TRP 4.3 4.9 - - - -
218A PRO* 3.4 22.6 - - + +
241A PHE* 2.9 47.6 + + - +
242A ALA* 3.7 9.4 + - - +
243A ALA 3.6 0.6 - - - +
244A MET* 1.3 82.1 - - - +
246A LYS* 1.3 61.8 + - - +
247A GLU 3.5 15.7 - - - +
248A LEU* 3.9 7.9 - - + +
271A VAL* 5.1 1.4 - - - +
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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