Contacts of the helix formed by residues 170 - 179 (chain A) in PDB entry 4IVR
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ILE* 3.0 23.9 + - + +
168A ALA 3.4 2.0 - - - -
169A LEU* 1.3 81.8 - - - +
171A CYS* 1.3 76.2 + - - +
173A PRO* 3.6 7.4 - - - +
174A ALA* 2.9 39.4 + - + +
187A VAL* 4.7 2.5 - - + +
191A VAL* 3.8 23.3 - - + -
194A ILE* 4.3 7.0 - - + -
242A LEU* 4.3 8.5 - - + -
288A LEU* 3.9 31.4 - - + -
292A PHE* 5.0 9.4 - - + -
315A LEU* 4.0 20.6 - - + -
319A LEU* 4.5 3.8 - - + -
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Residues in contact with CYS 171 (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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166A ILE* 2.8 22.6 + - - +
167A ALA 3.7 4.0 - - - +
170A LEU* 1.3 86.3 - - - +
172A TYR* 1.3 64.0 + - - +
175A ALA 3.0 18.0 + - - -
235A ILE* 3.7 5.1 - - - +
238A VAL* 3.5 25.6 - - + +
239A TYR* 3.5 49.4 - - + +
242A LEU* 3.7 20.6 - - - -
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Residues in contact with TYR 172 (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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57A PRO* 4.1 0.5 - - - +
58A HIS* 2.8 49.3 + + - +
101A TYR* 5.3 0.2 - - - -
125A GLN* 3.4 6.1 - - - +
163A ARG* 3.3 13.7 + - - -
167A ALA 3.0 21.4 + - - +
171A CYS* 1.3 69.4 - - - +
173A PRO* 1.3 73.1 - - + +
175A ALA* 3.1 3.2 + - - +
176A ARG* 2.9 25.9 + - - +
231A MET* 4.1 16.1 - - + +
235A ILE* 3.8 27.0 - - + +
239A TYR* 3.8 19.3 - + - -
501A N50 3.5 67.8 - + + +
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Residues in contact with PRO 173 (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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125A GLN* 3.4 16.6 - - - +
167A ALA 3.8 2.5 - - - +
168A ALA* 3.2 27.4 - - - +
169A LEU 4.7 0.2 - - - -
170A LEU* 3.6 20.4 - - - +
172A TYR* 1.3 92.7 - - + +
174A ALA* 1.3 63.6 + - - +
176A ARG* 2.9 13.7 + - + +
177A TYR* 2.9 13.7 + - - +
182A MET* 4.3 5.4 - - - +
187A VAL* 3.7 21.5 - - + +
190A PHE* 3.4 28.0 - - + -
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Residues in contact with ALA 174 (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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170A LEU* 2.9 27.0 + - + +
171A CYS 3.5 4.9 - - - +
172A TYR 3.3 0.2 - - - -
173A PRO* 1.3 75.3 - - - +
175A ALA* 1.3 63.5 + - - +
177A TYR* 3.3 10.7 + - - +
178A LEU* 3.0 23.9 + - - +
187A VAL* 4.2 15.2 - - + +
238A VAL* 4.1 17.3 - - + -
288A LEU* 5.4 1.1 - - + -
291A LEU* 4.1 18.1 - - + +
292A PHE* 5.7 1.1 - - + -
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Residues in contact with ALA 175 (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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171A CYS 3.0 13.6 + - - +
172A TYR 3.1 8.5 + - - +
174A ALA* 1.3 77.9 - - - +
176A ARG* 1.3 57.1 + - - +
178A LEU* 3.2 8.1 + - - +
179A MET* 3.0 31.8 + - - +
231A MET* 3.6 20.2 - - + -
234A ALA* 3.9 1.9 - - + +
235A ILE* 3.7 30.5 - - + +
238A VAL* 3.8 8.5 - - + +
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Residues in contact with ARG 176 (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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100A ILE* 3.3 27.7 - - - +
101A TYR* 3.5 28.1 + - - -
104A GLN* 2.9 39.4 + - - +
121A MET* 3.7 12.1 - - + +
125A GLN* 3.6 22.4 - - - +
172A TYR* 2.9 15.6 + - - +
173A PRO 2.9 9.0 + - - +
175A ALA* 1.3 72.9 - - - +
177A TYR* 1.3 64.3 + - - +
179A MET* 3.1 4.1 + - - -
180A GLY 3.0 4.7 + - - -
181A SER* 2.9 43.0 + - - +
182A MET* 4.0 13.2 - - + -
228A ASP* 4.9 1.8 + - - -
231A MET* 3.3 34.5 - - + +
501A N50 4.2 6.3 + - - -
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Residues in contact with TYR 177 (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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173A PRO 2.9 10.6 + - - +
174A ALA* 3.3 14.1 - - - +
176A ARG* 1.3 79.0 - - - +
178A LEU* 1.3 78.2 + - + +
180A GLY* 2.9 14.0 + - - -
182A MET* 3.2 30.8 - - - +
184A PRO* 3.6 35.9 - - + -
187A VAL* 3.9 16.2 - - + -
291A LEU* 3.4 31.5 + - + -
292A PHE* 6.0 3.6 - + - -
294A ALA* 3.3 26.3 - - - +
296A GLU* 4.5 3.0 + - - -
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Residues in contact with LEU 178 (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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174A ALA 3.0 15.7 + - - +
175A ALA 3.2 8.0 + - - +
177A TYR* 1.3 87.2 - - + +
179A MET* 1.3 60.7 + - - +
180A GLY 3.2 1.3 + - - -
234A ALA* 4.1 23.8 - - + +
237A ARG* 3.8 29.2 - - + +
238A VAL* 3.9 25.4 - - + -
291A LEU* 3.7 26.5 - - + -
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Residues in contact with MET 179 (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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104A GLN* 3.4 42.9 + - + +
107A LEU* 4.1 3.3 - - - +
108A ASP* 4.5 11.2 - - - +
175A ALA 3.0 17.8 + - - +
176A ARG* 3.1 10.7 + - - +
178A LEU* 1.3 77.0 - - - +
180A GLY* 1.3 60.6 + - - +
181A SER 3.3 0.2 - - - -
228A ASP* 3.7 30.1 - - - +
230A ALA* 3.6 35.7 - - + +
231A MET* 3.7 21.8 - - + +
234A ALA* 4.3 4.7 - - + -
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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