Contacts of the helix formed by residues 176 - 188 (chain A) in PDB entry 4FJV
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 ASP 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PHE* 6.1 0.7 - - + -
175A CYS* 1.3 74.5 - - - +
177A HIS* 1.3 81.6 + - - +
178A ILE 3.3 2.2 - - - +
179A GLN* 3.2 19.0 + - - +
180A ILE* 3.0 27.9 + - - +
42B ARG* 4.3 18.1 + - - -
70B VAL* 6.5 0.2 - - - -
71B LEU 3.3 10.3 - - - +
72B ARG* 4.8 1.0 - - - -
73B LEU 3.0 27.3 + - - -
74B ARG* 3.8 26.0 + - + +
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Residues in contact with HIS 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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176A ASP* 1.3 80.4 + - - +
178A ILE* 1.3 64.3 + - - +
180A ILE* 3.2 3.5 + - - +
181A THR* 2.9 23.6 + - + +
208A PHE* 3.7 28.2 - + - -
7B THR* 6.4 0.4 - - - -
8B LEU* 3.5 38.0 - - + +
9B THR* 6.1 3.6 - - + +
69B LEU 5.2 1.3 - - - -
70B VAL* 4.5 6.5 - - + -
71B LEU* 2.9 62.6 + - + +
73B LEU* 4.1 15.0 - - + +
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Residues in contact with ILE 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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143A ILE* 3.6 25.6 - - + -
150A PHE* 4.1 19.2 - - + +
153A PHE* 3.7 21.3 - - + +
154A ILE* 3.5 29.8 - - + -
163A PHE* 4.0 17.3 - - + -
176A ASP* 4.8 0.8 - - + +
177A HIS* 1.3 78.4 - - + +
179A GLN* 1.3 69.8 + - - +
181A THR* 3.4 8.8 - - - +
182A ALA* 2.9 25.5 + - - +
8B LEU* 4.2 17.7 - - + -
70B VAL* 4.6 9.2 - - + -
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Residues in contact with GLN 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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52A PHE* 5.0 1.3 - - - -
53A TYR* 3.4 27.1 - - + +
139A THR* 3.6 16.1 - - + +
143A ILE* 4.7 0.4 - - + -
163A PHE* 3.8 22.4 - - + -
167A GLU* 3.1 24.9 + - - +
168A VAL* 3.9 20.4 - - + -
174A GLU 3.8 13.9 + - - -
175A CYS* 4.2 2.9 - - + -
176A ASP* 3.2 35.2 + - - +
178A ILE* 1.3 78.4 - - - +
180A ILE* 1.3 58.4 + - - +
182A ALA* 3.2 0.7 + - - -
183A LEU* 2.9 30.3 + - - +
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.8 23.6 - - + -
175A CYS* 4.0 14.1 - - - -
176A ASP 3.0 29.0 + - - +
177A HIS* 3.2 4.5 + - - +
179A GLN* 1.3 76.7 - - - +
181A THR* 1.3 62.0 + - - +
183A LEU* 3.4 2.1 + - - +
184A SER* 3.1 22.0 + - - -
191A LEU* 3.6 28.3 - - + -
193A VAL* 5.2 3.1 - - + -
208A PHE* 4.2 18.8 - - + -
225A TYR* 3.4 32.1 - - + +
73B LEU* 4.0 13.9 - - + -
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Residues in contact with THR 181 (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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150A PHE* 4.8 6.7 - - + -
177A HIS* 2.9 31.9 + - + +
178A ILE* 3.4 5.2 - - - +
180A ILE* 1.3 78.6 - - - +
182A ALA* 1.3 65.2 + - - +
184A SER* 3.7 5.5 - - - -
185A GLN* 2.9 48.5 + - - +
208A PHE* 4.0 24.8 - - - +
8B LEU* 4.1 23.1 + - + +
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Residues in contact with ALA 182 (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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139A THR* 3.9 10.8 - - + +
142A PHE* 3.8 22.0 - - + -
143A ILE* 3.8 27.1 - - + -
150A PHE* 4.7 4.7 - - + -
178A ILE 2.9 20.1 + - - +
179A GLN 3.6 3.8 - - - +
181A THR* 1.3 78.8 - - - +
183A LEU* 1.3 57.0 + - - +
185A GLN* 3.4 3.0 + - - +
186A ALA* 2.8 30.2 + - - +
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Residues in contact with LEU 183 (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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52A PHE* 4.1 7.6 - - + -
53A TYR* 3.7 30.3 - - + -
56A LEU* 3.7 27.8 - - + +
135A LEU* 3.9 26.7 - - + +
138A LEU* 4.4 8.5 - - + -
139A THR* 3.3 23.5 + - - +
179A GLN 2.9 14.2 + - - +
180A ILE 4.0 2.5 - - - +
182A ALA* 1.3 72.9 - - - +
184A SER* 1.3 67.7 + - - +
186A ALA* 3.1 3.4 + - + -
187A LEU* 3.1 46.5 + - + +
189A ILE* 5.5 0.2 - - - +
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Residues in contact with SER 184 (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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56A LEU* 5.0 5.0 - - - +
180A ILE 3.1 17.1 + - - -
181A THR* 3.7 5.6 - - - -
183A LEU* 1.3 77.7 - - - +
185A GLN* 1.3 58.7 + - - +
188A SER* 2.9 24.9 + - - -
189A ILE* 2.8 38.2 + - - +
191A LEU* 5.0 7.2 - - - -
208A PHE* 3.4 30.2 + - - +
209A PRO* 4.1 4.3 - - - +
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Residues in contact with GLN 185 (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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77A ARG* 3.3 17.2 + - - -
142A PHE* 3.6 32.7 - - + -
150A PHE* 4.8 7.6 - - - -
181A THR* 2.9 46.5 + - - +
182A ALA* 3.8 1.7 - - - +
184A SER* 1.3 78.7 - - - +
186A ALA* 1.3 64.6 + - - +
187A LEU 3.3 0.7 + - - -
188A SER* 3.4 5.8 + - - +
209A PRO* 6.0 7.0 - - + -
8B LEU 4.8 9.3 + - - -
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Residues in contact with ALA 186 (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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77A ARG* 3.2 18.5 + - - +
81A THR* 5.2 3.6 - - - +
84A ASP* 5.4 2.6 - - - +
138A LEU* 4.0 30.2 - - + +
142A PHE* 3.7 28.6 - - + -
182A ALA 2.8 21.6 + - - +
183A LEU* 3.1 8.7 + - - +
185A GLN* 1.3 73.3 - - - +
187A LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 187 (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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56A LEU* 5.9 0.2 - - + -
60A TYR* 5.2 0.5 + - - -
74A PHE* 3.7 36.4 - - + -
77A ARG* 3.4 18.0 - - + +
78A VAL* 4.8 7.0 - - + -
81A THR* 4.4 11.4 - - + -
102A PHE* 4.6 6.5 - - + -
134A PHE* 5.6 0.4 - - + -
135A LEU* 3.8 29.4 - - + -
138A LEU* 3.5 26.9 - - + -
183A LEU* 3.1 20.5 + - + +
186A ALA* 1.3 77.2 - - - +
188A SER* 1.3 71.3 + - - +
189A ILE* 3.3 29.8 + - + +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 5.3 4.7 + - - -
77A ARG* 3.0 32.8 + - - -
184A SER 2.9 9.8 + - - -
185A GLN* 3.4 7.4 + - - +
187A LEU* 1.3 77.7 - - - +
189A ILE* 1.3 60.5 + - - +
190A ALA* 3.5 3.5 + - - +
209A PRO* 6.2 1.8 - - - -
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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