Contacts of the helix formed by residues 165 - 175 (chain A) in PDB entry 5E6J
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A TYR* 4.4 2.2 - - - -
158A LYS* 5.0 2.0 - - - +
164A GLY* 1.3 73.8 - - - -
166A VAL* 1.3 80.1 + - - +
167A ARG* 2.8 28.9 + - - +
168A GLU* 4.0 30.9 + - + +
169A THR* 3.0 25.3 + - - -
274A TYR* 3.4 9.1 + - - -
303A ASP* 4.9 0.5 - - - +
71B LEU 4.7 1.0 - - - +
72B ARG* 3.9 7.0 - - + -
73B LEU* 3.1 46.1 + - - +
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Residues in contact with VAL 166 (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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113A TYR* 3.6 28.5 - - + +
116A SER* 3.7 13.7 - - - -
117A VAL* 3.7 19.4 - - + +
165A ASP* 1.3 77.7 + - - +
167A ARG* 1.3 56.5 + - - +
169A THR* 3.4 2.7 + - - -
170A MET* 2.8 37.7 + - + +
244A MET* 4.5 1.3 - - + -
263A ASN* 3.7 17.9 - - - +
274A TYR* 3.3 32.5 + - + +
303A ASP* 3.7 15.7 - - - +
305A PHE* 5.5 0.4 - - + -
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Residues in contact with ARG 167 (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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165A ASP* 2.8 20.7 + - - +
166A VAL* 1.3 79.3 - - - +
168A GLU* 1.3 63.3 + - - +
170A MET* 3.2 4.0 + - - +
171A THR* 2.9 37.2 + - - -
207A MET* 3.9 19.6 - - + +
208A TYR 5.2 1.3 - - - -
209A MET* 3.6 39.1 - - - +
244A MET* 4.1 9.4 - - + -
246A SER* 3.4 36.8 - - - +
302A THR* 5.9 0.7 - - - -
303A ASP* 4.1 8.6 + - - +
42B ARG* 4.7 15.0 - - - +
44B ILE* 4.5 4.4 - - - +
49B GLN* 3.2 39.2 + - - +
70B VAL* 5.7 1.4 - - - +
73B LEU* 6.1 0.4 - - + -
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Residues in contact with GLU 168 (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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158A LYS* 5.9 3.6 - - + +
165A ASP* 3.6 22.9 + - + +
166A VAL 3.4 0.4 - - - -
167A ARG* 1.3 86.0 - - - +
169A THR* 1.3 58.2 + - - +
171A THR* 3.1 9.7 + - - -
172A HIS* 2.9 48.3 + - + +
42B ARG* 2.5 49.2 + - - +
72B ARG* 3.0 22.6 + - - +
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Residues in contact with THR 169 (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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113A TYR* 3.7 17.1 - - + -
114A LEU* 4.9 2.7 - - + -
117A VAL* 4.1 19.7 - - + -
152A ILE* 3.4 33.4 - - + -
156A SER* 3.9 14.3 + - - +
158A LYS* 4.7 7.4 - - - +
165A ASP 3.0 17.3 + - - -
166A VAL* 3.7 4.0 - - - -
168A GLU* 1.3 76.9 - - - +
170A MET* 1.3 58.2 + - - +
172A HIS* 3.2 2.7 + - - +
173A LEU* 2.8 37.7 + - + +
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Residues in contact with MET 170 (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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117A VAL* 3.8 31.2 - - + +
120A ALA* 4.9 1.6 - - + -
121A LEU* 4.3 20.9 - - + -
124A LEU* 4.2 14.1 - - + -
166A VAL* 2.8 29.9 + - + +
167A ARG 3.4 5.8 - - - +
169A THR* 1.3 76.7 - - - +
171A THR* 1.3 56.2 + - - +
173A LEU* 3.7 5.0 - - + +
174A LEU* 2.8 61.8 + - + +
207A MET* 4.5 1.6 - - + -
244A MET* 4.2 19.1 - - + -
305A PHE* 4.1 26.5 - - + -
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Residues in contact with THR 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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167A ARG* 2.9 21.1 + - - +
168A GLU* 3.3 10.0 - - - -
170A MET* 1.3 76.0 - - - +
172A HIS* 1.3 71.0 + - + +
174A LEU* 3.1 2.9 + - - +
175A GLN* 2.9 38.4 + - - +
203A VAL* 3.9 24.1 - - + +
204A GLU* 5.8 1.6 - - - +
207A MET* 3.3 16.0 - - + +
49B GLN* 5.8 6.4 - - + +
51B GLU* 4.8 13.7 - - - +
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Residues in contact with HIS 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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155A TYR* 4.2 14.3 + - - +
156A SER* 3.5 45.5 - - - +
157A ASN* 6.2 0.4 - - - -
158A LYS* 6.4 0.4 - - + -
168A GLU* 2.9 35.3 + - + +
169A THR 3.6 7.0 - - - +
171A THR* 1.3 81.6 - - + +
173A LEU* 1.3 62.7 + - - +
175A GLN* 3.3 23.0 - - + +
176A HIS* 4.1 10.7 - - - -
51B GLU* 5.8 4.1 + - - -
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Residues in contact with LEU 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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117A VAL* 5.3 2.5 - - + -
121A LEU* 3.4 34.1 - - + -
128A PHE* 3.9 22.3 - - + -
133A LEU* 4.7 8.7 - - + +
148A PHE* 4.3 3.4 - - + -
152A ILE* 3.8 40.2 - - + +
155A TYR* 5.1 7.2 - - + -
156A SER* 4.3 5.2 - - - +
169A THR* 2.8 37.2 + - + +
170A MET* 3.7 6.7 - - - +
172A HIS* 1.3 75.5 - - + +
174A LEU* 1.3 59.8 + - + +
175A GLN 3.0 4.3 - - - -
176A HIS* 2.8 27.6 + - - +
177A ALA 3.4 5.0 + - - -
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Residues in contact with LEU 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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121A LEU* 4.8 9.6 - - + -
126A VAL* 4.7 8.5 - - + -
128A PHE* 5.6 1.3 - - + -
170A MET* 2.8 42.4 + - + +
171A THR 3.8 2.9 - - - +
173A LEU* 1.3 69.9 - - + +
175A GLN* 1.3 66.6 + - - +
176A HIS 3.1 0.2 - - - -
177A ALA* 3.0 35.5 + - + +
179A LEU* 4.1 9.6 - - + +
203A VAL* 3.4 21.6 - - + +
206A VAL* 4.0 16.8 - - + -
207A MET* 4.1 17.9 - - - -
242A PHE* 3.8 33.4 - - + -
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Residues in contact with GLN 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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129A ASN* 5.3 1.0 + - - -
171A THR* 2.9 31.9 + - + +
172A HIS* 3.3 22.0 - - + +
174A LEU* 1.3 79.0 - - - +
176A HIS* 1.3 65.9 + - + +
177A ALA 3.6 4.5 + - - +
203A VAL* 3.6 21.7 - - - +
204A GLU* 4.4 9.9 + - - -
8C LEU* 6.2 0.2 - - - +
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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