Contacts of the helix formed by residues 164 - 175 (chain A) in PDB entry 2WL7
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 SER 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLY* 4.2 0.2 - - - -
118A THR* 3.4 10.9 + - - -
119A ASP* 3.5 20.9 - - - -
163A VAL* 1.3 81.9 - - - +
165A HIS* 1.3 64.1 + - - +
166A SER* 3.6 9.9 + - - -
167A LYS* 3.1 30.7 + - - +
168A ALA* 3.1 17.5 + - - +
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Residues in contact with HIS 165 (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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114A ILE* 3.5 42.7 + - + +
115A ALA* 4.0 6.7 - - - -
116A GLY 3.0 31.3 + - - +
117A GLY* 4.5 0.4 - - - -
119A ASP* 2.9 21.2 + - - +
120A ASN* 5.9 1.8 - - + -
129A ILE* 5.1 1.8 - - - +
163A VAL 3.9 0.2 + - - -
164A SER* 1.3 72.4 - - - +
166A SER* 1.3 64.3 + - - +
168A ALA* 3.1 7.7 + - - +
169A VAL* 3.0 43.1 + - + +
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 5.0 1.4 + - - -
164A SER* 3.2 10.0 + - - -
165A HIS* 1.3 80.3 - - - +
167A LYS* 1.3 59.7 + - - +
169A VAL* 3.3 9.2 + - - +
170A GLU* 3.0 28.2 + - - +
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Residues in contact with LYS 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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158A VAL* 5.7 0.3 - - - +
160A VAL* 5.0 0.8 - - - +
163A VAL* 3.9 18.6 - - + -
164A SER* 3.1 26.4 + - - +
166A SER* 1.3 77.2 - - - +
168A ALA* 1.3 61.4 + - - +
170A GLU* 3.0 39.4 + - - +
171A ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 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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114A ILE* 4.4 4.5 - - + -
129A ILE* 3.5 46.4 - - + -
155A VAL* 5.4 0.2 - - - +
160A VAL* 4.4 6.6 - - + +
163A VAL* 3.9 7.3 - - + +
164A SER 3.1 8.0 + - - +
165A HIS* 3.1 8.0 + - - +
167A LYS* 1.3 77.0 - - - +
169A VAL* 1.3 61.9 + - - +
171A ALA* 3.2 8.0 + - - +
172A LEU* 3.0 29.7 + - + +
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Residues in contact with VAL 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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114A ILE* 4.3 10.5 - - + -
165A HIS* 3.0 42.5 + - + +
166A SER* 3.6 9.0 - - - +
168A ALA* 1.3 75.5 - - - +
170A GLU* 1.3 58.6 + - - +
172A LEU* 3.2 11.2 + - - +
173A LYS* 2.8 32.4 + - + +
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Residues in contact with GLU 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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166A SER* 3.0 18.5 + - - +
167A LYS* 3.0 41.4 + - - +
168A ALA 3.3 0.2 - - - -
169A VAL* 1.3 77.8 - - - +
171A ALA* 1.3 63.5 + - - +
173A LYS* 4.3 8.3 - - + -
174A GLU* 3.0 52.1 + - - +
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Residues in contact with ALA 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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155A VAL* 3.7 11.4 - - + +
158A VAL* 3.9 36.2 - - + +
160A VAL* 4.0 12.6 - - + -
167A LYS 2.9 17.6 + - - +
168A ALA 3.5 4.9 - - - +
169A VAL 3.2 0.2 - - - -
170A GLU* 1.3 77.5 - - - +
172A LEU* 1.3 63.3 + - - +
174A GLU* 3.5 3.9 + - - +
175A ALA* 3.2 24.3 + - - +
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Residues in contact with LEU 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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105A ARG* 2.8 29.2 + - - -
110A LEU* 4.2 21.9 - - + +
112A PHE* 4.2 21.5 - - + -
114A ILE* 3.9 27.6 - - + -
129A ILE* 5.4 0.7 - - + -
152A ILE* 4.6 6.3 - - + -
155A VAL* 3.9 31.0 - - + -
168A ALA* 3.0 19.5 + - + +
169A VAL* 3.6 7.6 - - - +
171A ALA* 1.3 76.5 - - - +
173A LYS* 1.3 59.4 + - - +
175A ALA* 3.5 5.0 + - - +
179A VAL* 4.6 1.8 - - + -
181A LEU* 4.0 15.7 - - + -
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Residues in contact with LYS 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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105A ARG* 3.9 14.0 + - - +
169A VAL* 2.8 20.9 + - + +
170A GLU* 3.8 8.7 - - + +
172A LEU* 1.3 78.0 - - - +
174A GLU* 1.3 68.4 + - + +
175A ALA 3.2 1.1 + - - -
176A GLY* 4.1 2.9 + - - -
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Residues in contact with GLU 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 GLU* 3.0 44.9 + - + +
171A ALA* 3.9 4.4 - - - +
173A LYS* 1.3 84.7 - - + +
175A ALA* 1.3 60.9 + - - +
176A GLY* 3.1 7.8 + - - -
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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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155A VAL* 3.8 15.7 - - + -
156A ASN* 3.1 32.8 + - + +
171A ALA 3.2 16.1 + - - +
172A LEU 3.6 10.1 - - - +
173A LYS 3.2 2.0 - - - -
174A GLU* 1.3 77.3 - - - +
176A GLY* 1.3 60.9 + - - +
177A SER 4.0 0.2 + - - -
178A ILE 3.4 8.0 + - - +
179A VAL* 3.8 16.8 - - + -
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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