Contacts of the helix formed by residues 116 - 127 (chain A) in PDB entry 2WOK
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 THR 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.4 11.1 - - - +
114A PRO* 4.4 19.3 - - + +
115A ILE* 1.3 79.6 - - - +
117A SER* 1.3 60.5 + - - +
118A ASP* 3.5 16.0 + - - +
119A ASP* 2.9 40.5 + - - +
120A VAL* 3.7 4.3 + - - +
169A GLU* 3.6 37.7 + - + +
170A HIS* 5.9 1.8 - - + -
198A ARG* 5.9 1.6 + - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.3 12.0 - - - +
116A THR* 1.3 73.5 - - - +
118A ASP* 1.3 64.4 + - - +
120A VAL* 3.2 8.3 + - - +
121A ARG 3.0 17.5 + - - -
166A THR* 3.5 17.9 - - - +
168A ASP 2.7 23.5 + - - -
169A GLU* 2.8 20.0 + - - -
171A THR 3.2 28.3 + - - -
172A ILE* 3.9 6.1 - - - +
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR* 3.1 13.1 + - - +
117A SER* 1.3 82.0 + - - +
119A ASP* 1.3 55.6 + - - +
121A ARG* 3.4 18.2 + - - +
122A HIS* 2.8 34.2 + - - +
166A THR* 3.0 27.7 + - - -
169A GLU* 5.1 7.5 - - - +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 2.6 38.9 + - - +
114A PRO 3.5 4.3 - - - +
116A THR* 2.9 34.3 + - - +
118A ASP* 1.3 78.6 - - - +
120A VAL* 1.3 61.8 + - - +
122A HIS* 4.2 0.7 - - - -
123A ALA 3.0 21.0 + - - -
194A PRO* 3.4 7.7 - - + +
195A VAL 3.0 26.5 + - - +
196A PRO* 3.7 18.1 - - - +
197A ARG 4.7 1.7 + - - -
198A ARG* 4.3 5.6 + - - -
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.7 31.6 - - + -
85A LEU* 5.3 0.7 - - + -
103A LEU* 4.5 23.6 - - + -
115A ILE* 5.5 0.4 - - + -
116A THR 4.2 8.7 - - - +
117A SER* 3.2 6.7 + - - +
119A ASP* 1.3 74.0 - - - +
121A ARG* 1.3 67.7 + - - +
123A ALA* 3.2 2.9 + - - +
124A VAL* 3.1 26.0 + - + +
172A ILE* 3.9 14.6 - - + -
174A PHE* 4.5 6.1 - - + -
187A MET* 5.1 1.3 - - - -
192A ALA 4.0 14.6 - - - +
194A PRO* 4.1 24.5 - - + -
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER 3.0 12.9 + - - +
118A ASP* 3.4 21.0 + - - +
120A VAL* 1.3 78.1 - - - +
122A HIS* 1.3 57.4 + - - +
124A VAL* 3.2 3.6 + - - +
125A GLN* 2.8 55.0 + - + +
160A PRO* 3.6 31.6 - - - +
161A LEU 4.7 0.2 - - - -
164A VAL* 2.9 51.5 + - + -
165A LEU* 4.0 0.8 - - - +
166A THR* 3.1 38.3 + - + +
172A ILE* 3.7 6.7 - - - +
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Residues in contact with HIS 122 (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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118A ASP 2.8 19.4 + - - +
119A ASP* 3.8 0.9 - - - +
121A ARG* 1.3 73.2 - - - +
123A ALA* 1.3 57.3 + - - +
125A GLN* 3.1 13.9 + - - +
126A ARG* 2.9 41.4 + - - +
154A PRO* 3.8 31.4 - - + +
155A TYR* 5.1 2.9 - + - -
195A VAL* 3.3 28.5 - - + +
197A ARG* 3.7 43.2 - - + +
200A ASP* 2.8 34.0 + - + +
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Residues in contact with ALA 123 (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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49A ALA* 5.2 1.2 - - - +
119A ASP 3.0 18.0 + - - +
120A VAL 3.2 5.4 + - - +
122A HIS* 1.3 74.7 - - - +
124A VAL* 1.3 62.6 + - - +
126A ARG* 3.2 28.6 + - - +
127A VAL* 3.5 5.9 + - - +
191A CYS 3.6 19.2 - - - +
192A ALA 4.3 4.3 - - - -
193A ALA 3.0 32.3 - - - +
194A PRO* 4.1 0.2 - - + -
195A VAL* 3.9 6.9 + - + +
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Residues in contact with VAL 124 (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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120A VAL* 3.1 15.8 + - + +
121A ARG* 3.7 8.1 - - - +
123A ALA* 1.3 73.5 - - - +
125A GLN* 1.3 66.0 + - - +
127A VAL* 3.3 23.9 + - - +
128A PHE* 3.4 8.7 - - + -
140A LEU* 4.0 24.9 - - + -
144A LEU* 3.5 32.5 - - + -
161A LEU* 4.4 9.2 - - + -
164A VAL* 4.7 1.8 - - + -
174A PHE* 4.1 23.8 - - + -
187A MET* 4.6 1.6 - - + -
191A CYS 4.6 0.4 - - - -
192A ALA* 4.6 15.5 - - + -
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Residues in contact with GLN 125 (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 ARG* 2.8 40.0 + - + +
122A HIS* 3.4 17.5 + - - +
124A VAL* 1.3 76.4 - - - +
126A ARG* 1.3 57.1 + - - +
128A PHE* 2.9 30.9 + - - +
151A TYR* 3.3 32.7 + - + +
154A PRO* 3.3 21.7 - - + +
160A PRO* 3.3 13.0 - - - +
161A LEU* 2.8 39.8 - - + +
197A ARG* 5.7 2.3 + - - -
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 2.8 41.6 + - - -
49A ALA* 3.5 21.8 - - + +
122A HIS* 2.9 33.0 + - - +
123A ALA* 3.2 11.4 + - - +
125A GLN* 1.3 74.9 - - - +
127A VAL* 1.3 63.1 + - - +
129A ALA* 2.9 22.2 + - - +
133A LEU* 3.5 35.1 - - + +
154A PRO* 3.9 11.4 - - + +
155A TYR* 3.5 5.0 + - - +
195A VAL* 3.8 23.9 - - - +
200A ASP* 2.9 41.9 + - - +
205A TYR* 3.5 17.0 - - - +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 4.8 8.3 - - + +
123A ALA 3.6 14.6 - - - +
124A VAL* 3.4 13.9 - - - +
125A GLN 3.2 0.2 - - - -
126A ARG* 1.3 76.1 - - - +
128A PHE* 1.3 60.9 + - + +
130A GLN* 2.8 35.4 + - - +
133A LEU* 5.9 1.3 - - - -
137A PRO 3.6 20.0 - - - +
138A THR* 4.2 7.2 - - - -
140A LEU* 4.9 12.3 - - + -
141A ILE* 3.6 19.2 - - + +
191A CYS* 3.9 32.1 - - + +
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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