Contacts of the helix formed by residues 194 - 206 (chain A) in PDB entry 1WG8
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 ALA 194 (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* 4.1 15.0 - - + -
178A ALA* 3.9 25.1 - - - +
181A VAL* 3.8 12.3 - - + -
192A HIS* 2.9 26.5 + - + +
193A PRO* 1.3 77.3 - - - +
195A ARG* 1.3 64.5 + - - +
196A LYS 3.4 0.4 - - - -
197A THR* 3.3 4.2 + - - -
198A PHE* 2.9 29.8 + - + -
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Residues in contact with ARG 195 (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* 3.3 45.9 + - + +
190A ALA 4.2 6.1 + - - -
191A GLY* 3.8 16.4 - - - -
192A HIS* 3.0 29.7 + - - +
193A PRO 3.4 0.2 - - - -
194A ALA* 1.3 77.3 - - - +
196A LYS* 1.3 64.4 + - + +
198A PHE* 3.3 3.6 + - - +
199A GLN* 2.9 23.2 + - - +
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Residues in contact with LYS 196 (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 GLY* 3.1 27.8 - - - +
151A GLU* 2.9 28.6 + - - +
152A GLU* 3.6 26.9 - - + +
153A PRO* 4.1 11.6 - - + +
188A ARG* 4.0 12.3 - - - +
192A HIS 4.7 0.4 + - - -
193A PRO 4.4 2.0 + - - -
194A ALA 3.4 0.6 - - - -
195A ARG* 1.3 78.1 - - + +
197A THR* 1.3 63.1 - - - +
199A GLN* 3.2 8.4 + - - +
200A ALA* 2.9 24.8 + - - +
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Residues in contact with THR 197 (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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146A LEU* 3.8 28.5 - - + +
152A GLU* 4.6 2.9 + - - +
158A ILE* 3.8 26.0 - - - +
162A ILE* 4.8 7.0 - - + -
177A LEU* 4.5 9.2 - - + -
181A VAL* 4.0 24.9 - - + +
193A PRO 4.7 0.8 + - - -
194A ALA 3.3 9.0 + - - -
196A LYS* 1.3 78.3 - - - +
198A PHE* 1.3 63.2 + - + +
200A ALA* 3.3 2.8 + - - +
201A LEU* 3.0 39.5 + - + +
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Residues in contact with PHE 198 (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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111A PHE 3.6 22.4 - - - +
112A SER 3.7 6.3 - - - -
113A TYR* 3.4 42.2 - + + -
121A MET* 3.7 23.7 - - + +
174A THR* 3.6 35.4 - - + -
177A LEU* 3.8 31.0 - - + -
178A ALA 4.2 6.5 - - - -
194A ALA* 2.9 27.8 + - + +
195A ARG* 3.8 6.1 - - - +
197A THR* 1.3 80.0 - - + +
199A GLN* 1.3 55.8 + - - +
201A LEU* 3.4 4.8 + - - -
202A ARG* 2.9 30.7 + - - +
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Residues in contact with GLN 199 (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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149A LEU 3.1 20.1 - - - +
150A GLY* 4.2 7.5 - - - +
151A GLU* 5.6 2.1 - - - +
195A ARG 2.9 14.0 + - - +
196A LYS* 3.2 10.7 + - - +
198A PHE* 1.3 76.2 - - - +
200A ALA* 1.3 62.1 + - - +
202A ARG* 3.2 27.3 + - - +
203A ILE* 3.0 38.7 + - + +
235A HIS* 3.5 33.1 + - - +
236A SER 5.4 0.4 - - - +
237A LEU* 4.4 3.8 - - - +
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Residues in contact with ALA 200 (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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145A LEU* 3.6 24.8 - - + +
146A LEU* 4.1 8.3 - - + -
149A LEU* 3.7 16.4 + - + +
150A GLY* 3.5 24.2 - - - +
196A LYS 2.9 14.2 + - - +
197A THR 3.7 3.8 - - - +
199A GLN* 1.3 76.4 - - - +
201A LEU* 1.3 59.2 + - - +
203A ILE* 3.4 2.1 + - - +
204A TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 201 (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 MET* 3.8 24.2 - - + -
130A ALA* 4.7 7.0 - - + +
133A VAL* 3.8 31.2 - - + -
134A VAL* 3.6 19.5 - - + -
142A LEU* 5.1 5.8 - - + -
145A LEU* 4.2 15.7 - - + -
146A LEU* 5.1 1.1 - - + -
162A ILE* 6.0 0.7 - - + -
177A LEU* 3.6 31.6 - - + -
197A THR* 3.0 29.1 + - + +
198A PHE 3.9 0.2 - - - +
200A ALA* 1.3 77.7 - - - +
202A ARG* 1.3 58.2 + - - +
204A TYR* 3.7 2.4 - - + +
205A VAL* 2.9 36.5 + - + +
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Residues in contact with ARG 202 (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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98A GLY* 5.8 5.4 - - - -
99A VAL* 3.7 29.1 - - - +
111A PHE* 3.7 26.0 - - + -
121A MET* 3.8 11.6 - - - +
123A MET* 5.6 0.2 - - + -
198A PHE 2.9 19.5 + - - +
199A GLN* 3.6 37.7 - - - +
200A ALA 3.2 0.2 - - - -
201A LEU* 1.3 77.2 - - - +
203A ILE* 1.3 62.5 + - - +
205A VAL* 4.7 1.1 - - - -
206A ASN* 2.8 36.6 + - - +
208A GLU* 3.0 26.3 + - - +
235A HIS* 3.6 30.3 + - - -
238A GLU* 5.4 0.2 + - - -
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Residues in contact with ILE 203 (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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149A LEU* 3.5 37.5 - - + +
199A GLN* 3.0 23.8 + - + +
200A ALA 3.8 3.1 - - - +
201A LEU 3.3 0.2 - - - -
202A ARG* 1.3 80.3 - - - +
204A TYR* 1.3 57.6 + - - +
207A ASP* 2.8 25.5 + - - -
208A GLU* 2.9 42.8 + - + +
209A LEU* 4.1 24.2 - - + +
235A HIS* 3.5 32.3 - - + +
237A LEU* 4.3 5.8 - - + -
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Residues in contact with TYR 204 (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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133A VAL* 3.8 34.8 - - + -
137A LEU* 4.0 21.4 - - + +
145A LEU* 3.6 33.9 - - + -
149A LEU* 3.7 17.7 - - + -
200A ALA 2.9 17.5 + - - +
201A LEU* 3.7 3.6 - - - +
203A ILE* 1.3 75.6 - - - +
205A VAL* 1.3 69.4 + - + +
207A ASP* 3.2 14.2 + - - +
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Residues in contact with VAL 205 (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 ASP 4.2 2.0 - - - +
121A MET* 3.7 17.9 - - + +
122A ARG* 3.6 31.2 - - + -
126A GLU 4.1 14.2 - - - +
127A GLY* 5.4 1.0 - - - -
128A PRO* 3.9 9.7 - - - +
129A THR 4.2 2.9 - - - -
130A ALA* 3.7 34.8 - - + +
133A VAL* 4.3 13.2 - - + -
201A LEU* 2.9 24.8 + - - +
202A ARG* 4.0 2.5 - - - +
204A TYR* 1.3 77.2 - - + +
206A ASN* 1.3 60.7 + - - +
207A ASP* 3.8 0.7 + - - +
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Residues in contact with ASN 206 (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 GLN* 4.5 6.6 + - - +
74A ASN* 5.1 6.4 + - - -
76A ARG* 4.7 2.1 + - - -
121A MET 2.8 25.4 + - - -
122A ARG* 3.6 4.3 - - - +
123A MET* 2.9 44.0 + - + +
124A GLY 4.3 1.9 + - - -
202A ARG* 2.8 34.7 + - - +
205A VAL* 1.3 79.1 - - - +
207A ASP* 1.3 71.8 + - - +
208A GLU* 3.0 17.4 + - + +
211A ALA* 4.6 5.0 - - - +
3142A SAM 5.9 0.5 + - - -
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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