Contacts of the helix formed by residues 173 - 186 (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 THR 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLU* 3.9 24.0 + - + +
117A GLY 3.2 15.9 - - - +
118A PRO* 4.9 1.6 - - + -
119A LEU* 3.6 12.0 - - - +
172A GLU* 1.3 88.0 - - + +
174A THR* 1.3 64.0 + - - +
175A THR* 3.5 7.6 + - - -
176A GLN* 2.9 41.7 + - - +
177A LEU* 3.1 18.0 + - - +
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Residues in contact with THR 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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110A GLY* 3.3 39.7 - - - +
112A SER 3.2 21.5 + - - +
113A TYR 4.8 0.7 - - - -
115A LYS 2.9 22.4 + - - +
117A GLY 2.9 20.1 + - - +
118A PRO 4.2 1.3 - - - +
119A LEU* 3.7 16.3 - - + +
173A THR* 1.3 71.4 - - - +
175A THR* 1.3 62.9 + - - +
177A LEU 3.2 1.9 + - - -
178A ALA* 2.8 30.5 + - - +
198A PHE* 3.6 15.5 - - + -
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Residues in contact with THR 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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113A TYR 4.1 9.0 - - - +
114A GLN 4.0 13.9 - - - +
115A LYS 4.1 1.1 - - - -
116A GLU* 3.1 51.0 + - + +
173A THR* 3.5 4.9 + - - -
174A THR* 1.3 82.5 + - - +
176A GLN* 1.3 60.3 + - - +
178A ALA* 3.8 6.0 - - - +
179A GLU* 3.0 24.4 + - - +
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Residues in contact with GLN 176 (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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116A GLU* 5.8 0.4 - - - +
170A PRO 4.2 4.5 + - - +
171A ILE* 3.8 8.5 - - + -
172A GLU* 2.8 36.4 + - - +
173A THR* 2.9 32.2 + - - +
175A THR* 1.3 76.6 - - - +
177A LEU* 1.3 63.6 + - - +
179A GLU* 3.3 5.1 + - - +
180A ILE* 3.0 33.8 + - + +
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Residues in contact with LEU 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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119A LEU* 3.8 18.6 - - + -
121A MET* 4.8 0.2 - - + -
134A VAL* 4.3 9.2 - - + -
162A ILE* 4.0 32.8 - - + -
171A ILE* 4.1 23.7 - - + +
173A THR 3.1 13.2 + - - +
174A THR 3.6 6.5 - - - +
176A GLN* 1.3 76.6 - - - +
178A ALA* 1.3 64.5 + - - +
180A ILE* 3.1 5.2 + - + +
181A VAL* 3.0 27.6 + - + +
197A THR* 4.5 2.0 - - + -
198A PHE* 3.8 20.2 - - + -
201A LEU* 3.6 30.7 - - + -
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Residues in contact with ALA 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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113A TYR* 3.4 36.1 - - + +
174A THR 2.8 17.4 + - - +
175A THR* 3.8 4.9 - - - +
177A LEU* 1.3 77.0 - - - +
179A GLU* 1.3 58.1 + - - +
181A VAL* 3.4 1.7 + - - +
182A ARG* 2.9 29.9 + - - +
192A HIS* 4.0 10.7 - - + -
194A ALA* 3.9 14.1 - - + -
198A PHE* 4.2 2.0 - - + -
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Residues in contact with GLU 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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175A THR 3.0 17.8 + - - +
176A GLN* 3.8 4.9 - - - +
177A LEU 3.2 0.2 - - - -
178A ALA* 1.3 74.1 - - - +
180A ILE* 1.3 67.3 + - + +
182A ARG* 2.9 35.4 + - - -
183A LYS* 2.8 59.6 + - - +
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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
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161A ALA* 3.9 33.2 - - + +
162A ILE* 4.1 15.3 - - + +
165A ALA* 3.5 26.7 - - + -
171A ILE* 3.6 31.4 - - + -
176A GLN* 3.0 22.8 + - + +
177A LEU* 3.1 7.4 + - - +
179A GLU* 1.3 78.4 - - + +
181A VAL* 1.3 62.8 + - - +
183A LYS* 3.6 8.0 + - + +
184A ALA* 3.2 20.8 + - - +
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Residues in contact with VAL 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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158A ILE* 3.7 25.8 - - + -
161A ALA* 6.0 0.2 - - - -
162A ILE* 4.7 1.8 - - + -
177A LEU* 3.0 29.9 + - + +
178A ALA 3.9 4.3 - - - +
180A ILE* 1.3 73.4 - - - +
182A ARG* 1.3 64.7 + - - +
184A ALA* 3.2 5.4 + - - +
185A VAL* 3.0 32.9 + - + +
193A PRO 3.2 32.5 - - - +
194A ALA* 3.8 8.1 - - + -
197A THR* 4.0 27.6 - - + +
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Residues in contact with ARG 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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178A ALA 2.9 18.6 + - - +
179A GLU* 2.9 40.3 + - - +
181A VAL* 1.3 78.1 - - - +
183A LYS* 1.3 73.5 + - - +
186A GLY* 2.7 43.1 + - - +
192A HIS* 3.9 19.0 - - + +
193A PRO* 3.7 24.2 - - + -
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Residues in contact with LYS 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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157A ARG* 5.2 2.9 + - - -
179A GLU* 2.8 54.7 + - + +
180A ILE* 3.9 7.0 - - - +
182A ARG* 1.3 88.4 - - - +
184A ALA* 1.3 61.4 + - - +
185A VAL 4.8 0.2 - - - -
186A GLY* 4.4 3.1 + - - -
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Residues in contact with ALA 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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154A GLN* 4.7 0.5 + - - -
157A ARG* 2.8 48.1 + - + +
158A ILE* 4.5 9.6 - - + -
161A ALA* 3.7 24.0 - - + -
180A ILE 3.2 13.7 + - - +
181A VAL* 3.2 7.2 + - - +
183A LYS* 1.3 79.8 - - - +
185A VAL* 1.3 62.5 + - + +
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Residues in contact with VAL 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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154A GLN* 3.1 33.7 + - + +
158A ILE* 3.6 36.3 - - + -
181A VAL* 3.0 21.7 + - + +
183A LYS 4.8 0.2 - - - -
184A ALA* 1.3 80.8 - - - +
186A GLY* 1.3 64.4 + - - +
187A PHE 3.9 6.7 + - - +
188A ARG* 3.8 20.4 - - - +
193A PRO* 3.5 21.3 - - + +
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Residues in contact with GLY 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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182A ARG* 2.7 31.1 + - - -
183A LYS 4.4 2.8 + - - -
184A ALA 3.8 0.6 - - - -
185A VAL* 1.3 73.9 - - - +
187A PHE* 1.3 66.8 + - - -
188A ARG 3.5 0.2 + - - -
193A PRO* 3.4 23.7 - - - +
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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