Contacts of the helix formed by residues 174 - 184 (chain A) in PDB entry 4WCX
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A THR* 1.3 85.2 + - - +
175A VAL* 1.3 66.1 + - - +
176A GLU* 3.5 11.2 + - - +
177A ASN* 3.0 37.5 + - - +
178A TYR* 3.0 17.0 + - - -
215A TYR* 3.7 15.3 - - - +
222A ARG* 4.4 2.9 - - - +
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Residues in contact with VAL 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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173A THR 4.1 0.4 + - - -
174A THR* 1.3 71.1 - - - +
176A GLU* 1.3 63.2 + - - +
178A TYR* 3.2 10.1 + - - +
179A LYS* 2.9 47.0 + - - +
222A ARG* 3.6 38.5 - - + +
225A GLU* 4.4 12.1 - - + -
226A ALA* 4.1 13.0 - - + +
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Residues in contact with GLU 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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174A THR* 3.0 10.4 + - - +
175A VAL* 1.3 81.1 - - - +
177A ASN* 1.3 70.2 + - - +
179A LYS* 3.3 11.3 + - - +
180A LYS* 3.2 34.2 + - - +
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Residues in contact with ASN 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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143A ILE* 3.6 41.3 - - + +
173A THR* 2.9 33.0 + - + +
174A THR* 3.0 17.6 + - - +
176A GLU* 1.3 82.8 - - - +
178A TYR* 1.3 66.7 + - - +
180A LYS* 3.2 12.4 + - - +
181A LEU* 3.1 24.9 + - - +
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Residues in contact with TYR 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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172A ALA* 3.5 3.8 - - - -
173A THR* 3.1 48.8 + - + -
174A THR 3.0 19.7 + - - -
175A VAL 3.2 1.3 + - - +
177A ASN* 1.3 73.8 - - - +
179A LYS* 1.3 59.9 + - - +
181A LEU* 3.2 13.0 + - + +
182A LYS* 2.9 25.3 + - - +
189A TYR* 2.9 50.1 + + - -
219A ALA* 3.6 24.6 - - - +
222A ARG* 3.7 8.5 - - + -
223A ALA* 3.5 18.6 - - + -
226A ALA* 3.3 20.4 - - + -
228A ILE* 3.6 23.8 - - + +
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Residues in contact with LYS 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 VAL* 2.9 37.1 + - + +
176A GLU* 3.4 13.5 - - - +
177A ASN 3.2 0.2 - - - -
178A TYR* 1.3 74.5 - - - +
180A LYS* 1.3 66.9 + - + +
182A LYS* 3.2 7.0 + - - +
183A LYS* 2.9 24.9 + - - +
225A GLU 4.9 2.8 + - - -
226A ALA* 3.7 25.1 - - + +
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Residues in contact with LYS 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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143A ILE* 3.9 21.4 - - + +
144A ASP* 2.8 36.7 + - - +
147A VAL* 3.9 18.2 - - + +
176A GLU* 3.2 26.0 + - + +
177A ASN* 3.2 14.6 + - - +
179A LYS* 1.3 79.1 - - + +
181A LEU* 1.3 62.0 + - - +
183A LYS* 3.2 9.5 + - + +
184A VAL* 3.1 22.5 + - - +
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Residues in contact with LEU 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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143A ILE* 3.9 19.5 - - + -
146A ILE* 4.1 9.2 - - + -
147A VAL* 4.6 5.8 - - + -
150A ILE* 3.9 25.8 - - + -
168A VAL* 4.6 7.0 - - + -
170A ILE* 4.2 18.2 - - + -
173A THR* 5.6 0.4 - - + -
177A ASN 3.1 12.0 + - - +
178A TYR* 3.2 29.6 + - + +
180A LYS* 1.3 77.0 - - - +
182A LYS* 1.3 63.7 + - - +
184A VAL* 3.3 18.9 - - - +
186A ILE* 3.3 29.0 + - + +
189A TYR* 4.5 14.8 - - + -
228A ILE* 4.2 2.5 - - + -
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Residues in contact with LYS 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 TYR 2.9 13.2 + - - +
179A LYS* 3.6 10.8 - - - +
181A LEU* 1.3 76.9 - - - +
183A LYS* 1.3 65.2 + - - +
185A GLY* 3.1 15.5 + - - -
186A ILE* 4.3 13.2 - - + +
226A ALA 4.3 9.6 - - - +
227A GLY* 3.4 28.9 + - - +
228A ILE* 4.1 14.3 - - + +
229A ASP* 5.9 2.7 - - - -
258C GLU 5.3 7.1 + - - -
259C LYS* 5.6 5.7 - - - +
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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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179A LYS 2.9 17.3 + - - +
180A LYS* 3.2 9.2 + - + +
182A LYS* 1.3 80.4 - - - +
184A VAL* 1.3 58.8 + - - +
185A GLY* 3.2 1.6 + - - -
225C GLU* 5.8 8.8 - - - +
259C LYS* 5.4 21.2 + - - +
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Residues in contact with VAL 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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147A VAL* 3.4 20.2 - - + +
150A ILE* 3.5 38.1 - - + -
151A LYS* 3.4 43.7 - - + +
154A TYR* 3.7 16.6 - - - -
180A LYS 3.1 12.6 + - - +
181A LEU* 3.3 15.9 - - - +
183A LYS* 1.3 76.6 - - - +
185A GLY* 1.3 57.5 + - - +
186A ILE* 4.2 1.8 - - + -
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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