Contacts of the helix formed by residues 165 - 184 (chain A) in PDB entry 5WS3
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 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 3.2 31.6 - - + +
161A MET* 6.1 3.4 - - + -
162A PHE 4.7 6.7 - - - +
163A LYS 4.0 4.6 + - - +
164A SER* 1.3 79.4 + - - +
166A ALA* 1.3 68.3 + - - +
167A LYS* 3.6 0.9 - - - +
168A ARG* 3.6 14.2 + - - +
169A ALA* 3.1 22.0 + - - +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 4.2 29.2 - - + +
165A THR* 1.3 81.4 + - - +
167A LYS* 1.3 62.4 + - - +
169A ALA* 3.2 5.1 + - - +
170A ARG* 2.9 27.3 + - - +
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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
----------------------------------------------------------
164A SER* 3.1 32.1 - - - +
166A ALA* 1.3 76.7 - - - +
168A ARG* 1.3 59.3 + - - +
170A ARG* 3.7 11.6 - - + +
171A ASN* 2.9 45.4 + - - +
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 4.2 8.6 - - + +
92A PHE* 5.8 1.5 - - + -
151A ASP* 2.5 39.2 + - - +
162A PHE* 3.4 49.3 + - - +
164A SER* 2.6 48.1 + - - +
165A THR* 3.7 24.2 - - - +
166A ALA 3.2 0.4 - - - -
167A LYS* 1.3 77.7 - - - +
169A ALA* 1.3 58.6 + - - +
171A ASN* 3.4 7.1 + - - +
172A SER* 2.9 39.6 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.8 19.7 - - + -
91A TYR* 4.1 27.8 - - + -
92A PHE* 4.1 15.7 - - + -
165A THR 3.1 14.4 + - - +
166A ALA 3.2 7.4 + - - +
168A ARG* 1.3 77.1 - - - +
170A ARG* 1.3 57.9 + - - +
172A SER* 3.2 1.9 + - - -
173A ILE* 2.9 36.5 + - + +
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Residues in contact with ARG 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 ALA 2.9 15.8 + - - +
167A LYS* 3.7 11.0 - - - +
168A ARG 3.3 0.2 - - - -
169A ALA* 1.3 75.7 - - - +
171A ASN* 1.3 68.5 + - - +
173A ILE* 3.2 9.0 + - - +
174A VAL* 3.0 40.3 + - + +
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Residues in contact with ASN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LYS* 2.9 32.7 + - - +
168A ARG* 3.8 6.9 - - - +
170A ARG* 1.3 80.7 - - - +
172A SER* 1.3 63.2 + - - +
174A VAL* 3.4 6.9 + - - +
175A ILE* 3.0 36.0 + - + +
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Residues in contact with SER 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.7 22.9 - - - -
147A CYS* 4.4 13.3 - - - +
168A ARG* 2.9 28.2 + - - +
169A ALA 3.5 4.7 - - - -
171A ASN* 1.3 76.2 - - - +
173A ILE* 1.3 57.3 + - - +
175A ILE* 3.3 10.4 + - - +
176A ILE* 2.9 33.8 + - - +
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Residues in contact with ILE 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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91A TYR* 3.8 30.1 - - + +
92A PHE* 3.8 20.6 - - + -
95A ASN* 3.3 34.8 - - + +
169A ALA 2.9 24.2 + - - +
170A ARG* 3.2 7.6 + - + +
172A SER* 1.3 71.9 - - - +
174A VAL* 1.3 69.5 + - + +
176A ILE* 3.2 8.3 + - + +
177A TRP* 3.0 37.2 + - + +
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Residues in contact with VAL 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 ARG* 3.0 30.6 + - + +
171A ASN* 3.9 6.5 - - - +
173A ILE* 1.3 80.6 - - + +
175A ILE* 1.3 64.1 + - + +
177A TRP* 3.3 6.7 + - + +
178A ILE* 2.9 43.9 + - + +
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 3.0 27.9 + - + +
172A SER* 3.5 7.9 - - - +
174A VAL* 1.3 76.1 - - + +
176A ILE* 1.3 67.7 + - + +
178A ILE* 4.6 6.1 - - + -
179A VAL* 2.9 40.2 + - + +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 4.9 4.5 - - + -
95A ASN* 4.3 5.4 - - - +
140A VAL* 3.8 37.2 - - + +
143A LEU* 3.4 46.0 - - + +
144A THR* 3.7 15.5 - - + +
147A CYS* 3.5 21.8 - - + -
172A SER 2.9 22.6 + - - +
173A ILE* 3.2 9.4 + - - +
175A ILE* 1.3 79.6 - - + +
177A TRP* 1.3 58.9 + - - +
179A VAL* 4.0 1.4 - - - +
180A SER* 2.9 34.3 + - - -
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Residues in contact with TRP 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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95A ASN* 2.6 32.6 + - - +
98A LEU* 5.1 7.4 - - + +
99A ALA* 4.5 19.7 - - + -
102A LEU* 4.1 25.4 - - + -
136A VAL* 4.2 17.9 - - + -
137A SER* 5.5 1.1 - - - -
140A VAL* 3.7 31.9 - - + -
173A ILE* 3.0 33.8 + - + +
174A VAL* 3.8 6.1 - - + +
176A ILE* 1.3 78.8 - - + +
178A ILE* 1.3 59.0 + - + +
180A SER* 3.3 2.8 + - - -
181A CYS* 2.9 47.1 + - - -
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Residues in contact with ILE 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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174A VAL* 2.9 39.4 + - + +
175A ILE* 3.9 7.0 - - + +
177A TRP* 1.3 73.8 - - + +
179A VAL* 1.3 70.7 + - + +
181A CYS* 3.9 4.4 - - - +
182A ILE* 3.0 40.4 + - + +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.1 19.5 - - + -
175A ILE* 2.9 34.6 + - + +
176A ILE 4.0 2.5 - - - +
178A ILE* 1.3 79.0 - - + +
180A SER* 1.3 59.1 + - - +
182A ILE* 3.2 5.8 + - - +
183A ILE* 2.9 52.7 + - + +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 3.6 8.0 - - - +
139A SER* 2.6 33.3 + - - -
140A VAL* 3.1 33.3 + - - +
143A LEU* 3.8 3.1 - - - +
176A ILE 2.9 22.3 + - - -
177A TRP 3.7 2.2 - - - -
178A ILE 3.2 0.2 - - - -
179A VAL* 1.3 79.3 - - - +
181A CYS* 1.3 63.0 + - - +
183A ILE* 3.4 3.7 - - - +
184A MET* 3.4 26.2 + - - +
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Residues in contact with CYS 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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132A TYR* 2.6 36.5 + - - +
136A VAL* 3.9 20.0 - - - -
177A TRP* 2.9 31.5 + - - +
178A ILE* 3.9 4.3 - - - +
180A SER* 1.3 77.5 - - - +
182A ILE* 1.3 65.1 + - + +
184A MET 4.0 0.5 + - - -
185A ILE* 3.4 12.1 - - - +
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Residues in contact with ILE 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 ILE* 3.0 32.7 + - + +
179A VAL* 3.8 5.4 - - - +
181A CYS* 1.3 80.0 - - + +
183A ILE* 1.3 70.5 + - + +
185A ILE* 3.2 40.1 + - + +
186A PRO* 4.2 1.9 - - - +
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 3.3 26.9 - - - +
143A LEU* 5.4 1.1 - - + -
179A VAL* 2.9 40.0 + - + +
180A SER* 3.4 7.9 - - - +
182A ILE* 1.3 81.1 - - + +
184A MET* 1.3 74.0 + - + +
185A ILE 3.3 0.9 - - - -
186A PRO* 3.3 17.5 - - - +
223A TYR* 5.2 3.8 + - - -
230A VAL* 4.3 23.1 - - + -
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Residues in contact with MET 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 3.3 18.0 - - + -
135A THR* 3.4 52.5 - - - +
136A VAL* 3.7 13.0 - - + +
139A SER* 3.9 11.9 - - - -
180A SER 3.4 16.4 + - - +
181A CYS 4.0 0.2 + - - -
182A ILE 3.2 1.4 - - - -
183A ILE* 1.3 88.8 - - + +
185A ILE* 1.3 62.6 + - - +
186A PRO 3.4 2.0 - - - -
187A GLN* 3.2 16.5 + - + +
188A ALA 3.3 0.7 + - - -
223A TYR* 4.6 5.8 - - - -
227A PHE* 3.7 31.9 - - + -
230A VAL* 6.0 0.2 - - + -
231A THR* 3.8 19.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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