Contacts of the helix formed by residues 171 - 191 (chain A) in PDB entry 2W99
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 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLU* 1.3 74.5 - - - +
172A GLU* 1.3 56.8 + - - +
173A GLU* 2.9 29.6 - - - +
174A ASN* 2.6 36.3 + - - +
175A LYS 2.9 9.2 + - - -
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Residues in contact with GLU 172 (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 GLU 3.6 2.6 + - - -
171A ALA* 1.3 71.5 - - - +
173A GLU* 1.3 68.0 + - - +
175A LYS* 3.8 22.7 + - + +
176A GLN* 3.1 32.2 + - - +
179A ARG* 3.4 23.2 + - - -
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 2.9 29.2 + - - +
172A GLU* 1.3 84.3 + - + +
174A ASN* 1.3 68.2 + - - +
176A GLN* 3.4 17.6 + - - +
177A ILE* 3.5 14.8 + - + +
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU* 3.6 20.4 - - + +
171A ALA* 2.6 25.7 + - - +
173A GLU* 1.3 76.8 - - - +
175A LYS* 1.3 65.0 + - - +
176A GLN 3.1 1.6 - - - -
177A ILE* 3.0 17.8 + - - +
178A ILE* 3.0 17.5 + - - +
222A ASN* 2.8 41.0 + - - +
223A PHE* 3.6 28.0 - - + -
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Residues in contact with LYS 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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165A LEU* 3.1 46.9 + - + +
166A SER* 4.2 10.1 + - - +
168A MET* 3.4 17.3 + - + -
170A GLU* 3.1 38.6 + - + +
171A ALA 2.9 6.9 + - - +
172A GLU* 3.9 24.7 + - + +
174A ASN* 1.3 75.6 - - - +
176A GLN* 1.3 57.5 + - - +
178A ILE* 3.8 10.1 - - + +
179A ARG* 2.8 47.2 + - - +
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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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172A GLU* 3.1 27.1 + - + +
173A GLU* 3.4 11.2 - - - +
174A ASN 3.1 0.8 - - - -
175A LYS* 1.3 77.3 - - - +
177A ILE* 1.3 58.2 + - + +
179A ARG* 3.4 28.9 + - - +
180A LYS* 3.0 27.6 + - - +
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Residues in contact with ILE 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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173A GLU* 3.6 16.4 - - + +
174A ASN* 3.0 8.6 + - - +
176A GLN* 1.3 76.5 - - + +
178A ILE* 1.3 64.5 + - - +
180A LYS* 3.5 7.3 + - + +
181A HIS* 2.5 55.8 + - + -
215A LEU* 3.9 21.8 - - + -
218A ARG* 5.6 4.3 - - - +
223A PHE* 4.5 14.6 - - + -
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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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165A LEU* 3.9 24.9 - - + -
168A MET* 5.5 3.8 - - - -
170A GLU* 4.4 15.7 - - + -
174A ASN 3.0 21.4 + - - +
175A LYS* 3.8 10.5 - - + +
177A ILE* 1.3 73.5 - - - +
179A ARG* 1.3 60.2 + - - +
181A HIS* 3.3 1.6 + - - +
182A ALA* 2.9 29.3 + - + +
208A VAL* 4.5 11.2 - - + -
211A ALA* 4.1 7.7 - - + +
212A VAL* 3.3 39.5 - - + -
215A LEU* 3.6 19.7 - - + -
223A PHE* 4.0 14.4 - - + -
225A SER* 6.0 0.2 - - - -
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Residues in contact with ARG 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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161A ILE* 4.4 5.4 - - + -
162A GLU* 2.6 53.3 + - - +
165A LEU* 3.6 21.6 - - + +
172A GLU* 3.4 28.5 + - - -
175A LYS* 2.8 31.5 + - - +
176A GLN* 3.5 31.2 + - - +
177A ILE 3.2 0.2 - - - -
178A ILE* 1.3 78.4 - - - +
180A LYS* 1.3 62.1 + - - +
182A ALA* 3.7 3.8 + - - +
183A GLN* 3.2 47.9 + - - +
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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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176A GLN 3.0 16.9 + - - +
177A ILE* 3.5 9.9 - - + +
179A ARG* 1.3 80.5 - - - +
181A HIS* 1.3 74.8 + - + +
183A GLN* 3.3 7.8 + - - +
184A THR* 3.3 22.6 + - - +
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Residues in contact with HIS 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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177A ILE* 2.5 47.4 + - + +
180A LYS* 1.3 86.0 - - + +
182A ALA* 1.3 67.1 - - - +
184A THR* 3.1 18.4 + - - -
185A PHE* 3.1 27.6 + + + -
211A ALA* 3.8 19.1 - - + -
215A LEU* 4.2 17.7 - - + +
218A ARG* 4.7 7.5 + - - -
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Residues in contact with ALA 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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161A ILE* 3.9 24.2 - - + -
178A ILE 2.9 18.7 + - - +
179A ARG 4.0 3.4 - - - +
181A HIS* 1.3 75.1 - - - +
183A GLN* 1.3 56.7 + - - +
185A PHE* 3.1 10.4 + - - +
186A VAL* 2.8 31.6 + - - +
207A SER* 3.5 25.1 - - - +
208A VAL* 4.2 12.8 - - + +
211A ALA* 3.9 1.8 - - + +
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Residues in contact with GLN 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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75A GLU* 3.6 25.6 - - + +
158A HIS* 3.5 34.0 + - + +
161A ILE* 4.3 11.0 - - + +
162A GLU* 4.5 2.4 - - - +
179A ARG* 3.2 42.6 + - + +
180A LYS* 3.7 6.4 + - - +
181A HIS 3.1 0.8 - - - -
182A ALA* 1.3 72.9 - - - +
184A THR* 1.3 65.6 + - - +
186A VAL* 3.8 9.1 - - - +
187A ALA* 3.3 19.2 + - - +
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Residues in contact with THR 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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180A LYS* 3.3 14.9 + - - +
181A HIS* 3.1 13.8 + - - -
183A GLN* 1.3 73.2 - - - +
185A PHE* 1.3 70.6 + - + +
187A ALA* 2.9 17.5 + - - +
188A LEU* 3.0 23.2 + - + +
255A LEU* 5.6 6.1 - - + -
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Residues in contact with PHE 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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181A HIS* 3.1 29.6 + + + -
182A ALA* 3.1 6.2 + - - +
184A THR* 1.3 80.9 - - + +
186A VAL* 1.3 58.2 + - - +
188A LEU* 3.1 17.5 + - + +
189A CYS* 2.8 31.5 + - - -
207A SER* 3.5 30.1 - - - +
210A ALA* 4.0 16.4 - - + -
211A ALA* 3.7 25.4 - - + -
251A ILE* 3.0 32.1 - - + -
252A GLU* 5.2 2.5 - - + -
255A LEU* 3.6 35.2 - - + -
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Residues in contact with VAL 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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79A PRO* 4.5 7.9 - - + -
157A PRO* 3.2 44.6 - - + -
158A HIS* 3.9 15.9 - - + -
161A ILE* 3.8 17.7 - - + -
182A ALA 2.8 24.8 + - - +
183A GLN* 3.9 8.3 - - - +
184A THR 3.2 0.2 - - - -
185A PHE* 1.3 72.4 - - - +
187A ALA* 1.3 55.4 + - - +
189A CYS* 3.3 3.5 + - - +
190A ALA* 2.9 26.7 + - - +
195A PHE* 4.6 1.5 - - + -
203A VAL* 4.2 9.9 - - + +
207A SER* 3.4 16.2 - - - +
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Residues in contact with ALA 187 (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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65A LEU* 4.1 26.9 - - + -
78A PHE* 4.0 16.1 - - + -
183A GLN 3.3 10.5 + - - +
184A THR* 2.9 12.4 + - - +
186A VAL* 1.3 77.7 - - - +
188A LEU* 1.3 66.0 + - - +
190A ALA* 3.0 12.5 + - - +
191A THR* 3.3 17.8 + - - +
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Residues in contact with LEU 188 (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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184A THR* 3.0 21.2 + - + +
185A PHE* 3.2 24.0 - - + +
187A ALA* 1.3 75.3 - - + +
189A CYS* 1.3 63.1 + - - +
191A THR* 3.1 18.8 + - - +
192A ASP* 3.7 4.2 + - - +
251A ILE* 4.8 0.9 - - + +
254A LEU* 3.6 26.2 - - + +
255A LEU* 3.6 48.2 - - + +
258A SER* 3.8 16.6 - - - +
261A GLN* 5.9 3.1 - - - +
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Residues in contact with CYS 189 (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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185A PHE 2.8 23.4 + - - -
186A VAL 3.5 7.6 - - - +
188A LEU* 1.3 72.3 - - - +
190A ALA* 1.3 56.1 + - - +
192A ASP* 2.8 33.2 + - - +
194A LYS* 4.0 18.4 - - + -
195A PHE* 3.3 11.5 + - + +
203A VAL* 3.9 27.1 - - + -
207A SER* 4.6 0.2 - - - -
251A ILE* 3.6 33.4 - - - -
254A LEU* 3.8 11.4 - - - -
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Residues in contact with ALA 190 (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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57A ARG* 2.9 26.7 + - - -
78A PHE* 3.5 29.6 - - + -
79A PRO* 4.8 4.0 - - + -
82A MET* 3.2 19.3 - - + +
186A VAL 2.9 17.2 + - - +
187A ALA* 3.0 1.3 + - - +
189A CYS* 1.3 77.5 - - - +
191A THR* 1.3 59.2 + - - +
192A ASP 3.1 0.2 - - - -
195A PHE* 3.6 24.7 - - + -
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Residues in contact with THR 191 (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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57A ARG* 3.5 6.8 + - - -
58A LYS* 2.9 41.3 + - - +
61A ALA* 3.6 22.0 - - + -
62A THR* 3.6 32.5 - - + +
65A LEU* 4.6 7.9 - - + -
78A PHE* 3.7 17.9 - - + -
187A ALA 3.3 7.4 + - - +
188A LEU* 3.1 17.2 + - - +
189A CYS 3.2 0.2 - - - -
190A ALA* 1.3 76.0 - - - +
192A ASP* 1.3 55.8 + - - +
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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