Contacts of the helix formed by residues 170 - 187 (chain A) in PDB entry 2W7P
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 ASN 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 4.7 7.0 - - - +
168A PRO 3.8 2.7 + - - +
169A PRO* 1.3 73.2 - - - +
171A PHE* 1.3 51.8 + - - +
172A ASP* 2.7 19.5 + - - +
173A LYS* 2.6 54.6 + - + +
174A TYR* 2.9 21.6 + - + +
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Residues in contact with PHE 171 (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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112A TYR* 3.9 35.0 - + - -
137A SER* 6.1 2.9 - - - -
169A PRO* 3.9 31.4 - - + -
170A ASN* 1.3 71.3 - - - +
172A ASP* 1.3 56.9 + - - +
173A LYS 3.1 0.4 - - - -
174A TYR* 3.2 10.9 - + - -
175A ARG* 2.9 54.8 + - - +
197A LEU* 5.1 7.9 - - + +
1521A DTP 6.6 0.4 - + - -
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Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASN* 2.7 19.5 + - - +
171A PHE* 1.3 75.8 - - - +
173A LYS* 1.3 62.6 + - - +
175A ARG* 4.2 21.4 + - - +
176A ALA* 3.6 15.9 + - - +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.7 20.2 - - + -
116A GLU* 3.0 30.5 + - - +
118A ARG* 5.7 0.4 - - - +
119A ASP* 2.9 35.5 + - - +
170A ASN* 2.6 41.7 + - + +
172A ASP* 1.3 69.6 - - - +
174A TYR* 1.3 68.8 + - + +
176A ALA* 2.8 16.8 + - - +
177A VAL* 2.9 22.0 + - + +
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Residues in contact with TYR 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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111A PHE* 4.5 11.5 - + + -
112A TYR* 3.2 59.9 - + + -
115A VAL* 4.3 20.4 - - + -
116A GLU* 3.6 21.0 + - + +
130A VAL* 3.7 9.4 - - - +
169A PRO* 3.5 12.7 - - + +
170A ASN* 2.9 54.4 + - + -
171A PHE* 3.2 13.5 - - - +
173A LYS* 1.3 72.7 - - + +
175A ARG* 1.3 68.4 + - - +
176A ALA 2.7 1.2 + - - -
177A VAL* 2.8 20.2 + - - +
178A SER* 2.9 13.0 + - - -
197A LEU* 4.1 18.4 - - + -
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Residues in contact with ARG 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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171A PHE* 2.9 47.3 + - - +
172A ASP* 4.2 22.0 + - - +
174A TYR* 1.3 73.5 - - - +
176A ALA* 1.3 59.8 + - - +
178A SER* 3.4 15.1 - - - -
179A LYS* 3.5 20.3 + - - +
182A LYS* 5.8 0.3 + - - -
197A LEU* 4.2 19.1 - - + +
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Residues in contact with ALA 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 ASP 3.6 11.2 - - - +
173A LYS* 2.8 13.9 + - - +
174A TYR 2.7 0.6 + - - -
175A ARG* 1.3 77.9 - - - +
177A VAL* 1.3 62.4 + - + +
178A SER 3.0 2.4 + - - -
179A LYS* 3.4 15.2 + - - +
180A GLU* 3.6 19.0 + - - +
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Residues in contact with VAL 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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108A MET* 5.8 0.9 - - + -
111A PHE* 4.0 19.7 - - + -
115A VAL* 4.2 11.2 - - + -
118A ARG* 4.3 23.8 - - - +
173A LYS* 2.9 27.4 + - + +
174A TYR* 2.8 9.7 + - - +
176A ALA* 1.3 73.5 - - + +
178A SER* 1.3 63.1 + - - +
180A GLU* 3.5 20.7 + - - +
181A VAL* 3.5 10.0 + - - +
305A THR* 4.0 15.7 - - + +
307A LEU* 4.0 20.6 - - + -
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Residues in contact with SER 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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111A PHE* 4.4 7.4 - - - -
174A TYR 2.9 9.9 + - - -
175A ARG* 3.4 14.6 - - - -
177A VAL* 1.3 74.9 - - - +
179A LYS* 1.3 55.0 + - - +
180A GLU 3.0 4.0 - - - -
181A VAL* 2.5 45.9 + - - +
182A LYS* 2.9 26.3 + - - -
196A SER 4.8 0.2 + - - -
197A LEU* 3.4 33.3 + - - +
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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
----------------------------------------------------------
175A ARG* 3.5 17.4 + - - +
176A ALA* 3.4 11.7 + - - +
178A SER* 1.3 78.8 - - - +
180A GLU* 1.3 59.9 + - + +
182A LYS* 3.7 26.0 - - + +
183A GLU* 3.2 29.7 + - - +
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Residues in contact with GLU 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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118A ARG* 4.5 8.0 + - - -
176A ALA* 3.8 16.7 - - - +
177A VAL* 3.5 14.9 + - - +
178A SER 2.7 2.4 + - - -
179A LYS* 1.3 76.2 - - + +
181A VAL* 1.3 59.2 + - - +
183A GLU* 4.0 9.8 + - - +
184A ILE* 3.1 24.6 + - - +
304A LYS* 3.4 31.9 + - - +
305A THR* 4.0 21.4 - - + +
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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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106A ILE* 6.1 0.7 - - + -
108A MET* 3.4 27.8 - - + -
111A PHE* 6.0 0.2 - - + -
177A VAL 3.5 6.1 + - - +
178A SER* 2.5 36.0 + - - +
180A GLU* 1.3 73.4 - - - +
182A LYS* 1.3 72.2 + - + +
184A ILE* 3.4 15.1 + - - +
185A LEU* 3.4 19.2 + - + +
197A LEU 5.2 4.3 - - - +
301A ILE* 3.1 43.0 - - + +
305A THR* 5.6 3.6 - - + +
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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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175A ARG 5.8 0.2 + - - -
178A SER* 2.9 36.8 + - - +
179A LYS* 3.8 25.5 - - + +
180A GLU 3.3 0.2 - - - -
181A VAL* 1.3 78.7 - - + +
183A GLU* 1.3 53.1 - - - +
184A ILE 2.5 5.7 + - - -
185A LEU* 2.4 39.7 + - + +
186A ALA 3.0 8.7 + - - -
192A PHE* 4.0 31.1 - - + -
194A ALA* 4.6 20.9 - - - +
196A SER 5.0 4.9 + - - -
197A LEU* 6.0 1.4 - - - +
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Residues in contact with GLU 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 3.2 19.0 + - - +
180A GLU* 4.0 12.1 - - - +
181A VAL 3.5 0.2 - - - -
182A LYS* 1.3 76.8 - - - +
184A ILE* 1.3 59.4 + - + +
186A ALA* 3.7 18.1 - - - +
187A ASP* 3.8 12.8 - - - +
300A ARG* 5.5 0.5 + - - -
304A LYS* 5.4 6.4 + - - +
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Residues in contact with ILE 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 GLU 3.1 22.2 - - - +
181A VAL* 3.4 11.7 - - + +
182A LYS 2.5 5.1 + - - -
183A GLU* 1.3 74.5 - - + +
185A LEU* 1.3 63.8 + - + +
186A ALA 3.3 0.2 - - - -
187A ASP* 3.5 7.3 + - - +
188A TYR* 3.0 27.5 - - + -
297A ILE* 5.1 3.8 - - + -
300A ARG* 3.7 50.3 - - + +
301A ILE* 3.7 39.9 - - + +
304A LYS* 4.2 18.8 - - + -
305A THR* 6.5 1.6 - - + -
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Residues in contact with LEU 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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106A ILE* 3.1 33.2 - - + -
181A VAL* 3.5 19.5 - - + +
182A LYS* 2.4 24.1 + - + +
184A ILE* 1.3 70.2 - - + +
186A ALA* 1.3 54.6 + - - +
188A TYR* 2.6 37.4 + - - +
189A ASP 3.2 6.6 + - - -
192A PHE* 4.0 17.0 - - + -
200A ALA* 4.0 20.6 - - + -
202A LEU* 3.7 32.9 - - + +
297A ILE* 3.9 15.5 - - + -
301A ILE* 5.2 2.5 - - + -
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Residues in contact with ALA 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 LYS 3.0 7.5 + - - +
183A GLU* 3.7 17.5 - - - +
185A LEU* 1.3 76.5 - - - +
187A ASP* 1.3 55.9 + - - +
188A TYR 2.5 12.6 + - - -
189A ASP 3.0 26.1 + - - -
190A PRO* 3.8 9.0 - - + +
192A PHE* 4.1 12.0 - - + -
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Residues in contact with ASP 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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183A GLU 3.8 13.9 - - - +
184A ILE 3.5 9.9 + - - +
185A LEU 3.0 1.4 + - - -
186A ALA* 1.3 73.7 - - - +
188A TYR* 1.3 65.8 + - + +
207A HIS* 4.1 9.7 + - - -
300A ARG* 3.3 34.6 + - - +
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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