Contacts of the helix formed by residues 171 - 183 (chain A) in PDB entry 2W7W
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 VAL 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A TYR* 5.0 0.7 - - - -
168A PHE* 3.0 24.3 + - - +
169A ARG* 3.2 2.8 + - + -
170A ASN* 1.3 89.5 - - - +
172A ARG* 1.3 65.6 + - - +
173A PRO* 3.8 17.5 - - + -
174A ASP* 3.1 41.6 + - - +
175A TYR* 3.3 8.2 + - - -
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Residues in contact with ARG 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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115A ALA 2.9 20.0 + - - -
116A ILE* 3.1 33.7 + - + +
118A ASN* 2.7 30.5 + - - +
120A GLY 3.2 16.0 + - - +
159A LEU* 3.2 36.0 + - + +
161A GLU* 5.5 2.2 - - - +
164A TYR* 3.0 41.1 + - + +
170A ASN 3.3 5.8 + - - +
171A VAL* 1.3 73.1 - - - +
173A PRO* 1.4 66.6 - - + +
175A TYR* 3.1 9.5 + - + +
176A MET* 2.8 35.2 + - + +
160B TRP* 6.3 0.6 - - - -
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Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 5.9 0.4 - - + -
116A ILE* 3.9 33.7 - - + -
171A VAL* 3.4 16.6 - - + -
172A ARG* 1.4 94.5 - - + +
174A ASP* 1.3 57.6 + - - +
176A MET* 3.5 4.2 + - + +
177A GLY* 3.1 22.0 + - - -
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Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.5 31.7 - - + +
171A VAL* 3.1 34.0 + - + +
173A PRO* 1.3 76.9 - - - +
175A TYR* 1.3 65.0 + - - +
177A GLY* 3.2 4.3 + - - -
178A ALA 3.1 16.5 + - - -
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Residues in contact with TYR 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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19A ILE* 4.4 13.7 - - + -
77A TYR* 2.9 26.0 + - - -
157A VAL* 3.4 24.8 - - + +
158A ASP 2.5 30.4 + - - -
159A LEU* 4.0 8.7 - - + -
163A ALA* 3.6 21.1 - - + +
164A TYR* 3.4 40.2 - + + -
168A PHE* 3.7 22.7 - + + -
171A VAL 3.3 6.9 + - - +
172A ARG* 3.1 11.8 + - - +
174A ASP* 1.3 75.3 - - - +
176A MET* 1.3 69.0 + - - +
178A ALA* 3.1 5.1 + - + +
179A PHE* 2.8 28.8 + + + +
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Residues in contact with MET 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 4.0 18.8 - - + -
112A THR* 4.3 26.5 - - + +
115A ALA* 3.9 26.2 - - + -
116A ILE* 4.5 9.6 - - + -
157A VAL* 4.0 22.0 - - + -
159A LEU* 4.3 2.5 - - + -
172A ARG* 2.8 27.5 + - + +
173A PRO 3.9 4.9 - - - +
175A TYR* 1.3 80.4 - - + +
177A GLY* 1.3 62.7 + - - +
179A PHE* 3.3 24.8 - - + +
180A TRP* 3.0 41.1 + - + +
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Residues in contact with GLY 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 PRO 3.1 14.1 + - - -
174A ASP* 3.2 5.9 + - - -
176A MET* 1.3 76.6 - - - +
178A ALA* 1.3 59.8 + - - +
180A TRP* 3.5 8.3 + - - +
181A SER* 3.3 23.6 + - - -
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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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18A HIS* 3.7 27.1 - - + +
19A ILE* 4.5 6.7 - - + -
168A PHE* 3.6 31.2 - - + -
174A ASP 3.1 4.6 + - - -
175A TYR* 3.1 9.4 + - + +
177A GLY* 1.3 73.9 - - - +
179A PHE* 1.3 66.6 + - - +
181A SER* 3.0 16.7 + - - -
182A LEU* 3.0 18.8 + - - +
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Residues in contact with PHE 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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19A ILE* 5.7 1.7 - - - +
77A TYR* 4.8 3.8 - + - -
80A CYS* 5.0 2.0 - - + -
81A LEU* 4.0 23.3 - - + -
111A PHE* 3.7 20.4 - + - -
155A LEU* 3.9 23.8 - - + -
156A THR 3.3 28.0 - - - -
157A VAL* 3.7 24.2 - - + -
175A TYR* 2.8 20.9 + + + +
176A MET* 3.3 31.2 - - + +
178A ALA* 1.3 71.6 - - - +
180A TRP* 1.3 74.1 + + - +
182A LEU* 2.9 23.1 + - - +
183A VAL* 3.0 31.7 + - + +
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Residues in contact with TRP 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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86A GLY* 3.3 17.7 - - - -
87A GLY* 3.5 9.0 + - - +
104A PHE* 4.3 20.9 - + + -
107A PHE* 3.7 30.1 - + - -
108A LYS* 3.6 45.4 - - + +
111A PHE* 3.5 34.5 - + + -
112A THR* 2.9 30.6 + - + -
155A LEU* 4.8 2.0 - - + -
176A MET* 3.0 34.1 + - + +
177A GLY* 4.0 6.7 - - - +
179A PHE* 1.3 92.4 - + - +
181A SER* 1.3 60.3 + - - +
182A LEU 3.4 0.2 + - - -
183A VAL* 3.8 17.2 + - + +
185A TRP* 4.5 7.2 - + - -
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Residues in contact with SER 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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18A HIS* 3.5 38.7 + - - -
82A ALA 4.7 1.2 - - - +
85A ALA 3.8 6.9 + - - +
86A GLY* 3.5 15.3 + - - -
87A GLY 4.9 1.6 - - - +
177A GLY 3.3 13.6 + - - -
178A ALA 3.0 10.8 + - - -
180A TRP* 1.3 75.4 - - - +
182A LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 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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15A LEU* 3.7 34.1 - - + +
18A HIS* 3.7 29.6 - - + -
19A ILE* 3.5 39.5 - - + -
80A CYS 4.3 0.9 - - - -
81A LEU* 3.5 17.4 - - + -
82A ALA* 2.9 41.5 + - - +
83A PRO* 5.3 2.5 - - + -
86A GLY 4.0 2.0 - - - -
178A ALA 3.0 16.7 + - - +
179A PHE 2.9 6.2 + - - +
181A SER* 1.3 80.7 - - - +
183A VAL* 1.3 66.9 + - - +
184A ASN 3.1 0.5 + - - -
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Residues in contact with VAL 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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80A CYS 3.5 4.0 - - - -
81A LEU* 5.4 0.2 - - - -
85A ALA* 3.2 1.9 - - - +
86A GLY* 2.7 27.4 + - - -
155A LEU* 3.8 20.6 - - + -
179A PHE* 3.0 53.4 + - + +
180A TRP* 4.0 17.7 - - + +
181A SER 3.7 2.2 - - - -
182A LEU* 1.3 74.3 - - - +
184A ASN* 1.3 61.9 + - - +
185A TRP* 3.3 49.0 + - + +
188A VAL* 4.5 0.2 - - + -
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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