Contacts of the helix formed by residues 161 - 173 (chain A) in PDB entry 2WWA
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 GLY 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU 5.4 0.2 - - - -
80A LEU* 6.3 0.9 - - - -
128A TYR* 3.0 47.1 - - - -
157A LEU 3.0 10.7 + - - -
158A VAL 3.2 2.0 + - - -
160A ALA* 1.4 79.7 - - - +
162A ILE* 1.3 61.3 + - - +
163A PHE 3.1 0.9 - - - -
164A THR* 3.3 16.7 + - - +
165A THR* 3.4 6.1 + - - -
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Residues in contact with ILE 162 (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 PRO 5.4 7.2 - - - +
19A GLU* 5.3 3.6 - - - -
20A VAL* 3.4 38.8 - - + +
125A ILE* 3.9 36.3 - - + -
128A TYR* 4.9 4.9 - - + -
158A VAL* 3.0 38.7 + - + +
159A GLY* 5.1 5.8 - - - +
161A GLY* 1.3 75.5 - - - +
163A PHE* 1.4 57.0 + - - +
165A THR* 3.1 17.5 + - - +
166A LEU* 3.2 20.0 + - + +
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Residues in contact with PHE 163 (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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42A ILE* 3.5 31.0 - - + -
43A TYR* 5.4 0.4 - - - -
159A GLY 4.5 5.6 + - - +
160A ALA* 3.7 26.4 - - + +
161A GLY 3.7 0.4 - - - +
162A ILE* 1.4 77.7 - - - +
164A THR* 1.4 60.3 + - - +
166A LEU* 3.2 9.7 + - + +
167A LEU* 3.0 61.1 + - + +
64C VAL* 3.8 34.1 - - + -
65C LEU* 5.4 0.2 - - - -
67C LEU* 4.7 10.3 - - + +
68C SER* 3.2 39.0 - - - -
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Residues in contact with THR 164 (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 LEU* 5.5 8.0 - - + +
83A GLY* 3.2 34.3 - - - +
84A LEU* 4.9 8.4 - - + +
128A TYR* 3.5 7.0 - - + +
160A ALA 3.9 7.1 + - - +
161A GLY* 3.3 18.2 + - - +
163A PHE* 1.4 79.4 - - - +
165A THR* 1.4 62.0 + - + +
167A LEU* 3.7 16.7 + - - +
168A ALA* 3.5 16.6 + - - +
184A ILE* 3.3 29.6 - - - +
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Residues in contact with THR 165 (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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20A VAL* 5.6 2.3 - - - +
83A GLY 5.2 0.9 - - - +
84A LEU* 6.1 1.3 - - + -
87A ASN* 3.7 35.4 - - + +
121A LYS* 6.5 0.9 - - - -
124A ALA* 4.7 8.5 - - + -
125A ILE* 4.8 9.8 - - + +
128A TYR* 4.2 15.3 - - + -
161A GLY 3.4 10.1 + - - +
162A ILE* 3.1 22.7 + - - +
164A THR* 1.4 78.8 - - + +
166A LEU* 1.4 62.0 + - - +
167A LEU 3.4 0.2 - - - -
168A ALA* 3.7 8.5 + - - +
169A GLU* 3.4 30.9 + - - +
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Residues in contact with LEU 166 (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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20A VAL* 3.8 35.4 - - + -
21A GLU 4.2 7.0 - - - +
22A LEU* 4.2 24.5 - - + -
162A ILE* 3.2 21.3 + - + +
163A PHE* 3.2 17.6 + - + +
165A THR* 1.4 75.5 - - - +
167A LEU* 1.4 57.1 + - - +
169A GLU* 3.3 8.7 + - - +
170A VAL* 2.9 37.9 + - + +
64C VAL* 3.9 39.9 - - + -
67C LEU* 5.9 5.6 - - + -
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Residues in contact with LEU 167 (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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39A ALA* 3.9 43.1 - - + +
42A ILE* 4.7 3.1 - - + -
43A TYR* 5.0 10.8 - - + -
163A PHE* 3.0 53.4 + - + +
164A THR* 3.8 21.5 - - - +
165A THR 3.4 0.2 - - - -
166A LEU* 1.4 75.0 - - - +
168A ALA* 1.4 61.0 + - - +
170A VAL* 4.1 7.1 - - + +
171A ILE* 3.4 36.4 + - + +
180A GLY* 4.8 2.9 - - - +
184A ILE* 5.1 5.4 - - + -
64C VAL* 5.6 2.5 - - + -
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Residues in contact with ALA 168 (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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84A LEU* 5.1 4.0 - - + -
87A ASN* 4.6 16.4 - - - +
164A THR 3.5 10.6 + - - +
165A THR* 3.7 12.3 - - - +
167A LEU* 1.4 79.4 - - - +
169A GLU* 1.4 61.9 + - + +
172A ASP* 3.3 22.0 + - - +
179A SER* 4.7 2.1 + - - +
180A GLY* 3.9 20.5 + - - -
181A ALA* 4.5 15.0 - - + +
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Residues in contact with GLU 169 (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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20A VAL* 4.9 2.1 - - - +
22A LEU* 3.6 34.3 - - + +
23A PRO* 5.7 0.2 - - - -
121A LYS* 3.2 42.9 + - - +
165A THR* 3.4 17.6 + - - +
166A LEU* 3.3 16.8 + - - +
168A ALA* 1.4 76.6 - - + +
170A VAL* 1.4 62.8 + - - +
172A ASP* 3.1 8.0 + - - +
173A LYS* 3.1 39.9 + - - +
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Residues in contact with VAL 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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23A PRO* 3.9 31.0 - - + +
35A TYR* 5.8 6.7 - - + +
166A LEU* 2.9 26.4 + - + +
167A LEU* 3.6 10.3 + - + +
168A ALA 3.6 0.2 - - - -
169A GLU* 1.4 73.2 - - + +
171A ILE* 1.4 65.5 + - + +
173A LYS* 3.4 12.4 + - - +
175A PHE* 3.6 28.9 + - + +
61C SER* 3.6 22.0 - - - +
64C VAL* 4.4 17.5 - - + -
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Residues in contact with ILE 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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35A TYR 5.2 1.8 - - - +
36A THR* 3.7 21.5 - - - +
39A ALA* 3.8 25.6 - - + -
167A LEU* 3.4 21.2 + - + +
169A GLU 3.4 0.2 - - - -
170A VAL* 1.4 79.8 - - + +
172A ASP* 1.4 59.7 + - - +
174A GLY* 3.4 6.6 + - - -
175A PHE 5.5 0.4 - - - -
176A GLY* 3.2 27.7 + - - +
177A PHE 3.2 27.4 - - - +
178A SER 3.6 7.9 - - - +
179A SER 3.8 0.7 - - - -
180A GLY* 3.6 33.0 - - - +
183A ILE* 4.2 9.9 - - + -
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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
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168A ALA 3.3 17.4 + - - +
169A GLU* 3.1 10.6 + - - +
171A ILE* 1.4 77.9 - - - +
173A LYS* 1.4 69.2 + - - +
174A GLY* 3.2 3.8 + - - -
178A SER 4.7 5.5 - - - +
179A SER* 4.2 18.8 + - - +
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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
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22A LEU* 3.6 30.0 - - + +
23A PRO* 3.9 28.3 - - + +
24A PHE 5.2 6.1 - - - +
25A GLU 6.1 0.4 - - - +
26A LYS* 3.6 23.2 - - + +
117A GLN* 5.5 4.6 + - - -
169A GLU* 3.1 32.1 + - - +
170A VAL 3.4 6.9 + - - +
171A ILE 3.3 1.2 - - - -
172A ASP* 1.4 90.1 + - - +
174A GLY* 1.4 58.1 + - - +
175A PHE* 3.6 0.9 - - + +
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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