Contacts of the helix formed by residues 164 - 182 (chain A) in PDB entry 2KWI
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 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 3.8 16.9 - - + +
156A GLU* 2.9 27.0 + - - +
157A THR* 3.5 13.4 - - + +
163A ALA* 1.3 77.2 - - - +
165A VAL* 1.3 62.5 + - - +
166A ASP* 3.4 3.7 + - - +
167A LYS* 3.5 17.2 + - + +
168A VAL* 3.3 18.7 + - - +
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.6 42.8 - - + +
33A GLN* 4.2 15.7 - - + -
34A PHE* 4.4 7.2 - - + +
157A THR* 4.8 1.6 - - - -
158A SER 3.9 22.7 - - - +
159A ALA* 4.9 2.5 - - - -
162A ARG* 4.3 7.4 - - + -
163A ALA* 3.9 11.2 - - - +
164A ASN* 1.3 76.4 - - - +
166A ASP* 1.3 69.9 + - - +
168A VAL* 3.2 10.2 - - - +
169A PHE* 2.9 37.1 - - + -
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 4.3 15.5 - - - -
164A ASN* 5.6 1.7 + - - -
165A VAL* 1.3 81.7 + - - +
167A LYS* 1.3 63.2 + - - +
169A PHE* 3.2 3.3 + - - +
170A PHE* 2.9 51.9 + - + -
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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
----------------------------------------------------------
124A LEU* 5.5 0.2 - - + -
153A GLN* 5.3 2.8 - - - +
155A VAL* 3.6 35.9 - - + -
164A ASN* 3.5 25.5 + - + +
166A ASP* 1.3 78.4 - - - +
168A VAL* 1.3 59.2 + - - +
170A PHE* 5.0 2.7 - - - -
171A ASP* 2.7 72.5 + - + +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 5.7 3.8 - - + -
90A LEU* 4.1 8.5 - - + +
124A LEU* 3.5 17.6 - - + +
126A VAL* 4.0 26.2 - - + -
155A VAL* 3.8 25.1 - - + -
157A THR* 3.8 19.3 - - + -
164A ASN 3.3 13.0 + - - +
165A VAL* 3.2 21.3 - - - +
167A LYS* 1.3 77.1 - - - +
169A PHE* 1.3 71.5 + - + +
172A LEU* 3.4 24.6 + - - +
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Residues in contact with PHE 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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17A VAL* 5.5 2.2 - - + +
19A MET* 3.6 30.7 - - + -
30A LEU* 3.7 31.9 - - + -
31A THR* 4.0 14.1 - - + -
34A PHE* 3.7 45.5 - + + -
64A ILE* 4.5 7.3 - - + +
66A ILE* 4.1 24.9 - - + -
90A LEU* 4.6 8.7 - - + -
165A VAL* 2.9 27.6 - - + -
166A ASP 3.2 5.5 + - - +
167A LYS 3.2 1.0 - - - -
168A VAL* 1.3 86.6 - - + +
170A PHE* 1.3 64.4 + - - +
172A LEU* 4.2 1.8 - - - +
173A MET* 3.2 28.9 + - + +
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Residues in contact with PHE 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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34A PHE* 3.6 30.1 - + - -
55A VAL* 4.3 12.3 - - + -
57A LEU* 3.8 33.4 - - + -
166A ASP* 2.9 43.7 + - + +
167A LYS* 4.1 2.7 - - - +
169A PHE* 1.3 73.0 - - - +
171A ASP* 1.3 67.3 + - - +
173A MET* 3.0 23.4 - - + +
174A ARG* 2.9 33.1 + - + +
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Residues in contact with ASP 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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124A LEU* 4.5 3.9 - - + +
153A GLN* 3.9 25.8 + - - +
167A LYS* 2.7 61.1 + - + +
168A VAL* 4.3 2.9 - - - +
170A PHE* 1.3 75.9 - - - +
172A LEU* 1.3 61.2 + - - +
174A ARG* 3.3 14.7 + - - +
175A GLU* 3.3 16.8 + - - +
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Residues in contact with LEU 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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17A VAL* 3.7 22.9 - - + -
88A GLY* 3.9 6.5 - - - -
89A PHE 3.8 15.3 - - - +
90A LEU* 3.5 30.1 - - + -
122A PRO* 3.7 34.3 - - + +
123A LEU 4.4 0.9 - - - +
124A LEU* 4.0 23.8 - - + +
153A GLN* 5.5 0.7 - - - +
168A VAL 3.4 16.3 + - - +
169A PHE* 4.2 2.5 - - - +
170A PHE 3.3 0.6 - - - -
171A ASP* 1.3 78.8 - - - +
173A MET* 1.3 63.8 + - - +
175A GLU* 3.2 23.8 + - - +
176A ILE* 3.2 12.6 + - + +
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Residues in contact with MET 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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15A HIS* 3.0 57.8 + - + +
17A VAL* 5.2 1.1 - - + +
34A PHE* 4.2 9.6 - - + -
55A VAL* 4.6 11.7 - - + -
57A LEU* 4.5 11.9 - - - -
62A VAL* 5.4 0.7 - - - -
64A ILE* 3.6 27.1 - - + -
169A PHE 3.2 20.5 + - - +
170A PHE* 3.0 49.8 + - + +
172A LEU* 1.3 78.1 - - - +
174A ARG* 1.3 68.0 + - + +
176A ILE* 3.2 17.9 - - - +
177A ARG 3.7 0.7 + - - -
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Residues in contact with ARG 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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15A HIS* 6.1 0.9 - - - -
57A LEU* 3.4 38.0 - - - +
58A ASP* 5.7 3.0 + - - -
60A GLU* 5.6 4.9 + - - -
170A PHE* 2.9 29.9 + - + +
171A ASP* 3.5 10.5 - - - +
172A LEU 3.2 0.4 - - - -
173A MET* 1.3 78.1 - - - +
175A GLU* 1.3 63.1 + - - +
177A ARG* 3.0 74.4 + - - +
178A THR* 3.7 6.3 + - - -
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Residues in contact with GLU 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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122A PRO* 3.7 18.0 - - + +
123A LEU 4.9 2.1 + - - +
152A VAL* 6.1 0.2 - - - +
153A GLN* 2.7 35.0 + - - +
171A ASP* 3.3 12.3 + - - +
172A LEU* 3.2 16.2 + - - +
174A ARG* 1.3 79.1 - - - +
176A ILE* 1.3 62.2 + - - +
178A THR* 3.0 20.7 + - - -
179A LYS* 2.6 49.1 + - - +
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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
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11A SER 5.3 1.1 - - - +
12A LEU* 6.3 0.2 - - - -
14A LEU 4.6 6.3 - - - +
15A HIS* 3.7 28.9 - - + +
16A LYS 3.9 20.9 - - - +
17A VAL* 4.0 9.2 - - + -
87A GLU* 3.8 33.9 - - + +
88A GLY* 4.3 7.0 - - - +
122A PRO* 4.6 6.7 - - + -
172A LEU 3.3 11.7 - - - +
173A MET* 3.2 25.1 - - - +
174A ARG 3.1 0.8 - - - -
175A GLU* 1.3 76.5 - - - +
177A ARG* 1.3 55.7 + - - +
179A LYS* 3.3 9.0 + - - +
180A LYS* 2.9 33.1 + - + +
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Residues in contact with ARG 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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9A GLN* 6.2 0.4 - - - +
12A LEU* 3.6 32.6 - - + +
15A HIS* 3.9 15.7 - - + -
60A GLU* 5.8 6.0 + - - -
173A MET 3.8 8.7 - - - +
174A ARG* 3.0 66.2 + - - +
176A ILE* 1.3 76.8 - - - +
178A THR* 1.3 58.2 + - - +
180A LYS 3.2 1.4 + - - -
181A MET* 2.8 50.4 + - + +
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Residues in contact with THR 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 ARG 3.9 6.8 + - - -
175A GLU* 3.0 14.7 + - - -
177A ARG* 1.3 78.3 + - - +
179A LYS* 1.3 64.6 + - + +
181A MET* 3.4 10.9 + - + +
182A SER* 3.1 28.0 + - - +
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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
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87A GLU* 4.6 9.2 - - - +
119A ASP* 3.8 16.8 - - + +
120A LYS* 3.4 51.6 - - + +
121A ILE 4.7 1.1 - - - -
122A PRO* 3.7 25.7 - - + +
175A GLU* 2.6 57.5 + - - +
176A ILE* 3.5 10.3 - - - +
178A THR* 1.3 85.3 - - + +
180A LYS* 1.3 61.8 + - - +
182A SER* 3.2 17.8 + - - +
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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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11A SER* 3.4 37.8 - - - +
12A LEU* 3.5 20.9 - - + -
14A LEU 6.1 0.2 - - - -
87A GLU* 2.6 43.6 + - - +
119A ASP* 6.3 0.4 - - - +
176A ILE* 2.9 21.9 + - + +
177A ARG 3.2 0.2 + - - -
179A LYS* 1.3 75.7 - - - +
181A MET* 1.3 62.4 + - - +
182A SER* 3.2 4.7 + - - -
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 5.4 3.8 - - - +
12A LEU* 3.6 31.0 - - + -
177A ARG* 2.8 36.2 + - + +
178A THR* 3.8 8.7 - - + +
179A LYS 3.2 0.2 - - - -
180A LYS* 1.3 76.5 - - - +
182A SER* 1.3 74.9 + - - +
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP* 2.7 28.4 + - - -
178A THR* 3.1 16.4 + - - +
179A LYS* 3.2 10.0 + - - +
180A LYS 4.0 4.9 + - - -
181A MET* 1.3 89.2 - - - +
183A GLU* 1.3 65.8 + - - +
184A ASN* 5.0 5.8 - - - -
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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
------------------------------------------------------------
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