Contacts of the helix formed by residues 162 - 180 (chain A) in PDB entry 2BKR
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 ASP 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PRO* 5.6 0.2 - - - +
157A GLN* 4.5 3.0 - - + +
159A ASN* 2.9 32.4 + - - +
160A SER 3.9 0.2 - - - -
161A TYR* 1.3 83.3 + - - +
163A CYS* 1.3 65.5 + - - +
164A GLY 3.2 2.9 - - - -
165A MET* 2.9 16.1 + - - +
166A TYR* 3.1 31.9 + - + -
192A PRO* 5.0 1.6 - - - +
195A ILE* 3.4 22.0 - - + +
196A THR* 4.3 10.4 + - - -
199A ARG* 2.7 34.5 + - - +
76B GLY 3.4 0.2 + - - -
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Residues in contact with CYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A HIS* 3.6 13.9 - - + -
103A TRP* 3.4 24.4 - - - +
120A SER* 3.6 13.2 + - - +
157A GLN* 3.4 15.4 + - - +
161A TYR 3.3 0.2 - - - -
162A ASP* 1.3 75.5 - - - +
164A GLY* 1.3 71.2 + - - +
166A TYR* 3.1 6.1 + - - +
167A VAL* 3.1 23.6 + - - +
75B GLY 3.3 5.4 - - - -
76B GLY* 1.8 73.5 + - - +
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Residues in contact with GLY 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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27A LEU* 3.6 18.9 - - - +
32A ILE* 4.1 5.1 - - - +
103A TRP* 3.6 26.2 - - - -
161A TYR 4.5 2.6 + - - -
162A ASP 3.2 0.6 - - - -
163A CYS* 1.3 85.4 - - - +
165A MET* 1.3 61.1 + - - +
167A VAL* 3.3 6.2 + - - +
168A ILE* 3.2 24.8 + - - +
75B GLY 4.6 0.6 + - - -
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Residues in contact with MET 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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21A LEU* 3.9 13.7 - - - -
27A LEU* 3.6 23.0 - - + +
162A ASP* 2.9 11.5 + - - +
164A GLY* 1.3 74.1 - - - +
166A TYR* 1.3 59.7 + - - +
168A ILE* 3.3 9.7 + - + +
169A CYS* 2.8 58.6 + - - -
195A ILE* 3.5 18.8 - - + +
198A LYS* 4.1 11.9 - - + -
199A ARG* 3.7 41.3 - - + +
202A TRP* 3.9 24.7 - - + +
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Residues in contact with TYR 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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120A SER* 3.5 24.0 - - - +
155A PRO* 3.7 42.0 - - + -
156A ALA 3.5 12.1 + - - -
157A GLN* 3.6 24.9 - - + -
158A GLN 4.5 1.1 + - - -
162A ASP* 3.1 39.6 + - + -
163A CYS 3.1 7.2 + - - +
165A MET* 1.3 72.9 - - - +
167A VAL* 1.3 61.8 + - + +
169A CYS 4.6 0.2 - - - +
170A ASN* 2.8 43.8 + - - +
190A LEU* 3.9 11.6 + - + -
191A THR 4.2 0.2 - - - -
192A PRO* 3.8 21.3 - - - +
195A ILE* 3.4 34.4 - - + +
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Residues in contact with VAL 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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32A ILE* 4.4 8.7 - - + -
36A PHE* 4.2 8.3 - - + -
89A ALA* 4.1 17.9 - - + -
103A TRP* 3.7 9.9 - - + +
104A SER* 3.4 44.6 - - - +
105A LEU* 3.9 27.7 - - + +
118A TYR 5.4 0.7 - - - +
163A CYS 3.1 13.7 + - - +
164A GLY* 3.4 8.3 - - - +
165A MET 3.2 0.4 - - - -
166A TYR* 1.3 78.0 - - + +
168A ILE* 1.3 61.4 + - - +
170A ASN* 4.1 1.4 - - - +
171A THR* 2.9 29.8 + - - -
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Residues in contact with ILE 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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27A LEU* 3.6 31.0 - - + -
31A ILE* 4.2 9.2 - - + -
32A ILE* 4.0 24.2 - - + -
35A ALA* 3.7 24.0 - - + -
36A PHE* 5.1 2.0 - - + -
39A PHE* 3.7 5.6 - - + -
164A GLY 3.2 6.0 + - - +
165A MET* 3.3 15.9 + - + +
167A VAL* 1.3 75.8 - - - +
169A CYS* 1.3 59.5 + - - +
171A THR* 3.3 7.6 + - - -
172A GLU* 3.0 25.9 + - + +
202A TRP* 3.6 44.0 - - + +
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Residues in contact with CYS 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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165A MET* 2.8 33.1 + - - +
166A TYR 4.4 0.2 - - - +
168A ILE* 1.3 75.1 - - - +
170A ASN* 1.3 65.3 + - - +
172A GLU* 3.8 7.6 - - - +
173A ALA* 2.9 26.9 + - - +
190A LEU* 3.7 20.5 - - + +
194A TYR* 4.1 8.1 + - + +
195A ILE* 3.7 18.8 - - + -
198A LYS* 3.7 35.9 - - - -
202A TRP* 5.1 1.8 - - - -
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Residues in contact with ASN 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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105A LEU* 3.8 17.4 - - + +
118A TYR* 4.0 23.6 + - + +
120A SER 5.7 1.8 - - - +
154A ALA* 5.0 1.2 - - - +
155A PRO* 3.4 18.1 + - - +
166A TYR* 2.8 38.6 + - - +
167A VAL* 4.9 0.6 - - - +
169A CYS* 1.3 72.7 - - - +
171A THR* 1.3 57.8 + - - +
173A ALA* 3.8 0.5 - - - +
174A LEU* 2.9 39.1 + - + +
186A LEU* 3.4 23.8 - - + +
190A LEU* 3.2 19.6 - - - +
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Residues in contact with THR 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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36A PHE* 3.6 13.7 - - + -
39A PHE* 3.6 26.0 - - + -
53A PHE* 3.7 18.2 - - + -
87A PHE* 3.9 15.2 - - + -
105A LEU* 3.3 27.0 - - - +
167A VAL 2.9 17.5 + - - -
168A ILE 3.4 5.6 - - - -
170A ASN* 1.3 79.3 - - - +
172A GLU* 1.3 56.4 + - - +
174A LEU* 3.9 1.2 - - - +
175A CYS* 3.0 31.2 + - - -
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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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39A PHE* 3.1 24.5 - - + -
43A GLN* 2.7 46.0 + - - +
44A PHE* 4.4 1.8 - - - -
168A ILE 3.0 10.6 + - - +
169A CYS* 3.8 8.1 - - - +
171A THR* 1.3 78.4 - - - +
173A ALA* 1.3 60.1 + - - +
175A CYS* 3.3 7.0 + - - +
176A GLN* 2.9 53.1 + - + +
194A TYR* 5.1 9.9 - - - +
198A LYS* 5.3 10.8 - - - +
202A TRP* 4.9 4.4 - - + -
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Residues in contact with ALA 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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169A CYS 2.9 14.3 + - - +
172A GLU* 1.3 78.5 - - + +
174A LEU* 1.3 61.3 + - - +
176A GLN* 3.3 2.5 + - - -
177A ASN* 3.0 23.3 + - - -
184A GLU* 3.0 23.5 - - + +
186A LEU* 3.1 33.7 - - + -
189A LEU* 4.4 8.5 - - + -
190A LEU* 4.3 10.1 - - + -
194A TYR* 5.5 1.3 - - - +
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Residues in contact with LEU 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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87A PHE* 4.1 5.8 - - + -
105A LEU* 4.0 11.2 - - + -
107A VAL* 4.0 18.2 - - + -
118A TYR* 3.8 41.1 - - + +
170A ASN* 2.9 22.5 + - + +
171A THR 3.9 2.9 - - - +
173A ALA* 1.3 76.3 - - - +
175A CYS* 1.3 51.5 + - - +
177A ASN* 3.2 9.6 + - - +
178A PHE* 2.7 73.3 + - + -
186A LEU* 3.8 21.5 - - + -
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Residues in contact with CYS 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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39A PHE* 5.5 0.2 - - - -
44A PHE* 3.3 32.9 - - + -
53A PHE* 3.6 25.8 - - - -
87A PHE* 3.5 27.4 - - - -
171A THR 3.0 21.3 + - - +
172A GLU 3.6 0.7 - - - +
174A LEU* 1.3 73.7 - - - +
176A GLN* 1.3 60.4 + - - +
178A PHE* 4.8 0.2 - - - -
179A PHE* 2.8 49.2 + - + +
180A ARG 3.7 0.7 + - - -
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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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43A GLN* 3.1 14.1 + - - +
44A PHE* 3.8 9.1 - - - -
172A GLU* 2.9 43.0 + - + +
173A ALA* 3.5 2.0 - - - +
175A CYS* 1.3 77.0 - - - +
177A ASN* 1.3 55.0 + - - +
180A ARG* 3.0 52.2 + - - +
182A GLN* 3.3 22.9 + - + +
184A GLU* 3.1 32.3 - - - +
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Residues in contact with ASN 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 ALA 3.0 15.0 + - - -
174A LEU* 3.5 16.3 - - - +
176A GLN* 1.3 74.3 - - - +
178A PHE* 1.3 74.4 + - + +
181A GLN* 4.1 8.1 + - - -
182A GLN 3.1 22.3 - - - +
183A THR* 4.4 1.5 - - - -
184A GLU* 2.9 53.8 + - - +
186A LEU* 5.4 3.6 - - - +
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Residues in contact with PHE 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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84A ARG* 5.1 11.0 + - - +
85A VAL* 4.1 31.0 - - + -
87A PHE* 4.1 13.5 - + - -
107A VAL* 4.4 11.4 - - + -
109A LEU* 5.6 8.7 - - + -
118A TYR* 5.8 0.4 - - - -
174A LEU* 2.7 61.2 + - + +
177A ASN* 1.3 83.8 - - + +
179A PHE* 1.3 84.3 + + + +
181A GLN* 5.0 0.9 + - - +
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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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44A PHE* 4.7 6.5 - + + -
47A SER* 3.7 28.9 - - - +
50A HIS* 4.5 17.7 - + + -
51A VAL* 3.6 39.7 - - + -
84A ARG* 5.3 10.1 - - - -
85A VAL* 4.0 22.2 - - + -
87A PHE* 4.7 0.7 - + - -
175A CYS* 2.8 43.9 + - + +
178A PHE* 1.3 94.9 - + + +
180A ARG* 1.3 78.5 + - + +
181A GLN* 3.7 3.4 - - - +
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Residues in contact with ARG 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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43A GLN* 3.1 22.0 + - - +
44A PHE* 3.6 31.3 - - + +
46A ASP* 2.6 43.8 + - - -
47A SER* 4.2 6.3 + - - -
176A GLN* 3.0 36.9 + - - +
179A PHE* 1.3 92.2 + - - +
181A GLN* 1.3 63.8 + - - +
182A GLN* 2.8 33.3 + - + +
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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