Contacts of the helix formed by residues 156 - 173 (chain A) in PDB entry 2BQY
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY* 3.5 5.2 - - - -
121A ASP* 3.3 22.5 + - - +
122A ILE* 3.6 14.5 - - + +
123A ASP* 5.1 1.3 - - - +
155A GLU* 1.3 81.7 - - - +
157A LYS* 1.3 64.7 + - - +
158A GLU* 3.2 15.5 + - - +
159A SER* 3.0 25.3 + - - -
160A ALA 3.2 13.7 + - - -
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Residues in contact with LYS 157 (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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12A ALA* 5.3 3.1 - - - -
13A ASP* 3.0 34.0 + - - -
87A ARG* 6.0 1.6 - - - +
88A LEU* 3.6 25.0 + - + +
89A VAL* 3.4 15.7 + - - +
90A GLY* 4.0 2.0 - - - +
120A LYS 4.0 14.0 + - - +
121A ASP* 2.7 24.3 + - - +
156A ASN* 1.3 69.7 - - - +
158A GLU* 1.3 64.5 + - - +
159A SER 3.1 1.8 - - - -
160A ALA* 2.9 3.6 + - - +
161A ILE* 2.9 49.7 + - + +
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP* 5.3 0.6 + - - -
156A ASN* 3.2 14.8 + - - +
157A LYS* 1.3 79.2 - - - +
159A SER* 1.3 61.9 + - - +
161A ILE* 3.6 14.5 + - + +
162A LYS* 3.0 52.2 + - - +
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Residues in contact with SER 159 (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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91A VAL* 3.9 4.6 - - - +
155A GLU* 2.7 39.2 + - - +
156A ASN* 3.0 22.7 + - - -
158A GLU* 1.3 75.6 - - - +
160A ALA* 1.3 62.3 + - - +
162A LYS* 3.4 14.7 + - - +
163A VAL* 3.3 25.2 + - - +
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Residues in contact with ALA 160 (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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88A LEU* 4.2 12.6 - - + -
90A GLY* 3.1 40.4 - - - +
91A VAL* 4.0 11.6 - - + +
104A LEU* 3.8 10.6 - - + +
156A ASN 3.2 2.9 + - - +
157A LYS* 2.9 8.4 + - - +
159A SER* 1.3 78.8 - - - +
161A ILE* 1.3 65.0 + - - +
163A VAL* 3.1 4.8 + - - +
164A LEU* 2.9 23.9 + - - +
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Residues in contact with ILE 161 (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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12A ALA* 4.0 26.9 - - + -
88A LEU* 4.3 8.9 - - + +
157A LYS* 2.9 43.2 + - + +
158A GLU* 3.7 15.3 - - + +
160A ALA* 1.3 76.4 - - - +
162A LYS* 1.3 60.2 + - + +
164A LEU* 3.4 2.2 + - + +
165A GLU* 2.8 55.3 + - + +
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Residues in contact with LYS 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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158A GLU* 3.0 46.4 + - - +
159A SER* 3.4 11.5 + - - +
160A ALA 3.2 0.4 - - - -
161A ILE* 1.3 77.5 - - + +
163A VAL* 1.3 60.1 + - + +
165A GLU* 4.1 6.8 - - - +
166A LYS* 3.0 33.3 + - - +
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Residues in contact with VAL 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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68A VAL* 4.5 10.5 - - + -
91A VAL* 4.5 11.7 - - + -
93A ASN* 5.5 0.2 - - - +
102A GLU* 3.8 43.3 - - + +
104A LEU* 4.0 17.0 - - + -
155A GLU* 6.0 0.2 - - - +
159A SER* 3.3 19.3 + - - +
160A ALA* 3.1 10.0 + - - +
162A LYS* 1.3 76.5 - - + +
164A LEU* 1.3 58.9 + - - +
166A LYS* 3.5 9.7 + - + +
167A ALA* 3.0 27.1 + - + +
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Residues in contact with LEU 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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10A HIS* 4.0 19.5 - - + +
12A ALA* 4.1 15.5 - - + -
15A LEU* 4.4 9.0 - - + -
57A VAL* 4.3 23.1 - - + -
60A THR* 4.4 4.5 - - + -
68A VAL* 4.7 2.7 - - + -
88A LEU* 3.6 25.6 - - + -
104A LEU* 4.3 17.9 - - + +
160A ALA 2.9 12.4 + - - +
161A ILE* 3.6 7.4 - - + +
163A VAL* 1.3 75.8 - - - +
165A GLU* 1.3 62.7 + - + +
167A ALA* 2.9 8.1 + - - +
168A ILE* 2.9 51.2 + - + +
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Residues in contact with GLU 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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161A ILE* 2.8 44.3 + - + +
162A LYS* 4.1 6.5 - - - +
164A LEU* 1.3 76.2 - - + +
166A LYS* 1.3 61.4 + - - +
168A ILE* 3.4 15.6 + - + +
169A LYS* 3.2 22.7 + - - +
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Residues in contact with LYS 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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102A GLU* 5.4 8.1 - - - +
162A LYS 3.0 20.2 + - - +
163A VAL* 3.7 8.1 - - + +
165A GLU* 1.3 76.7 - - - +
167A ALA* 1.3 63.7 - - - +
169A LYS* 3.6 5.3 + - - +
170A ALA* 3.2 24.2 + - + +
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Residues in contact with ALA 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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60A THR* 3.3 17.3 - - - -
61A LEU* 2.7 44.4 + - - +
62A GLY* 4.7 2.2 - - - +
68A VAL* 4.1 20.4 - - + -
163A VAL* 3.0 13.9 + - + +
164A LEU 2.9 10.2 + - - +
166A LYS* 1.3 78.4 - - - +
168A ILE* 1.3 61.8 + - - +
170A ALA 3.8 0.5 + - - -
171A TYR 3.5 7.1 + - - -
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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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10A HIS* 3.5 48.7 - - + +
59A ASN 4.3 2.4 - - - +
60A THR* 3.7 22.0 - - + -
164A LEU* 2.9 34.3 + - + +
165A GLU* 3.7 13.7 - - + +
166A LYS 3.3 0.2 - - - -
167A ALA* 1.3 77.2 - - - +
169A LYS* 1.3 66.3 + - - +
171A TYR* 3.3 5.9 + - - +
172A GLN* 3.3 39.1 + - + +
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Residues in contact with LYS 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 GLU 3.2 13.9 + - - +
166A LYS* 4.0 5.6 - - - +
168A ILE* 1.3 75.9 - - - +
170A ALA* 1.3 66.7 + - - +
172A GLN* 3.0 27.3 + - + +
173A GLY* 3.3 10.4 + - - -
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Residues in contact with ALA 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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61A LEU* 3.7 39.1 - - + +
166A LYS* 3.2 17.8 + - + +
167A ALA 3.9 0.9 - - - +
168A ILE 3.3 0.2 - - - -
169A LYS* 1.3 79.6 - - - +
171A TYR* 1.3 60.2 + - - +
173A GLY* 4.0 10.8 + - - +
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Residues in contact with TYR 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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33A LYS* 3.7 19.9 + - - -
59A ASN* 3.4 47.2 + - + +
60A THR* 3.7 26.2 - - - -
61A LEU* 3.9 15.7 - - + +
167A ALA 3.5 1.4 + - - -
168A ILE 3.3 9.3 + - - +
169A LYS 3.1 0.6 - - - -
170A ALA* 1.3 80.8 - - - +
172A GLN* 1.3 68.3 + - + +
173A GLY* 3.4 6.6 + - - +
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Residues in contact with GLN 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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59A ASN 5.9 0.2 - - - +
168A ILE* 3.4 25.9 - - + +
169A LYS* 3.0 21.0 + - + +
171A TYR* 1.3 85.9 - - + +
173A GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 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 LYS 3.3 11.2 + - - -
170A ALA 4.0 7.7 + - - +
171A TYR 3.4 8.3 - - - +
172A GLN* 1.3 82.2 - - - +
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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