Contacts of the helix formed by residues 149 - 163 (chain A) in PDB entry 2GB0
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 SER 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A HIS 2.9 24.3 + - - -
47A ASP 3.1 17.2 + - - -
49A ARG* 3.5 32.1 + - - +
147A LEU 3.3 3.0 + - - -
148A PHE* 1.3 70.3 - - - +
150A GLU* 1.3 65.3 + - - +
152A CYS* 3.2 2.9 + - - +
153A ILE* 3.2 26.6 + - - +
347A PHE* 3.5 26.6 - - - -
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PRO* 3.5 29.0 - - + +
39A HIS 5.3 1.8 - - - +
40A THR* 5.5 3.8 - - - +
44A HIS* 3.7 15.7 - - + +
45A HIS* 3.7 12.2 - - + +
46A GLY 3.1 9.4 + - - -
47A ASP* 2.8 41.4 + - - +
148A PHE 3.5 0.6 - - - -
149A SER* 1.3 76.5 + - - +
151A ASN* 1.3 59.6 + - - +
153A ILE* 3.4 1.5 + - - -
154A ARG* 2.9 49.0 + - - +
311A ARG* 4.5 5.1 + - - -
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Residues in contact with ASN 151 (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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81A HIS* 4.2 10.2 + - + +
82A LYS* 2.9 43.5 + - - +
83A ILE* 4.1 2.0 - - - +
148A PHE* 3.1 22.1 + - - +
150A GLU* 1.3 79.1 - - - +
152A CYS* 1.3 52.6 + - - +
154A ARG* 3.0 17.8 + - - +
155A ALA* 2.8 36.6 + - - +
801A PO4 2.9 32.1 + - - -
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Residues in contact with CYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A TRP* 3.4 40.2 - - + -
75A LEU* 4.0 1.9 - - - +
83A ILE* 3.9 28.7 - - - -
147A LEU* 4.4 4.7 - - - -
148A PHE 3.0 20.6 + - - -
149A SER 3.2 8.3 + - - +
151A ASN* 1.3 76.1 - - - +
153A ILE* 1.3 56.8 + - - +
155A ALA* 3.3 2.3 + - - +
156A TYR* 2.9 36.2 + - + +
347A PHE* 3.8 19.1 - - + -
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Residues in contact with ILE 153 (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 ALA 4.4 1.3 - - - +
12A GLY 3.9 2.2 - - - +
13A SER* 3.6 28.5 - - - +
16A MET* 3.6 18.7 - - + +
37A PRO* 4.0 26.7 - - + -
38A PRO* 4.0 9.9 - - + -
44A HIS* 3.2 50.5 - - + +
149A SER 3.2 9.7 + - - +
150A GLU 3.9 6.1 - - - +
152A CYS* 1.3 79.3 - - + +
154A ARG* 1.3 58.4 + - - +
156A TYR* 3.4 6.5 + - + +
157A ARG* 2.9 28.6 + - - +
347A PHE* 4.3 6.1 - - + -
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Residues in contact with ARG 154 (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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38A PRO* 3.6 33.6 + - + +
81A HIS* 3.3 27.4 - - - +
150A GLU* 2.9 39.7 + - - +
151A ASN* 3.0 30.0 + - - +
153A ILE* 1.3 77.3 - - - +
155A ALA* 1.3 56.5 + - - +
157A ARG* 3.3 5.6 + - - +
158A GLU* 2.9 50.1 + - + +
801A PO4 3.5 13.1 + - - -
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Residues in contact with ALA 155 (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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75A LEU* 4.0 14.1 - - + -
79A THR* 3.7 36.3 - - + +
81A HIS* 4.1 10.1 - - + -
83A ILE* 4.3 1.3 - - + -
151A ASN 2.8 20.4 + - - +
152A CYS 3.7 3.8 - - - +
154A ARG* 1.3 71.2 - - - +
156A TYR* 1.3 66.3 + - - +
158A GLU* 3.2 4.4 + - - +
159A LEU* 2.9 30.5 + - - +
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Residues in contact with TYR 156 (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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13A SER 5.3 1.8 - - - -
16A MET* 3.8 21.5 - - + +
17A ALA* 3.6 29.8 - - + -
20A TYR* 3.4 46.5 - + + +
21A GLN* 5.2 3.0 + - + -
71A LEU* 4.6 9.0 + - - +
72A TRP* 3.7 24.9 - + - -
75A LEU* 3.9 26.4 - - + +
152A CYS* 2.9 23.8 + - + +
153A ILE* 4.5 2.9 - - + -
155A ALA* 1.3 75.1 - - - +
157A ARG* 1.3 58.0 + - - +
159A LEU* 3.9 2.5 - - - +
160A ALA* 2.8 32.3 + - - +
350A SER* 5.4 0.2 - - - -
351A SER* 3.1 27.9 + - - -
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Residues in contact with ARG 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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16A MET* 3.6 35.2 - - + +
36A ASP* 2.5 31.9 + - - -
37A PRO* 3.0 27.3 + - - +
153A ILE 2.9 19.0 + - - +
154A ARG* 3.6 5.8 - - - +
156A TYR* 1.3 74.9 - - - +
158A GLU* 1.3 63.5 + - + +
160A ALA* 3.8 1.5 - - - +
161A GLU* 2.8 59.3 + - + +
167A VAL* 4.0 18.6 + - + +
169A THR* 3.7 15.8 - - - +
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A THR* 4.5 1.9 + - - -
80A HIS* 3.8 11.7 - - - -
81A HIS* 2.9 38.4 + - - -
154A ARG* 2.9 29.2 + - + +
155A ALA* 3.8 3.7 - - - +
157A ARG* 1.3 78.1 - - + +
159A LEU* 1.3 62.0 + - + +
161A GLU* 4.0 4.9 - - - +
162A ALA* 3.0 29.1 + - - +
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Residues in contact with LEU 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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20A TYR* 3.8 22.7 - - + -
75A LEU* 3.6 29.6 - - + -
78A GLU* 3.9 39.7 - - + +
79A THR* 4.7 8.3 - - - -
155A ALA* 2.9 21.3 + - - +
156A TYR 3.9 0.2 - - - +
158A GLU* 1.3 75.7 - - + +
160A ALA* 1.3 64.9 + - - +
162A ALA* 3.5 7.5 + - + +
163A ARG* 3.3 37.9 + - - +
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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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16A MET* 5.1 2.7 - - - +
19A GLY* 4.0 3.1 - - - +
20A TYR* 3.7 27.5 - - - +
23A ALA* 3.7 8.7 - - - +
31A LEU* 5.1 4.3 - - + -
156A TYR 2.8 19.5 + - - +
157A ARG* 3.8 5.2 - - - +
159A LEU* 1.3 78.1 - - - +
161A GLU* 1.3 62.7 + - + +
163A ARG* 3.0 12.4 + - - +
164A GLY 3.3 0.5 + - - -
165A ALA* 3.0 33.8 + - + +
167A VAL* 6.2 0.7 - - + -
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Residues in contact with GLU 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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157A ARG* 2.8 55.6 + - - +
158A GLU* 4.1 5.1 - - - +
160A ALA* 1.3 72.8 - - + +
162A ALA* 1.3 66.3 + - - +
164A GLY* 3.0 13.9 + - - -
165A ALA 3.5 21.0 + - - +
166A LYS* 5.5 0.2 - - - -
167A VAL* 3.8 25.7 + - + +
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A GLU 3.0 19.3 + - - +
159A LEU* 3.7 10.5 - - + +
160A ALA 3.2 0.2 - - - -
161A GLU* 1.3 77.3 - - - +
163A ARG* 1.3 62.8 + - + +
164A GLY 3.6 0.5 + - - -
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Residues in contact with ARG 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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20A TYR* 5.3 6.1 - - - -
23A ALA* 3.9 21.6 - - + +
24A LYS* 3.7 41.8 - - - +
26A GLY* 5.8 1.6 - - - -
159A LEU* 3.3 24.1 + - - +
160A ALA* 3.0 11.9 + - - +
161A GLU 3.0 0.8 - - - -
162A ALA* 1.3 82.0 - - + +
164A GLY* 1.3 56.3 + - - +
165A ALA 3.6 0.4 - - - -
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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