Contacts of the helix formed by residues 148 - 163 (chain B) 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 PHE 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ASP* 3.1 24.7 - - - +
48B THR* 3.5 27.4 - - + -
82B LYS* 3.6 37.2 - - + +
83B ILE 3.0 18.4 + - - -
85B THR* 3.3 33.7 - - - -
146B VAL* 4.3 4.9 - - + -
147B LEU* 1.3 69.5 - - - +
149B SER* 1.3 60.6 + - - +
150B GLU 3.5 1.1 - - - -
151B ASN* 3.0 18.5 + - + +
152B CYS* 2.9 28.0 + - - -
259B PHE* 4.4 30.7 - + + -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS 2.9 24.6 + - - -
47B ASP 3.1 15.4 + - - -
49B ARG* 3.6 25.0 + - - +
147B LEU 3.3 3.4 + - - -
148B PHE* 1.3 70.7 - - - +
150B GLU* 1.3 64.9 + - - +
152B CYS* 3.2 3.6 + - - +
153B ILE* 3.1 27.6 + - - +
347B PHE* 3.4 35.8 - - - -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PRO* 3.5 28.0 - - + +
39B HIS 5.3 1.5 - - - +
40B THR* 5.4 4.0 - - - +
44B HIS* 3.5 17.0 - - + +
45B HIS* 3.6 14.2 - - + +
46B GLY 3.0 9.4 + - - -
47B ASP* 2.7 41.9 + - - +
148B PHE 3.5 0.6 - - - -
149B SER* 1.3 75.5 + - - +
151B ASN* 1.3 58.3 + - - +
153B ILE* 3.4 0.7 + - - -
154B ARG* 2.9 48.7 + - - +
311B ARG* 4.6 4.3 + - - -
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Residues in contact with ASN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 6.1 0.9 - - - -
81B HIS* 4.2 9.3 + - + +
82B LYS* 3.0 42.2 + - - +
83B ILE* 4.2 2.2 - - - +
148B PHE* 3.0 21.8 + - - +
150B GLU* 1.3 77.2 - - - +
152B CYS* 1.3 56.0 + - - +
154B ARG* 3.1 15.7 + - - +
155B ALA* 2.8 36.4 + - - +
804B PO4 2.8 33.7 + - - -
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Residues in contact with CYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TRP* 3.4 37.7 - - + -
75B LEU* 4.1 1.7 - - - +
83B ILE* 3.9 28.9 - - - -
147B LEU* 4.5 4.3 - - - -
148B PHE 2.9 20.8 + - - -
149B SER 3.2 7.8 + - - +
151B ASN* 1.3 76.3 - - - +
153B ILE* 1.3 59.3 + - + +
155B ALA* 3.3 1.7 + - - +
156B TYR* 2.9 36.3 + - + +
347B PHE* 3.7 21.1 - - + -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 4.4 1.1 - - - +
12B GLY 3.8 2.0 - - - +
13B SER* 3.5 29.6 - - - +
16B MET* 3.6 20.4 - - + +
37B PRO* 4.1 25.1 - - + -
38B PRO* 4.1 10.5 - - + -
44B HIS* 3.2 49.8 - - + +
149B SER 3.1 13.4 + - - +
150B GLU 3.9 2.5 - - - +
152B CYS* 1.3 76.7 - - + +
154B ARG* 1.3 58.8 + - - +
156B TYR* 3.4 6.5 + - + -
157B ARG* 2.9 28.8 + - - +
347B PHE* 4.3 5.8 - - + -
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PRO* 3.5 35.2 + - + +
81B HIS* 3.5 26.0 - - - +
150B GLU* 2.9 40.5 + - - +
151B ASN* 3.1 29.5 + - - +
153B ILE* 1.3 78.6 - - - +
155B ALA* 1.3 56.7 + - - +
157B ARG* 3.3 4.8 + - - +
158B GLU* 2.9 51.2 + - + +
804B PO4 3.5 13.5 + - - -
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 4.1 9.6 - - + -
79B THR* 3.7 36.8 - - + +
81B HIS* 4.0 11.2 - - + -
83B ILE* 4.3 4.0 - - + -
151B ASN 2.8 20.7 + - - +
152B CYS 3.7 3.8 - - - +
154B ARG* 1.3 70.8 - - - +
156B TYR* 1.3 66.7 + - - +
158B GLU* 3.3 4.2 + - - +
159B LEU* 2.9 30.3 + - - +
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER 5.3 1.6 - - - -
16B MET* 3.9 19.1 - - + +
17B ALA* 3.7 29.8 - - + -
20B TYR* 3.3 47.3 - + + +
21B GLN* 5.2 3.4 + - + -
71B LEU* 4.5 8.3 + - - +
72B TRP* 3.8 24.4 - + - -
75B LEU* 3.8 27.1 - - + +
152B CYS 2.9 23.2 + - - +
153B ILE* 3.9 6.3 - - + +
155B ALA* 1.3 75.3 - - - +
157B ARG* 1.3 58.0 + - - +
159B LEU* 3.8 2.0 - - - +
160B ALA* 2.9 32.1 + - - +
350B SER* 5.5 0.2 - - - -
351B SER* 3.2 27.8 + - - -
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B MET* 3.5 33.8 - - + +
36B ASP* 2.6 26.7 + - - -
37B PRO* 2.9 28.1 + - - +
38B PRO* 5.6 0.4 - - - -
153B ILE 2.9 19.3 + - - +
154B ARG* 3.6 5.6 - - - +
156B TYR* 1.3 77.8 - - - +
158B GLU* 1.3 60.9 + - + +
160B ALA* 3.2 2.0 + - - +
161B GLU* 2.8 64.6 + - + +
167B VAL* 3.9 18.6 + - + +
169B THR* 3.6 18.8 - - - +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 4.6 1.6 + - - -
80B HIS* 3.8 11.2 - - - -
81B HIS* 2.8 37.4 + - - -
154B ARG* 2.9 29.6 + - + +
155B ALA* 3.8 4.1 - - - +
157B ARG* 1.3 79.4 - - + +
159B LEU* 1.3 60.0 + - + +
161B GLU* 3.9 6.1 - - - +
162B ALA* 3.0 30.2 + - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B TYR* 3.8 28.5 - - + -
75B LEU* 3.7 28.5 - - + -
78B GLU* 4.0 30.5 - - + +
79B THR* 4.6 8.5 - - - +
155B ALA* 2.9 21.3 + - - +
156B TYR 3.9 0.2 - - - +
158B GLU* 1.3 74.5 - - + +
160B ALA* 1.3 67.1 + - - +
162B ALA* 3.5 8.0 + - + +
163B ARG* 3.3 39.2 + - - +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 5.2 2.2 - - - +
19B GLY* 4.0 4.3 - - - +
20B TYR* 3.8 26.9 - - - +
23B ALA* 3.7 9.2 - - - +
31B LEU* 5.0 4.3 - - + -
156B TYR 2.9 19.1 + - - +
157B ARG* 3.8 4.9 - - - +
159B LEU* 1.3 74.2 - - - +
161B GLU* 1.3 67.4 + - + +
163B ARG* 3.0 12.0 + - - +
164B GLY 3.3 0.3 + - - -
165B ALA* 3.0 34.8 + - + +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ARG* 2.8 52.8 + - - +
158B GLU* 4.0 4.9 - - - +
160B ALA* 1.3 74.8 - - + +
162B ALA* 1.3 65.1 + - - +
164B GLY* 2.9 14.6 + - - -
165B ALA* 3.5 21.9 - - + +
167B VAL* 3.8 27.5 + - + +
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU 3.0 19.4 + - - +
159B LEU* 3.7 10.8 - - + +
160B ALA 3.3 0.2 - - - -
161B GLU* 1.3 78.1 - - - +
163B ARG* 1.3 63.3 + - + +
164B GLY 3.3 0.6 + - - -
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 5.5 5.3 - - - -
23B ALA* 4.0 20.5 - - + +
24B LYS* 3.8 38.9 - - - +
26B GLY* 5.9 1.4 - - - -
159B LEU* 3.3 24.3 + - - +
160B ALA* 3.0 10.3 + - - +
161B GLU 3.0 0.8 - - - -
162B ALA* 1.3 82.5 - - + +
164B GLY* 1.3 56.8 + - - +
165B ALA 3.6 0.6 + - - -
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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
------------------------------------------------------------
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