Contacts of the helix formed by residues 152 - 165 (chain A) in PDB entry 1GTA
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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.4 21.6 - - - +
143A LEU* 2.9 32.2 + - - +
144A ASN 4.7 0.2 + - - -
147A HIS 4.1 0.5 - - - +
148A VAL* 3.5 6.9 - - + -
149A THR* 2.9 36.2 + - - +
151A PRO* 1.3 77.7 - - - +
153A PHE* 1.4 52.1 + - + +
155A LEU 3.4 1.0 + - - -
156A TYR* 2.8 30.1 + - - +
179A PHE* 3.1 33.3 - - + -
183A ILE* 4.4 11.4 - - + +
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Residues in contact with PHE 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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16A PRO* 3.8 24.8 - - + +
19A LEU* 3.8 24.2 - - + +
20A LEU* 4.0 23.1 - - + -
23A TYR* 3.8 36.1 - + + -
72A ILE* 5.7 0.2 - - + -
148A VAL* 3.3 32.3 - - + -
149A THR 4.1 8.3 - - - -
150A HIS* 3.1 7.8 + - - +
152A ASP* 1.4 71.4 - - - +
154A MET* 1.4 62.1 + - - +
156A TYR* 3.4 4.0 + - - +
157A ASP* 3.2 23.4 + - - +
183A ILE* 3.8 33.9 - - + -
186A ILE* 4.5 4.9 - - + -
189A ILE* 4.0 14.4 - - + -
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Residues in contact with MET 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 3.8 24.7 - - + +
69A MET* 4.0 14.4 - - + +
72A ILE* 4.3 6.1 - - + -
96A GLU* 3.4 50.7 - - + +
99A VAL* 3.6 20.2 - - + +
100A LEU* 3.7 24.7 - - + -
103A ARG* 5.8 0.7 - - - +
150A HIS* 3.2 26.6 + - - +
151A PRO* 3.5 12.1 - - + +
153A PHE* 1.4 73.2 - - - +
155A LEU* 1.3 65.3 + - - +
157A ASP* 3.5 3.1 + - - +
158A ALA* 3.1 18.5 + - - +
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Residues in contact with LEU 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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99A VAL* 3.9 15.1 - - + +
102A ILE* 4.7 9.6 - - + -
130A LEU* 5.6 0.7 - - + -
133A PHE* 4.2 37.5 - - + -
143A LEU* 4.2 16.4 - - + -
151A PRO 2.9 17.6 + - - +
152A ASP 3.7 6.7 - - - +
154A MET* 1.3 71.9 - - - +
156A TYR* 1.3 64.2 + - - +
158A ALA* 4.5 3.6 - - + -
159A LEU* 3.1 45.3 + - + +
176A LEU* 4.4 15.7 - - + -
179A PHE* 3.6 29.8 - - + -
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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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19A LEU* 3.8 26.2 - - + -
152A ASP 2.8 17.3 + - - +
153A PHE* 3.8 7.9 - - - +
154A MET 3.3 1.0 - - - -
155A LEU* 1.3 76.7 - - - +
157A ASP* 1.3 60.3 + - - +
159A LEU* 3.4 5.2 + - - +
160A ASP* 2.9 36.0 + - + +
179A PHE* 4.2 5.3 - + - -
180A LYS* 3.6 35.1 + - + -
183A ILE* 3.8 32.5 - - + -
184A GLU* 2.6 47.3 + - + +
189A ILE* 5.7 1.3 - - + -
193A LEU* 3.9 17.5 - - + +
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Residues in contact with ASP 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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11A LYS* 4.8 6.1 - - - +
12A GLY 4.3 4.1 - - - +
15A GLN* 3.5 25.0 - - + +
16A PRO* 3.7 29.7 - - + +
19A LEU* 5.1 1.6 - - + -
103A ARG* 3.4 25.5 + - - +
153A PHE 3.2 14.2 + - - +
154A MET 4.0 1.9 - - - +
156A TYR* 1.3 80.3 - - + +
158A ALA* 1.3 65.4 + - - +
160A ASP* 3.4 8.5 + - - +
161A VAL* 3.1 31.0 + - - +
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Residues in contact with ALA 158 (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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99A VAL* 4.6 5.8 - - + -
102A ILE* 4.2 24.0 - - + -
103A ARG* 4.2 24.9 - - + +
154A MET 3.1 17.9 + - - +
155A LEU* 3.9 12.6 - - + +
157A ASP* 1.3 75.2 + - - +
159A LEU* 1.4 61.3 + - - +
161A VAL* 3.0 3.9 + - - +
162A VAL* 3.0 27.4 + - - +
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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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102A ILE* 6.0 0.2 - - + -
130A LEU* 4.4 13.0 - - + -
155A LEU* 3.1 37.3 + - + +
156A TYR* 3.7 4.9 - - - +
158A ALA* 1.4 71.1 - - + +
160A ASP* 1.3 64.1 + - - +
162A VAL* 3.9 7.9 - - + +
163A LEU* 3.3 30.4 + - - +
170A LEU* 3.8 34.8 - - + -
176A LEU* 4.0 33.4 - - + +
179A PHE* 4.1 19.1 - - + -
180A LYS* 4.5 15.7 - - + -
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Residues in contact with ASP 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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11A LYS* 3.0 33.3 + - - +
156A TYR* 2.9 26.7 + - + +
157A ASP* 3.5 11.1 - - - +
159A LEU* 1.3 80.3 - - - +
161A VAL* 1.3 59.0 + - - +
163A LEU* 3.8 9.2 - - - +
164A TYR* 3.2 33.8 + - - -
180A LYS* 3.8 24.8 + - - +
198A TYR* 5.2 2.6 + - - -
203A LEU* 4.6 2.4 - - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.6 2.5 - - + -
103A ARG* 3.7 45.1 - - - +
106A VAL* 4.0 24.2 - - + -
157A ASP* 3.1 23.7 + - - +
158A ALA* 3.0 6.9 + - - +
160A ASP* 1.3 77.6 - - - +
162A VAL* 1.4 56.6 + - + +
163A LEU 3.1 0.9 - - - -
164A TYR* 3.0 30.0 + - - +
165A MET 3.8 1.9 + - - -
203A LEU* 3.9 21.3 - - + -
204A GLN* 4.7 0.7 - - - +
210A PHE* 3.9 10.4 - - + -
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Residues in contact with VAL 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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102A ILE* 3.8 28.0 - - + -
106A VAL* 4.3 17.3 - - + -
122A PHE* 4.4 6.3 - - + -
123A LEU* 5.7 0.8 - - + +
126A LEU* 4.0 24.6 - - + +
130A LEU* 5.1 3.6 - - + -
158A ALA 3.0 19.3 + - - +
159A LEU* 3.9 20.0 - - + +
161A VAL* 1.4 67.2 - - + +
163A LEU* 1.3 57.6 + - - +
164A TYR 3.3 0.2 - - - -
165A MET* 3.5 11.4 + - + +
166A ASP* 2.9 23.0 + - - +
169A CYS* 3.4 23.8 - - - -
170A LEU* 5.2 1.1 - - + -
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Residues in contact with LEU 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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159A LEU 3.3 22.9 + - - +
160A ASP* 3.8 6.7 - - - +
161A VAL 3.1 0.8 + - - -
162A VAL* 1.3 78.8 - - + +
164A TYR* 1.4 59.4 + - + +
166A ASP 3.9 6.3 - - - +
167A PRO* 3.4 42.2 - - + +
169A CYS* 3.6 22.4 - - - -
170A LEU* 3.8 33.9 - - + +
180A LYS* 4.3 20.6 - - + +
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Residues in contact with TYR 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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11A LYS* 5.2 1.8 + - - -
160A ASP* 3.2 41.1 + - - -
161A VAL 3.0 8.3 + - - +
163A LEU* 1.4 73.4 - - + +
165A MET* 1.3 63.4 + - - +
167A PRO* 4.6 4.6 - - - +
200A ALA* 4.6 7.6 + - - +
201A TRP* 3.7 24.4 - + - -
203A LEU* 3.8 27.6 - - + -
210A PHE* 3.7 15.0 - - + -
215A HIS 5.6 1.3 - - - -
217A PRO* 3.1 41.3 - - + +
218A LYS* 3.1 22.0 + - - +
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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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106A VAL* 4.7 8.5 - - - -
109A ILE* 5.0 2.5 - - - -
115A PHE* 4.3 22.0 - - + -
119A LYS* 3.9 23.5 - - + +
122A PHE* 3.4 29.4 - - + -
123A LEU* 3.2 46.0 - - + +
161A VAL 3.8 0.2 + - - -
162A VAL* 3.7 13.0 - - + +
164A TYR* 1.3 80.5 - - - +
166A ASP* 1.3 59.7 + - - +
167A PRO* 4.1 1.8 - - - +
210A PHE* 3.4 30.0 - - + -
218A LYS* 4.6 9.9 - - + +
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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