Contacts of the helix formed by residues 157 - 177 (chain A) in PDB entry 2GFP
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 THR 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.4 2.1 - - - +
150A LEU* 3.1 46.2 - - + +
151A ILE* 3.0 24.3 - - - +
154A LEU 4.7 2.7 - - - +
155A LEU 2.7 14.3 + - - +
156A ASP* 1.3 66.9 - - - +
158A MET* 1.3 69.5 + - - +
160A ASN* 3.3 35.9 - - - +
161A TRP* 3.0 24.3 + - - +
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Residues in contact with MET 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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34A MET* 5.2 15.9 - - + -
88A LEU* 3.5 44.0 - - + -
156A ASP* 2.8 51.0 + - + +
157A THR* 1.3 74.5 - - - +
159A TRP* 1.3 62.6 + - + +
160A ASN* 3.0 7.4 + - - -
161A TRP* 3.1 36.7 + - + -
162A ARG* 3.1 15.3 + - - +
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Residues in contact with TRP 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 5.3 0.4 - - - +
158A MET* 1.3 78.8 - - + +
160A ASN* 1.3 81.6 + - - +
161A TRP 3.4 0.2 - - - -
162A ARG* 3.2 18.7 - - + +
163A ALA* 2.8 27.6 + - + +
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Residues in contact with ASN 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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150A LEU* 4.2 8.1 + - + +
154A LEU* 4.8 13.7 + - - +
156A ASP 4.6 1.2 - - - +
157A THR* 3.3 43.7 - - + +
158A MET 3.0 1.1 + - - -
159A TRP* 1.3 95.7 + - - +
161A TRP* 1.3 60.7 + - - +
163A ALA* 3.1 6.8 + - - +
164A CYS* 2.8 31.8 + - - +
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Residues in contact with TRP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 6.2 1.6 - - + -
26A ILE* 4.7 19.7 - - + -
30A ALA* 5.9 9.2 - - + -
84A MET* 3.4 14.5 - - + +
87A THR* 3.0 38.2 - - + +
88A LEU* 3.5 37.2 - - + -
91A VAL* 4.2 9.2 - - + -
103A SER* 5.8 1.6 - - - -
150A LEU* 4.8 4.3 - - + -
157A THR* 3.0 34.4 + - - +
158A MET* 3.3 34.3 - - + -
160A ASN* 1.3 73.6 - - - +
162A ARG* 1.3 74.1 + - - +
164A CYS* 4.4 6.5 - - - -
165A TYR* 3.0 26.1 + - + +
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Residues in contact with ARG 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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84A MET* 2.7 55.7 + - - +
85A LEU* 3.1 43.9 + - - +
87A THR* 3.6 4.9 - - - +
88A LEU* 4.4 13.8 - - + +
158A MET 3.1 15.7 - - - +
159A TRP* 3.2 21.5 - - + +
161A TRP* 1.3 92.8 - - - +
163A ALA* 1.3 61.5 + - - +
166A LEU* 3.0 35.5 + - - +
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Residues in contact with ALA 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 TRP* 2.8 15.4 + - + +
160A ASN* 3.1 11.0 + - - +
162A ARG* 1.3 73.9 - - - +
164A CYS* 1.3 62.7 + - - +
166A LEU* 4.9 0.7 - - - -
167A PHE* 2.6 47.4 + - + +
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Residues in contact with CYS 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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19A VAL* 3.8 3.5 - - - +
22A MET* 3.2 40.6 - - + -
146A LEU* 5.5 7.6 - - - -
150A LEU* 4.0 18.4 - - + -
160A ASN 2.8 17.9 + - - +
161A TRP* 4.0 6.7 - - - +
163A ALA* 1.3 71.5 - - - +
165A TYR* 1.3 63.5 + - - +
167A PHE* 4.1 9.6 - - - -
168A LEU* 3.0 33.7 + - - +
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Residues in contact with TYR 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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19A VAL* 3.2 15.3 - - + +
22A MET* 5.2 0.4 - - - +
23A ALA* 3.4 28.7 - - + -
80A MET* 3.1 35.5 + - - +
81A SER* 3.6 18.6 + - - -
84A MET* 3.0 40.2 - - + -
106A GLN* 4.0 16.7 + - + +
107A GLY* 4.7 0.2 - - - -
110A THR* 2.9 27.3 + - - +
161A TRP* 3.0 8.8 + - + +
164A CYS* 1.3 77.0 - - - +
166A LEU* 1.3 66.9 + - - +
169A LEU* 2.9 52.3 + - + +
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Residues in contact with LEU 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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81A SER* 3.7 27.1 - - - -
84A MET* 3.7 14.4 - - - -
85A LEU* 3.7 24.5 - - + -
162A ARG* 3.0 22.3 + - - +
163A ALA* 4.9 0.4 - - - -
165A TYR* 1.3 79.7 - - - +
167A PHE* 1.3 56.8 + - - +
169A LEU* 4.7 0.9 - - - -
170A VAL* 2.7 64.3 + - + +
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Residues in contact with PHE 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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163A ALA* 2.6 36.1 + - + +
164A CYS* 4.0 9.0 - - - -
166A LEU* 1.3 73.5 - - - +
168A LEU* 1.3 88.6 + - + -
170A VAL* 3.3 10.7 - - - +
171A LEU* 2.9 60.4 + - + +
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Residues in contact with LEU 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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15A LEU* 3.6 27.4 - - + +
18A ALA* 3.5 31.0 - - + -
19A VAL* 3.7 10.5 - - + -
22A MET* 3.6 21.1 - - - -
142A LEU* 6.4 0.2 - - + -
146A LEU* 5.9 3.6 - - + -
164A CYS* 3.0 23.5 + - - +
167A PHE* 1.3 95.9 - - + +
169A LEU* 1.3 56.2 + - - +
171A LEU* 3.2 25.7 - - + +
172A CYS* 3.0 22.2 + - - +
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Residues in contact with LEU 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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16A LEU* 4.8 4.0 - - + -
19A VAL* 3.4 13.2 - - + +
76A ILE 5.0 0.4 - - - +
77A LEU* 3.3 55.4 - - + +
78A VAL* 5.1 0.4 - - - -
80A MET* 5.6 0.2 - - + -
81A SER* 3.6 15.0 - - - +
110A THR* 3.7 22.0 - - + -
165A TYR* 2.9 45.9 + - + +
166A LEU 4.5 0.2 - - - +
168A LEU* 1.3 72.9 - - - +
170A VAL* 1.3 70.3 + - + +
171A LEU 3.1 1.8 - - - -
172A CYS* 3.0 10.2 + - - +
173A ALA* 2.9 23.8 + - + +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 5.1 3.1 - - - +
166A LEU* 2.7 54.8 + - + +
167A PHE* 3.3 17.3 - - - +
169A LEU* 1.3 80.3 - - + +
171A LEU* 1.3 60.3 + - + +
173A ALA* 3.5 10.6 - - + +
174A GLY* 2.8 26.7 + - - -
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Residues in contact with LEU 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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15A LEU* 3.7 18.8 - - + -
167A PHE* 2.9 48.4 + - + +
168A LEU* 3.2 24.2 - - + +
170A VAL* 1.3 76.9 - - + +
172A CYS* 1.3 68.0 - - - +
174A GLY* 3.3 2.7 + - - -
175A VAL* 3.1 34.0 + - + +
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Residues in contact with CYS 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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12A MET* 3.0 22.2 - - - +
15A LEU* 3.5 13.2 - - + +
16A LEU* 3.1 47.8 - - + +
77A LEU* 5.3 1.3 - - - -
168A LEU 3.0 6.5 + - - +
169A LEU 3.0 10.3 - - - +
171A LEU* 1.3 75.9 - - - +
173A ALA* 1.3 53.6 + - - +
175A VAL 2.8 4.2 + - - -
176A THR* 2.5 65.4 + - - +
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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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73A ARG* 5.6 3.1 - - + +
77A LEU* 3.6 29.8 - - + +
78A VAL* 5.6 2.9 - - + -
169A LEU 2.9 10.3 + - - +
170A VAL* 3.5 14.1 - - + +
172A CYS* 1.3 74.9 - - - +
174A GLY* 1.3 64.4 + - - +
176A THR* 2.7 26.0 + - - -
177A PHE* 3.3 8.0 + - - -
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Residues in contact with GLY 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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170A VAL 2.8 20.6 + - - -
171A LEU* 3.3 2.6 + - - -
173A ALA* 1.3 73.0 - - - +
175A VAL* 1.3 62.0 + - - +
177A PHE* 4.1 9.9 - - - +
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Residues in contact with VAL 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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11A LEU* 6.0 6.3 - - + -
12A MET* 3.2 18.9 - - + +
15A LEU* 4.4 13.7 - - + -
171A LEU* 3.1 26.0 - - + +
172A CYS 2.8 4.0 + - - +
174A GLY* 1.3 79.8 - - - +
176A THR* 1.3 61.0 + - - +
177A PHE* 3.1 24.7 - - + -
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Residues in contact with THR 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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12A MET* 3.4 33.5 - - + +
16A LEU* 5.2 0.2 - - + -
72A ARG* 5.1 13.5 - - - -
73A ARG* 4.9 7.8 - - - +
77A LEU* 5.3 1.5 - - + +
172A CYS* 2.5 49.7 + - - +
173A ALA* 2.7 29.1 + - - -
175A VAL* 1.3 74.7 - - - +
177A PHE* 1.3 78.9 + - - +
178A SER* 2.8 20.3 + - - -
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Residues in contact with PHE 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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12A MET* 3.9 12.8 - - + -
73A ARG* 6.0 4.0 - - - +
173A ALA 3.3 7.3 + - - +
174A GLY 4.1 6.7 - - - +
175A VAL* 3.1 42.0 - - + -
176A THR* 1.3 91.5 + - - +
178A SER* 1.3 58.1 + - - +
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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