Contacts of the helix formed by residues 158 - 172 (chain C) in PDB entry 2GTP
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 158 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C PHE* 4.5 10.5 - + + -
105C CYS* 3.6 24.7 - - + -
108C TYR* 3.7 49.7 - + + -
120C ALA* 3.5 26.2 - - - -
123C ILE* 3.6 32.3 - - + -
124C TYR 4.5 3.6 - - - -
128C VAL* 4.5 4.9 - - + -
146C THR* 3.9 18.8 - - + -
150C ILE* 3.8 20.9 - - + -
155C PRO 5.0 0.4 + - - -
156C THR 3.2 0.4 - - - -
157C CYS* 1.3 77.8 - - - +
159C ASP* 1.3 60.5 + - - +
160C GLU 3.2 3.3 + - - -
161C ALA* 3.3 6.6 + - + +
162C GLN* 2.8 31.1 + - - +
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Residues in contact with ASP 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LYS* 3.8 29.7 + - - +
155C PRO 4.3 0.9 - - - +
156C THR* 3.0 44.6 + - - +
157C CYS 3.5 0.2 - - - -
158C PHE* 1.3 77.2 + - - +
160C GLU* 1.3 56.8 + - - +
162C GLN* 3.7 7.1 - - - +
163C LYS* 2.9 32.5 + - - +
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Residues in contact with GLU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ARG 5.4 0.3 - - - +
142C THR* 4.2 23.1 + - + +
145C SER* 2.7 34.3 + - - -
146C THR* 4.8 3.4 + - - +
149C LYS* 3.6 18.5 + - - +
156C THR 4.8 0.4 + - - -
157C CYS 4.9 2.5 + - - +
158C PHE 3.3 0.6 - - - -
159C ASP* 1.3 78.8 - - - +
161C ALA* 1.3 61.8 + - - +
163C LYS* 3.4 6.2 + - - +
164C VAL* 3.3 27.3 + - + +
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Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 3.8 22.0 - - + -
128C VAL* 5.5 1.6 - - + -
136C ILE* 4.3 9.9 - - + -
138C ILE* 4.6 5.1 - - + +
142C THR* 4.0 15.4 - - + +
146C THR* 4.1 21.5 + - + +
158C PHE* 3.3 9.1 + - + +
160C GLU* 1.3 75.5 - - - +
162C GLN* 1.3 65.8 + - - +
164C VAL* 3.3 4.7 + - - +
165C ILE* 3.1 27.0 + - - +
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Residues in contact with GLN 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 3.8 10.6 - - - -
102C TRP* 3.2 50.9 + - + +
105C CYS* 3.6 20.2 - - + +
106C GLU* 3.0 23.0 + - - -
109C LYS* 2.7 30.4 + - - -
158C PHE 2.8 20.1 + - - +
159C ASP* 3.7 9.0 - - - +
161C ALA* 1.3 73.2 - - - +
163C LYS* 1.3 56.8 + - - +
165C ILE* 3.3 2.1 + - - +
166C TYR* 2.8 28.9 + - + +
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Residues in contact with LYS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ASP 2.9 17.7 + - - +
160C GLU* 3.6 7.0 - - - +
162C GLN* 1.3 75.9 - - - +
164C VAL* 1.3 57.4 + - + +
166C TYR* 3.2 8.6 + - + +
167C THR* 2.9 37.1 + - - +
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ASN 4.5 8.1 - - - +
138C ILE* 3.9 25.4 - - + -
139C ASP* 5.6 1.1 - - - +
142C THR* 4.4 18.6 - - + +
160C GLU* 3.3 16.9 + - + +
161C ALA 3.3 7.4 + - - +
163C LYS* 1.3 77.4 - - + +
165C ILE* 1.3 58.7 + - - +
167C THR* 3.7 6.8 + - - -
168C LEU* 3.1 25.6 + - + +
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Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ASN* 3.4 57.4 - - + +
101C PHE* 3.8 12.1 - - + -
102C TRP* 5.2 1.8 - - + +
136C ILE* 3.8 31.6 - - + -
137C ASN 4.0 11.2 - - - +
138C ILE* 4.0 13.2 - - + -
161C ALA 3.1 16.6 + - - +
162C GLN* 3.9 3.6 - - + +
164C VAL* 1.3 75.5 - - - +
166C TYR* 1.3 67.1 + - - +
168C LEU* 3.7 9.3 - - + +
169C MET* 3.0 26.1 + - + +
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Residues in contact with TYR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C SER* 5.5 0.3 - - - -
73C LEU* 3.6 25.6 + - + +
74C GLU* 2.9 39.1 + - + +
77C LEU* 4.2 10.5 - - + -
102C TRP* 3.7 29.4 - + + +
162C GLN* 2.8 16.9 + - + +
163C LYS* 3.2 10.1 + - + +
165C ILE* 1.3 76.6 - - - +
167C THR* 1.3 56.2 + - - +
169C MET* 3.0 12.0 + - + +
170C GLU* 2.7 64.6 + - - +
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Residues in contact with THR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LYS* 2.9 22.9 + - - +
164C VAL* 3.8 8.6 - - - -
166C TYR* 1.3 77.9 - - - +
168C LEU* 1.3 57.1 + - - +
170C GLU* 3.7 14.4 + - - +
171C LYS* 2.8 44.3 + - + +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LYS* 3.5 48.9 - - + +
182B THR* 4.0 22.7 - - + -
98C ASN* 3.5 30.5 - - - +
137C ASN* 4.1 24.2 - - + +
164C VAL* 3.1 19.2 + - + +
165C ILE* 3.7 11.7 - - + +
166C TYR 3.2 0.2 - - - -
167C THR* 1.3 72.7 - - - +
169C MET* 1.3 66.9 + - - +
171C LYS* 5.0 1.8 - - - -
172C ASP* 3.0 30.5 + - - +
173C SER* 4.4 0.6 + - - -
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Residues in contact with MET 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 3.9 9.0 - - + -
77C LEU* 4.4 13.0 - - + -
86C PHE* 3.8 28.5 - - + -
90C LEU* 4.2 4.0 - - + -
98C ASN* 3.8 17.9 - - + +
99C ILE* 3.9 26.5 - - + -
102C TRP* 4.2 29.8 - - + -
165C ILE* 3.0 24.3 + - + +
166C TYR* 3.0 16.0 + - + +
168C LEU* 1.3 76.5 - - - +
170C GLU* 1.3 61.1 + - - +
173C SER* 3.2 15.5 + - - +
174C TYR* 2.9 29.5 + - - +
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Residues in contact with GLU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C SER* 5.7 2.6 - - - -
73C LEU* 3.6 26.8 + - + +
166C TYR* 2.7 49.0 + - + +
167C THR* 3.7 12.4 + - - +
169C MET* 1.3 73.3 - - - +
171C LYS* 1.3 62.0 + - + +
174C TYR* 3.6 12.6 - - + +
175C PRO* 3.1 23.9 - - - +
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Residues in contact with LYS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B VAL* 6.1 5.7 - - + +
75B SER* 5.6 6.1 - - - +
179B VAL* 3.7 25.8 - - + +
180B LYS 6.1 0.2 - - - +
167C THR* 2.8 35.7 + - + +
168C LEU* 4.4 2.2 - - - +
170C GLU* 1.3 80.7 - - + +
172C ASP* 1.3 58.3 + - + +
175C PRO* 3.4 16.1 - - - +
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Residues in contact with ASP 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.8 13.4 - - + +
180B LYS 3.2 22.9 - - - +
181B THR* 3.2 9.1 + - - +
182B THR* 3.0 29.9 + - + +
168C LEU* 3.0 15.5 + - + +
171C LYS* 1.3 78.2 - - - +
173C SER* 1.3 66.0 + - - +
174C TYR 3.5 0.7 - - - -
175C PRO* 3.6 8.0 - - - +
176C ARG* 2.8 53.7 + - - +
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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