Contacts of the helix formed by residues 158 - 172 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D PHE* 4.3 13.9 - + + -
105D CYS* 3.6 24.0 - - + -
108D TYR* 4.2 16.1 - + + -
109D LYS* 6.1 0.2 - - - -
120D ALA* 3.4 29.8 - - + -
123D ILE* 3.9 28.9 - - + -
124D TYR 4.1 1.6 - - - -
128D VAL* 4.1 14.1 - - + -
146D THR* 3.6 32.3 - - + -
150D ILE* 3.4 22.9 - - + -
155D PRO 5.0 0.8 + - - -
156D THR 3.2 0.4 - - - -
157D CYS* 1.3 86.4 - - + +
159D ASP* 1.3 65.6 + - - +
160D GLU 3.2 3.7 + - - -
161D ALA* 3.2 7.0 + - + +
162D GLN* 2.8 24.9 + - - +
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Residues in contact with ASP 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LYS* 3.4 30.5 + - - +
156D THR* 3.0 43.5 + - - +
157D CYS 3.4 0.2 - - - -
158D PHE* 1.3 76.7 - - - +
160D GLU* 1.3 58.4 + - - +
162D GLN* 3.5 5.9 - - - +
163D LYS* 2.9 32.8 + - - +
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Residues in contact with GLU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ARG 5.5 0.2 - - - +
142D THR* 4.4 17.0 + - + -
145D SER* 2.6 30.3 + - - -
146D THR* 5.1 4.6 + - - +
149D LYS* 3.7 20.6 + - - +
156D THR 4.8 0.2 + - - -
157D CYS 4.8 4.4 + - - +
158D PHE 3.2 0.6 - - - -
159D ASP* 1.3 81.1 - - - +
161D ALA* 1.3 63.5 + - - +
163D LYS* 3.4 5.7 + - - +
164D VAL* 3.3 23.4 + - - +
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PHE* 3.9 23.3 - - + -
128D VAL* 5.4 1.1 - - + -
136D ILE* 4.3 0.9 - - + -
138D ILE* 4.3 14.1 - - + -
142D THR* 4.0 16.1 - - + +
146D THR* 4.1 18.6 + - + +
158D PHE* 3.2 10.0 + - + +
160D GLU* 1.3 76.5 - - - +
162D GLN* 1.3 66.9 + - - +
164D VAL* 3.3 4.1 + - - +
165D ILE* 3.0 27.0 + - - +
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Residues in contact with GLN 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PHE* 3.9 10.6 - - - -
102D TRP* 3.2 54.5 + - + +
105D CYS* 3.5 19.3 - - + +
106D GLU* 3.3 17.0 + - - -
109D LYS* 2.6 33.0 + - - -
158D PHE 2.8 20.9 + - - +
159D ASP* 3.5 9.0 + - - +
161D ALA* 1.3 73.4 - - - +
163D LYS* 1.3 57.6 + - - +
165D ILE* 3.2 2.1 + - - +
166D TYR* 2.8 28.9 + - + +
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ASP 2.9 16.6 + - - +
160D GLU* 3.7 6.5 - - - +
161D ALA 3.3 0.2 - - - -
162D GLN* 1.3 75.5 - - - +
164D VAL* 1.3 61.0 + - + +
166D TYR* 3.3 8.2 + - + +
167D THR* 2.9 41.9 + - - +
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Residues in contact with VAL 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASN 4.3 8.1 - - - +
138D ILE* 3.8 28.7 - - + -
139D ASP 5.6 0.9 - - - +
142D THR* 4.6 15.3 - - + +
160D GLU 3.3 11.6 + - - +
161D ALA* 3.3 8.2 + - - +
162D GLN 3.3 0.8 - - - -
163D LYS* 1.3 81.3 - - + +
165D ILE* 1.3 58.4 + - - +
167D THR* 3.6 6.6 + - - -
168D LEU* 3.0 27.3 + - + +
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASN* 3.4 51.4 - - + +
101D PHE* 3.9 10.8 - - + -
102D TRP* 5.2 2.5 - - + +
136D ILE* 3.8 37.5 - - + -
137D ASN 3.8 12.1 - - - +
138D ILE* 3.8 15.9 - - + -
161D ALA 3.0 16.9 + - - +
162D GLN* 4.0 2.7 - - - +
164D VAL* 1.3 73.7 - - - +
166D TYR* 1.3 66.7 + - - +
168D LEU* 3.8 9.7 - - + +
169D MET* 3.0 25.8 + - + +
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Residues in contact with TYR 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D SER* 5.6 0.2 - - - -
73D LEU* 3.4 30.0 + - + +
74D GLU* 2.9 42.2 + - + +
77D LEU* 4.2 12.6 - - + -
102D TRP* 4.0 27.7 - + + +
162D GLN* 2.8 18.0 + - + +
163D LYS* 3.3 8.9 + - + +
165D ILE* 1.3 77.5 - - - +
167D THR* 1.3 56.2 + - - +
169D MET* 3.2 9.5 + - + +
170D GLU* 2.6 62.2 + - - +
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Residues in contact with THR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LYS* 2.9 28.0 + - - +
164D VAL* 3.9 7.9 - - - +
166D TYR* 1.3 78.3 - - - +
168D LEU* 1.3 57.6 + - - +
170D GLU* 3.8 13.8 + - - +
171D LYS* 2.8 36.9 + - + +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LYS* 3.6 40.4 - - + +
182A THR* 3.8 24.0 - - + -
98D ASN* 3.8 20.0 - - - +
137D ASN* 4.0 27.4 - - + +
164D VAL* 3.0 19.3 + - + +
165D ILE* 3.8 22.9 - - + +
166D TYR 3.2 0.2 - - - -
167D THR* 1.3 74.5 - - - +
169D MET* 1.3 63.2 + - - +
171D LYS* 5.1 1.3 - - - -
172D ASP* 3.2 22.2 + - + +
173D SER* 3.9 0.7 + - - -
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Residues in contact with MET 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D LEU* 4.0 8.1 - - + -
77D LEU* 4.1 20.2 - - + -
86D PHE* 3.9 25.1 - - + -
90D LEU* 4.1 5.6 - - + -
98D ASN* 3.7 20.4 - - + +
99D ILE* 3.6 29.2 - - - -
102D TRP* 4.1 25.8 - - + -
165D ILE 3.0 22.5 + - - +
166D TYR* 3.6 15.3 - - + +
168D LEU* 1.3 77.4 - - - +
170D GLU* 1.3 61.1 + - - +
173D SER* 3.2 12.6 + - - +
174D TYR* 2.9 29.9 + - - +
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D SER* 6.0 1.4 - - - -
73D LEU* 3.4 28.3 + - + +
166D TYR* 2.6 46.3 + - - +
167D THR* 3.8 11.6 + - - +
169D MET* 1.3 74.5 - - - +
171D LYS* 1.3 57.1 + - + +
174D TYR* 3.6 13.5 - - + +
175D PRO* 3.3 21.3 - - - +
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Residues in contact with LYS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.6 24.2 - - + +
167D THR* 2.8 27.3 + - + +
168D LEU* 4.7 2.0 - - - +
170D GLU* 1.3 75.5 - - + +
172D ASP* 1.3 56.9 + - + +
175D PRO* 3.4 15.4 - - - +
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Residues in contact with ASP 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.5 13.0 - - + +
180A LYS 3.1 25.5 - - - +
181A THR* 3.3 10.8 + - - +
182A THR* 3.1 27.4 + - - +
168D LEU* 3.2 16.4 + - + +
171D LYS* 1.3 78.4 - - + +
173D SER* 1.3 67.4 + - - +
174D TYR 3.5 0.9 - - - -
175D PRO* 3.3 9.5 - - - +
176D ARG* 3.0 52.8 + - - +
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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