Contacts of the helix formed by residues 174 - 184 (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 PRO 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLU* 3.5 7.4 - - - +
172A ALA* 3.3 13.7 - - - +
173A PHE* 1.3 88.1 - - - +
175A LYS* 1.3 63.8 + - + +
177A VAL* 3.3 10.8 + - + +
178A CYS* 3.0 33.3 + - - -
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Residues in contact with LYS 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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134A GLU* 2.8 28.5 + - - +
137A LEU* 3.8 33.4 + - + +
138A CYS* 3.2 45.9 + - - -
174A PRO* 1.3 74.3 - - + +
176A LEU* 1.3 54.8 + - - +
178A CYS* 3.3 6.8 + - - +
179A PHE* 2.8 34.8 + - - +
182A ARG* 5.0 1.7 + - - -
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Residues in contact with LEU 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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130A LEU* 3.7 36.1 - - + +
133A PHE* 3.9 18.6 - - + -
134A GLU* 3.0 20.5 + - + +
137A LEU* 3.9 20.9 - - + -
155A LEU* 4.4 13.9 - - + -
159A LEU* 4.0 23.3 - - + +
170A LEU* 4.5 10.5 - - + -
173A PHE* 3.4 26.7 - - + +
174A PRO 3.3 0.2 - - - -
175A LYS* 1.3 77.1 - - - +
177A VAL* 1.3 55.5 + - - +
179A PHE* 3.2 5.2 + - + +
180A LYS* 3.0 26.7 + - - +
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Residues in contact with VAL 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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170A LEU* 3.6 35.4 - - + +
171A ASP* 5.7 0.9 - - - -
173A PHE 3.2 16.3 + - - +
174A PRO* 3.5 11.4 - - + +
176A LEU* 1.3 70.9 - - - +
178A CYS* 1.3 65.6 + - - +
180A LYS* 3.3 6.3 + - - +
181A LYS* 3.1 51.8 + - - +
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Residues in contact with CYS 178 (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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174A PRO* 3.0 20.8 + - - +
175A LYS* 3.8 8.1 - - - +
177A VAL* 1.3 76.0 - - - +
179A PHE* 1.3 64.7 + - - +
181A LYS* 3.0 20.4 + - - +
182A ARG* 2.8 42.5 + - - +
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Residues in contact with PHE 179 (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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137A LEU* 3.8 29.4 - - + -
141A THR 4.2 9.0 - - - -
142A TYR* 4.1 16.2 - + - -
143A LEU* 4.4 2.9 - - + -
152A ASP* 3.1 53.8 - - + -
155A LEU* 3.6 31.0 - - + -
156A TYR* 4.2 7.0 - - - -
159A LEU* 4.1 11.2 - - + -
175A LYS 2.8 22.2 + - - +
176A LEU* 3.2 4.0 + - + +
178A CYS* 1.3 70.9 - - - +
180A LYS* 1.3 65.4 + - - +
182A ARG* 3.1 16.9 + - - +
183A ILE* 3.0 35.4 + - + +
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Residues in contact with LYS 180 (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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156A TYR* 3.6 33.0 + - + -
159A LEU* 4.5 18.8 - - + -
160A ASP* 3.8 27.2 + - - +
163A LEU* 4.3 24.5 - - + +
170A LEU* 5.0 3.8 - - + -
176A LEU 3.0 13.2 + - - +
177A VAL* 3.7 10.3 - - - +
178A CYS 3.2 0.4 - - - -
179A PHE* 1.3 80.3 - - - +
181A LYS* 1.3 63.3 + - + +
183A ILE 3.2 0.5 + - - -
184A GLU* 3.2 44.6 + - - +
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A VAL* 3.1 39.8 + - - +
178A CYS* 3.0 15.8 + - - +
180A LYS* 1.3 75.4 - - + +
182A ARG* 1.4 57.7 + - - +
184A GLU* 3.3 15.6 + - - +
185A ALA* 2.9 29.3 + - - +
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Residues in contact with ARG 182 (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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137A LEU* 5.3 2.2 - - - +
140A LYS 5.0 2.0 + - - -
141A THR* 2.9 54.2 + - - +
142A TYR* 3.7 20.2 - - + +
175A LYS 5.0 1.4 + - - -
178A CYS* 2.8 35.2 + - - +
179A PHE* 3.1 33.0 + - - +
181A LYS* 1.4 73.9 - - - +
183A ILE* 1.4 60.6 + - - +
185A ALA* 3.2 15.4 + - + +
186A ILE* 3.7 11.8 + - - +
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Residues in contact with ILE 183 (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* 5.7 0.2 - - + -
142A TYR* 4.0 22.9 - - + -
148A VAL* 4.9 0.9 - - + -
152A ASP* 4.4 10.3 - - + +
153A PHE* 3.8 30.5 - - + -
156A TYR* 3.8 33.7 - - + -
179A PHE* 3.0 43.6 + - + +
180A LYS 3.8 0.7 - - - +
182A ARG* 1.4 73.0 - - - +
184A GLU* 1.3 65.2 + - - +
186A ILE* 3.1 28.0 + - + +
189A ILE* 3.5 19.9 - - + +
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Residues in contact with GLU 184 (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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156A TYR* 2.6 38.7 + - + +
180A LYS* 3.2 35.6 + - - +
181A LYS* 3.3 15.9 + - - +
183A ILE* 1.3 76.9 - - - +
185A ALA* 1.3 58.5 + - - +
186A ILE 3.2 0.9 + - - -
189A ILE* 4.2 7.0 - - + -
190A ASP* 3.6 24.8 + - - +
193A LEU* 4.0 15.0 - - + -
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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