Contacts of the helix formed by residues 174 - 185 (chain A) in PDB entry 10GS
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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130A GLU* 3.6 8.7 - - - +
171A ASP 4.5 4.5 - - - +
172A ALA 3.4 11.7 - - - +
173A PHE* 1.3 84.7 - - - +
175A LEU* 1.3 66.6 + - + +
177A SER* 3.6 6.2 + - - -
178A ALA* 3.1 28.2 + - - +
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Residues in contact with LEU 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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130A GLU* 3.0 26.6 + - + +
133A LEU* 3.7 13.7 - - + +
134A SER* 3.7 40.4 - - - +
138A GLY 4.1 20.2 - - - +
139A GLY* 4.3 10.3 - - - +
174A PRO* 1.3 85.4 - - + +
176A LEU* 1.3 61.4 + - - +
178A ALA* 3.4 5.4 + - + +
179A TYR* 2.9 29.5 + - - +
182A ARG* 4.8 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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126A LEU* 3.9 31.2 - - + +
129A PHE* 3.9 22.2 - - + -
130A GLU* 3.0 20.2 + - - +
133A LEU* 3.7 19.3 - - + -
155A LEU* 5.0 2.9 - - + -
159A LEU* 4.2 28.5 - - + -
170A LEU* 4.5 13.2 - - + -
173A PHE* 3.2 27.5 + - + +
175A LEU* 1.3 75.0 - - - +
177A SER* 1.3 57.6 + - - +
179A TYR* 3.2 6.5 + - + +
180A VAL* 2.9 36.3 + - - +
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Residues in contact with SER 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* 2.7 43.9 + - - +
171A ASP* 4.6 2.3 + - - -
173A PHE 3.0 9.4 + - - -
174A PRO* 3.8 7.6 - - - +
176A LEU* 1.3 75.9 - - - +
178A ALA* 1.3 61.9 + - - +
180A VAL* 3.4 4.4 + - - +
181A GLY* 3.0 19.6 + - - -
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Residues in contact with ALA 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 3.1 15.5 + - - +
175A LEU* 3.8 6.1 - - + +
177A SER* 1.3 78.8 - - - +
179A TYR* 1.3 53.3 + - - +
181A GLY* 3.3 1.4 + - - -
182A ARG* 2.8 53.4 + - - +
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Residues in contact with TYR 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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133A LEU* 3.8 24.7 - - + -
141A THR 4.1 3.4 - - - -
142A PHE* 4.3 4.5 - - - -
143A ILE* 3.9 13.1 - - + +
152A ASP* 2.5 47.6 + - - +
155A LEU* 3.8 33.6 - - + +
156A LEU* 4.7 5.6 - - + -
159A LEU* 3.9 18.6 - - + -
175A LEU 2.9 19.6 + - - +
176A LEU 3.3 3.4 - - - +
178A ALA* 1.3 76.4 - - - +
180A VAL* 1.3 59.7 + - - +
182A ARG* 3.3 25.1 + - - +
183A LEU* 3.0 54.3 + - + +
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Residues in contact with VAL 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 LEU* 4.1 13.6 - - + +
159A LEU* 3.6 32.5 - - + -
160A LEU* 4.0 20.6 - - + -
163A GLU* 6.0 2.9 - - + -
170A LEU* 3.7 19.7 - - + -
176A LEU 2.9 20.5 + - - +
177A SER 3.7 5.4 - - - +
179A TYR* 1.3 76.3 - - - +
181A GLY* 1.3 55.4 - - - +
183A LEU* 4.0 0.7 - - - +
184A SER* 2.7 45.9 + - - +
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Residues in contact with GLY 181 (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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177A SER 3.0 14.5 + - - -
178A ALA* 3.8 2.9 - - - -
180A VAL* 1.3 78.4 - - - +
182A ARG* 1.3 61.6 + - - +
184A SER* 3.5 6.2 + - - -
185A ALA* 3.2 23.9 + - - +
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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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139A GLY 2.9 23.4 + - - -
140A LYS* 3.4 23.2 + - - +
141A THR* 2.8 33.4 + - - +
142A PHE* 6.2 1.8 - - - -
175A LEU 4.8 0.2 + - - -
178A ALA* 2.8 43.6 + - - +
179A TYR* 3.6 22.1 - - - +
181A GLY* 1.3 77.0 - - - +
183A LEU* 1.3 68.8 + - + +
185A ALA* 3.2 18.6 + - - +
186A ARG* 3.7 7.6 + - - +
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Residues in contact with LEU 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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141A THR 5.4 1.8 - - - +
142A PHE* 3.7 32.3 - - + -
148A ILE* 4.2 5.8 - - + -
152A ASP* 4.3 20.2 - - + +
153A TYR* 5.9 0.7 - - + -
156A LEU* 4.0 21.3 - - + -
179A TYR* 3.0 58.2 + - + +
180A VAL 4.2 1.3 - - - +
182A ARG* 1.3 78.6 - - + +
184A SER* 1.3 61.1 + - - +
185A ALA 3.0 6.4 + - - -
186A ARG* 3.1 34.9 + - - +
189A LEU* 3.5 12.8 - - + +
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Residues in contact with SER 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 LEU* 4.3 8.3 - - - +
160A LEU* 4.6 5.9 - - - +
180A VAL* 2.7 33.4 + - - +
181A GLY* 3.8 6.7 - - - -
182A ARG 3.4 0.2 - - - -
183A LEU* 1.3 75.5 - - - +
185A ALA* 1.3 56.5 + - - +
186A ARG 3.4 0.7 - - - -
189A LEU* 4.9 1.8 - - - -
190A LYS* 3.4 29.0 - - - +
193A LEU* 4.5 21.5 - - - +
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Residues in contact with ALA 185 (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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181A GLY 3.2 15.8 + - - +
182A ARG* 3.5 9.9 - - - +
183A LEU 3.0 1.4 - - - -
184A SER* 1.3 76.1 - - - +
186A ARG* 1.3 64.7 + - - +
187A PRO* 3.2 7.8 - - - +
190A LYS* 4.4 13.1 - - - +
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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