Contacts of the helix formed by residues 174 - 185 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 3.6 9.0 - - - +
171B ASP 4.5 4.9 - - - +
172B ALA 3.4 12.6 - - - +
173B PHE* 1.3 83.3 - - - +
175B LEU* 1.3 67.3 + - + +
177B SER* 3.6 6.4 + - - -
178B ALA* 3.1 27.7 + - - +
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 3.0 26.4 + - + +
133B LEU* 3.7 13.7 - - + +
134B SER* 3.7 41.3 - - - +
138B GLY 4.1 20.2 - - - +
139B GLY* 4.3 10.6 - - - +
174B PRO* 1.3 84.1 - - + +
176B LEU* 1.3 61.1 + - - +
178B ALA* 3.4 5.3 + - + +
179B TYR* 2.9 30.0 + - - +
182B ARG* 4.8 1.9 + - - -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 3.9 30.7 - - + +
129B PHE* 3.9 22.0 - - + -
130B GLU* 3.0 21.2 + - - +
133B LEU* 3.7 19.5 - - + -
155B LEU* 4.9 2.7 - - + -
159B LEU* 4.1 28.7 - - + -
170B LEU* 4.5 12.8 - - + -
173B PHE* 3.2 26.4 + - + +
175B LEU* 1.3 74.8 - - - +
177B SER* 1.3 58.4 + - - +
179B TYR* 3.2 6.5 + - + +
180B VAL* 2.8 36.4 + - - +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 2.6 44.1 + - - +
171B ASP* 4.6 2.4 + - - -
173B PHE 3.0 9.8 + - - -
174B PRO* 3.8 7.2 - - - -
176B LEU* 1.3 77.1 - - - +
178B ALA* 1.3 62.6 + - - +
180B VAL* 3.4 3.8 + - - +
181B GLY* 3.0 19.2 + - - -
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B PRO 3.1 16.2 + - - +
175B LEU* 3.8 6.1 - - + +
177B SER* 1.3 78.0 - - - +
179B TYR* 1.3 53.2 + - - +
181B GLY* 3.3 1.7 + - - -
182B ARG* 2.8 54.2 + - - +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 3.8 24.2 - - + -
141B THR 4.1 2.7 - - - -
142B PHE* 4.3 4.7 - - - -
143B ILE* 3.9 14.1 - - + +
152B ASP* 2.5 47.4 + - - +
155B LEU* 3.8 32.8 - - + +
156B LEU* 4.7 5.4 - - + -
159B LEU* 3.9 19.3 - - + -
175B LEU 2.9 19.2 + - - +
176B LEU* 3.3 3.4 - - + +
178B ALA* 1.3 77.1 - - - +
180B VAL* 1.3 60.1 + - - +
182B ARG* 3.3 25.5 + - - +
183B LEU* 3.0 53.7 + - + +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.1 11.4 - - + +
159B LEU* 3.6 33.0 - - + -
160B LEU* 4.0 20.9 - - + -
163B GLU* 6.0 2.9 - - + -
170B LEU* 3.7 20.0 - - + -
176B LEU 2.8 20.3 + - - +
177B SER 3.7 5.6 - - - +
179B TYR* 1.3 75.9 - - + +
181B GLY* 1.3 55.8 + - - +
183B LEU* 3.5 0.9 + - - +
184B SER* 2.7 46.2 + - - +
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B SER 3.0 14.2 + - - -
178B ALA* 3.8 2.2 - - - -
180B VAL* 1.3 78.8 - - - +
182B ARG* 1.3 62.7 + - - +
184B SER* 3.6 5.9 + - - -
185B ALA* 3.2 23.7 + - - +
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Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLY 2.9 24.4 + - - -
140B LYS* 3.4 22.9 + - - +
141B THR* 2.8 33.4 + - - +
142B PHE* 6.2 1.6 - - - -
178B ALA* 2.8 42.7 + - - +
179B TYR* 3.6 22.0 + - - +
181B GLY* 1.3 77.0 - - - +
183B LEU* 1.3 68.4 + - + +
185B ALA* 3.2 18.6 + - - +
186B ARG* 3.7 7.6 + - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B THR 5.4 1.8 - - - +
142B PHE* 3.7 32.3 - - + -
148B ILE* 4.2 4.7 - - + -
152B ASP* 4.3 19.5 - - + +
153B TYR* 5.9 1.1 - - + -
156B LEU* 4.0 22.0 - - + -
179B TYR* 3.0 58.0 + - + +
180B VAL 4.2 1.3 - - - +
182B ARG* 1.3 79.0 - - + +
184B SER* 1.3 61.6 + - - +
185B ALA 3.0 6.4 + - - -
186B ARG* 3.1 36.4 + - + +
189B LEU* 3.5 12.2 - - + +
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Residues in contact with SER 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.3 7.4 - - - +
160B LEU* 4.6 5.7 - - - +
180B VAL* 2.7 32.2 + - - +
181B GLY* 3.8 7.4 - - - -
183B LEU* 1.3 75.5 - - - +
185B ALA* 1.3 57.3 + - - +
186B ARG 3.4 0.9 - - - -
189B LEU* 4.9 1.3 - - - -
190B LYS* 3.4 29.0 - - - +
193B LEU* 4.5 23.0 - - - +
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLY 3.2 16.7 + - - +
182B ARG* 3.5 9.4 - - - +
183B LEU 3.0 0.8 - - - -
184B SER* 1.3 76.0 - - - +
186B ARG* 1.3 66.2 + - - +
187B PRO* 3.2 7.3 - - - +
190B LYS* 4.4 13.7 - - - +
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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