Contacts of the helix formed by residues 172 - 184 (chain A) in PDB entry 1V1A
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 SER 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A TYR* 3.4 2.0 - - - -
168A GLN 5.3 0.4 - - - -
171A TRP* 1.3 76.1 - - - +
173A PRO* 1.3 63.4 - - - +
174A GLU* 2.8 26.8 + - - +
175A GLU* 2.7 43.5 + - - +
176A ALA* 2.8 27.9 + - - +
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Residues in contact with PRO 173 (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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166A TYR* 3.3 13.0 - - + +
168A GLN* 5.6 1.3 - - - +
172A SER* 1.3 83.5 - - - +
174A GLU* 1.3 67.2 + - - +
176A ALA* 3.0 3.1 + - + +
177A ARG* 2.5 67.6 + - - +
199A LEU* 4.1 15.7 - - + +
200A LEU* 3.3 26.3 - - + +
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Residues in contact with GLU 174 (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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172A SER* 2.8 34.0 + - - +
173A PRO* 1.3 85.8 - - - +
175A GLU* 1.3 56.9 + - + +
176A ALA 2.9 4.2 + - - -
177A ARG* 2.9 34.7 + - - +
178A GLY* 2.7 33.4 + - - -
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Residues in contact with GLU 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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143A ARG* 4.1 17.3 + - - +
170A LEU 4.9 0.2 - - - +
171A TRP* 3.4 36.4 - - + +
172A SER* 2.7 52.3 + - - +
174A GLU* 1.3 76.4 - - + +
176A ALA* 1.3 58.1 + - - +
178A GLY* 4.1 1.6 - - - -
179A PHE* 3.5 13.5 + - - +
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Residues in contact with ALA 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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164A VAL* 6.3 0.7 - - + -
166A TYR* 3.5 29.2 - - + -
171A TRP* 3.8 17.9 - - + -
172A SER 2.8 13.4 + - - +
173A PRO* 3.2 9.0 - - + +
174A GLU 2.9 0.4 + - - -
175A GLU* 1.3 75.3 - - - +
177A ARG* 1.3 66.2 + - - +
178A GLY 3.1 0.7 - - - -
179A PHE* 3.0 5.5 + - - +
180A LEU* 2.8 29.0 + - + +
200A LEU* 4.4 8.7 - - + -
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Residues in contact with ARG 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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173A PRO* 2.5 45.9 + - - +
174A GLU* 3.2 32.5 + - - +
176A ALA* 1.3 70.4 - - - +
178A GLY* 1.3 65.3 + - - +
180A LEU* 2.8 23.1 + - - +
181A GLU* 2.9 15.6 + - - +
199A LEU 4.1 3.2 + - - -
200A LEU* 2.8 30.8 + - + +
201A PHE* 3.9 27.7 - - + -
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Residues in contact with GLY 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 GLU 2.7 19.6 + - - -
175A GLU* 4.3 2.5 - - - -
177A ARG* 1.3 75.7 - - - +
179A PHE* 1.3 61.0 + - - +
181A GLU* 3.3 13.9 + - - +
182A ARG* 3.4 13.7 + - - +
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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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133A GLY* 5.4 2.0 - - - -
136A PRO* 3.2 42.6 - - + -
143A ARG* 3.6 30.6 - - + +
146A SER* 3.8 13.9 - - - -
147A LEU* 3.8 22.7 - - + -
150A MET* 4.5 4.0 - - + -
162A LEU* 4.8 15.5 - - + -
171A TRP* 3.5 31.2 - + + -
175A GLU 3.5 6.1 + - - +
176A ALA 3.0 4.5 + - - +
178A GLY* 1.3 75.5 - - - +
180A LEU* 1.3 66.3 + - + +
182A ARG* 3.6 5.4 + - + +
183A ALA* 2.9 54.3 + - + +
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Residues in contact with LEU 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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133A GLY* 6.0 3.8 - - - -
162A LEU* 4.9 13.0 - - + -
164A VAL* 4.6 26.7 - - + -
171A TRP* 5.9 2.5 - - + -
176A ALA* 2.8 25.1 - - + +
177A ARG* 2.8 20.4 + - - +
179A PHE* 1.3 86.3 - - + +
181A GLU* 1.3 56.8 + - - +
183A ALA* 4.4 2.5 - - - -
184A LEU* 2.8 38.7 + - + +
190A LEU* 6.0 2.2 - - + -
200A LEU* 4.4 14.6 - - + -
201A PHE* 4.0 22.7 - - + -
211A LEU* 4.2 22.2 - - + -
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Residues in contact with GLU 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 ARG 2.9 14.3 + - - +
178A GLY* 3.3 9.4 + - - +
180A LEU* 1.3 72.8 - - - +
182A ARG* 1.3 59.8 + - - +
184A LEU* 4.3 3.7 - - - +
185A PRO* 3.4 18.0 - - - +
210A ALA* 5.8 4.0 - - - +
211A LEU* 5.6 1.3 - - - +
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Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.5 45.4 - - + +
151A GLU* 5.8 1.4 + - - -
178A GLY 3.4 12.2 + - - +
179A PHE* 4.1 5.4 - - + +
180A LEU 3.2 0.2 - - - -
181A GLU* 1.3 78.0 - - - +
183A ALA* 1.3 64.9 + - - +
185A PRO* 3.5 10.1 - - - +
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Residues in contact with ALA 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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147A LEU* 4.5 7.6 - - + -
150A MET* 4.1 17.1 - - + +
162A LEU* 4.6 9.6 - - + -
179A PHE* 2.9 46.7 + - + +
180A LEU* 3.9 3.4 - - - +
182A ARG* 1.3 76.3 - - - +
184A LEU* 1.3 53.7 + - - +
185A PRO* 2.9 4.1 - - - +
186A GLY* 2.7 33.4 + - - -
187A VAL* 3.8 5.2 + - - +
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Residues in contact with LEU 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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162A LEU* 5.6 1.7 - - + +
180A LEU* 2.8 23.4 + - + +
181A GLU* 4.3 4.7 - - - +
183A ALA* 1.3 71.5 - - - +
185A PRO* 1.3 68.2 - - + +
186A GLY 3.0 0.2 - - - -
187A VAL* 2.9 23.9 + - + +
190A LEU* 4.3 22.9 - - + -
210A ALA 4.8 3.4 - - - +
211A LEU* 4.1 38.8 - - + -
212A SER 4.3 7.0 - - - +
213A ALA* 3.9 31.4 - - + +
214A PRO* 5.7 0.2 - - + -
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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