Contacts of the helix formed by residues 165 - 179 (chain A) in PDB entry 2A79
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ASN 4.1 4.7 - - - +
164A THR* 1.3 92.5 - - + +
166A MET* 1.3 66.4 + - - +
167A GLU* 4.2 8.1 - - + +
168A GLU* 3.0 34.2 + - + +
169A THR* 3.1 9.5 + - - -
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Residues in contact with MET 166 (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 THR 3.3 4.4 + - - -
165A PRO* 1.3 72.1 - - - +
167A GLU* 1.3 62.7 + - - +
169A THR* 3.2 13.9 + - + -
170A VAL* 2.9 51.5 + - + +
185A TRP* 4.6 0.7 - - + -
190A TRP* 3.3 42.2 - - + -
194A GLU* 4.4 2.7 - - - +
197A GLU* 3.0 41.3 + - - +
198A ALA* 3.7 21.5 - - + -
201A VAL* 3.9 11.0 - - + -
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Residues in contact with GLU 167 (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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165A PRO* 3.1 6.3 - - + +
166A MET* 1.3 79.0 - - - +
168A GLU* 1.3 57.9 + - - +
170A VAL* 3.8 0.7 - - - +
171A ARG* 2.8 69.2 + - + +
201A VAL* 3.8 14.7 - - + +
205A PHE* 3.5 40.4 - - + -
207A LEU* 5.4 0.2 - - + -
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Residues in contact with GLU 168 (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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132A SER* 3.2 13.7 - - - -
133A ARG* 2.7 42.9 + - + +
134A LYS 4.7 0.2 + - - -
164A THR* 3.9 10.3 - - + +
165A PRO* 3.0 29.7 + - + +
167A GLU* 1.3 80.1 - - - +
169A THR* 1.3 57.2 + - - +
171A ARG* 3.6 6.8 - - - +
172A ALA* 2.9 27.8 + - - +
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Residues in contact with THR 169 (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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131A LEU* 2.9 46.0 + - + +
136A ILE* 4.0 15.9 - - + +
164A THR* 3.4 11.1 + - - +
165A PRO 3.1 5.0 + - - -
166A MET* 3.6 25.8 - - + -
168A GLU* 1.3 75.8 - - - +
170A VAL* 1.3 65.9 + - - +
172A ALA* 3.2 3.5 + - - +
173A MET* 3.0 33.5 + - + +
185A TRP* 4.8 1.8 - - + -
190A TRP* 4.5 4.9 - - + -
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Residues in contact with VAL 170 (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 MET* 2.9 44.2 + - + +
167A GLU 4.1 1.8 - - - +
169A THR* 1.3 72.3 - - - +
171A ARG* 1.3 65.1 + - - +
173A MET* 3.8 5.5 - - - +
174A THR* 2.9 28.6 + - - -
185A TRP* 4.0 13.9 - - + -
198A ALA* 4.0 17.9 - - - +
201A VAL* 4.2 7.4 - - + -
202A ALA* 4.0 17.9 - - + +
207A LEU* 3.6 30.1 - - + -
208A ILE 4.2 9.6 - - - +
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Residues in contact with ARG 171 (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 ARG* 3.8 11.9 + - - +
167A GLU* 2.8 52.3 + - - +
168A GLU* 3.6 6.3 - - - +
170A VAL* 1.3 78.8 - - - +
172A ALA* 1.3 56.3 + - - +
174A THR* 3.7 3.9 - - - +
175A HIS* 2.9 28.9 + - - +
205A PHE* 3.2 36.3 + - - +
207A LEU* 3.7 31.0 - - + +
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Residues in contact with ALA 172 (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 ARG* 3.8 41.0 - - + +
136A ILE* 3.9 23.6 - - + -
137A ILE* 5.1 2.0 - - + -
168A GLU 2.9 16.1 + - - +
169A THR* 3.2 4.2 + - - +
171A ARG* 1.3 73.0 - - - +
173A MET* 1.3 67.3 + - - +
175A HIS* 3.0 4.0 + - - +
176A VAL* 2.9 27.4 + - - +
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Residues in contact with MET 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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119A ILE* 5.8 2.7 - - + -
131A LEU* 5.0 0.7 - - + -
136A ILE* 3.7 34.5 - - + -
155A VAL* 4.1 15.7 - - + -
156A PHE 4.5 4.5 - - - +
157A ALA* 4.2 29.4 - - + +
169A THR* 3.0 21.3 + - + +
170A VAL 3.8 2.5 - - - +
172A ALA* 1.3 74.6 - - - +
174A THR* 1.3 64.5 + - - +
176A VAL* 3.1 21.8 - - - +
177A ILE* 3.1 15.8 + - - +
185A TRP* 3.3 65.7 - - + -
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Residues in contact with THR 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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170A VAL 2.9 19.0 + - - -
171A ARG 3.7 4.5 - - - +
173A MET* 1.3 75.1 - - - +
175A HIS* 1.3 61.3 + - - +
177A ILE* 3.5 4.7 + - - +
178A ASN* 2.8 42.9 + - - +
207A LEU* 3.4 24.9 - - + +
208A ILE* 2.9 53.6 + - + +
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Residues in contact with HIS 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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133A ARG* 3.4 26.1 + - - +
137A ILE* 3.4 37.4 - - + +
171A ARG 2.9 15.6 + - - +
172A ALA 3.0 8.0 + - - +
174A THR* 1.3 74.9 - - - +
176A VAL* 1.3 62.4 + - + +
178A ASN* 3.0 10.5 + - - +
179A GLN* 2.9 64.5 + - + +
181A MET* 5.9 0.9 - - - -
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Residues in contact with VAL 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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136A ILE* 4.3 14.1 - - + -
137A ILE* 4.2 24.0 - - + -
140A LEU* 3.8 25.1 - - + -
155A VAL* 4.4 13.7 - - + -
172A ALA 2.9 17.7 + - - +
173A MET* 3.1 23.1 - - - +
175A HIS* 1.3 77.9 - - + +
177A ILE* 1.3 56.4 + - - +
179A GLN* 3.5 1.4 + - - -
180A GLY 3.4 2.6 + - - -
181A MET* 2.7 58.4 + - + +
182A ALA* 3.4 3.9 + - + -
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Residues in contact with ILE 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 MET 3.1 18.3 + - - +
174A THR 3.7 4.5 - - - +
175A HIS 3.1 0.4 - - - -
176A VAL* 1.3 76.5 - - + +
178A ASN* 1.3 61.7 + - - +
179A GLN 3.1 0.2 - - - -
180A GLY* 2.8 19.1 + - - -
182A ALA* 3.4 33.3 - - + +
183A MET* 3.7 13.2 - - - +
184A TYR* 3.9 17.5 - - - -
185A TRP* 3.7 29.6 - - + +
208A ILE* 4.0 30.3 - - + -
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Residues in contact with ASN 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 THR* 2.8 36.0 + - - +
175A HIS* 3.0 10.2 + - - +
177A ILE* 1.3 73.1 - - - +
179A GLN* 1.3 65.0 + - - +
180A GLY* 2.9 7.3 + - - -
208A ILE* 4.4 10.5 - - - +
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Residues in contact with GLN 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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175A HIS* 2.9 51.8 + - + +
176A VAL* 3.8 6.3 - - - +
177A ILE 3.1 0.4 - - - -
178A ASN* 1.3 81.5 - - - +
180A GLY* 1.3 62.7 + - - +
181A MET* 3.4 21.3 + - + +
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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