Contacts of the helix formed by residues 170 - 181 (chain A) in PDB entry 1OBZ
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A SER* 4.2 5.4 - - - -
136A ILE* 4.0 0.8 - - - +
168A GLY 3.5 3.4 + - - -
169A TRP* 1.3 77.1 - - - +
171A SER* 1.3 64.0 + - - +
172A ASP* 3.5 10.0 + - - +
173A LYS* 3.0 25.5 + - - +
174A ALA* 3.0 22.2 + - - +
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Residues in contact with SER 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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129A LEU* 3.9 17.9 - - - +
130A LYS* 3.4 8.2 - - - +
131A SER* 2.8 34.6 + - - +
136A ILE* 4.8 0.9 - - - -
170A SER* 1.3 72.1 - - - +
172A ASP* 1.3 62.5 + - - +
174A ALA* 3.3 7.1 + - - +
175A HIS* 3.0 24.1 + - - +
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Residues in contact with ASP 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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170A SER* 3.2 8.8 + - - +
171A SER* 1.3 76.8 - - - +
173A LYS* 1.3 66.0 + - - +
175A HIS* 3.2 13.5 + - - +
176A LYS* 2.9 60.6 + - - +
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Residues in contact with LYS 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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164A GLU* 5.4 4.1 + - - -
169A TRP* 3.5 50.7 - - + +
170A SER* 3.0 25.2 + - - +
172A ASP* 1.3 77.7 + - - +
174A ALA* 1.3 64.2 + - - +
176A LYS* 3.2 10.4 + - + +
177A VAL* 2.9 35.8 + - + +
223B LYS* 5.5 6.9 - - - +
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Residues in contact with ALA 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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129A LEU* 3.9 26.2 - - + +
136A ILE* 4.1 17.9 - - + -
161A ILE* 5.0 1.1 - - + +
169A TRP* 3.9 19.5 - - + -
170A SER 3.0 13.2 + - - +
171A SER 3.6 7.6 - - - +
172A ASP 3.2 0.4 - - - -
173A LYS* 1.3 78.6 - - - +
175A HIS* 1.3 62.6 + - - +
177A VAL* 3.2 5.0 + - - +
178A LEU* 3.1 26.9 + - - +
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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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127A LEU 5.7 0.9 - - - -
128A ARG* 6.5 1.1 - - - -
129A LEU* 5.2 2.1 - - - +
171A SER 3.0 13.3 + - - +
172A ASP* 3.4 17.4 + - - +
174A ALA* 1.3 74.2 - - - +
176A LYS* 1.3 66.1 + - - +
178A LEU* 3.2 15.3 + - + +
179A LYS* 3.1 49.8 + - + +
1275A ACT 4.6 22.3 - - + +
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Residues in contact with LYS 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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172A ASP* 2.9 53.6 + - - +
173A LYS* 3.6 8.1 - - + +
175A HIS* 1.3 78.1 + - - +
177A VAL* 1.3 60.4 + - + +
179A LYS* 3.1 10.6 + - + +
180A GLN* 2.9 53.6 + - - +
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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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161A ILE* 3.9 26.9 - - + +
162A ASN* 5.5 3.8 - - + +
164A GLU* 4.6 10.8 - - - +
169A TRP* 3.8 32.1 - - + -
173A LYS* 2.9 30.4 + - + +
174A ALA 3.5 7.6 - - - +
176A LYS* 1.3 75.5 - - + +
178A LEU* 1.3 64.4 + - - +
180A GLN* 3.8 6.8 - - - +
181A ALA* 3.0 24.0 + - + +
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Residues in contact with LEU 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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119A LYS* 4.1 7.6 - - - -
123A GLY 5.3 1.4 - - - +
125A ILE* 4.0 34.3 - - + -
127A LEU* 4.7 10.3 - - + +
129A LEU* 3.8 27.8 - - + -
161A ILE* 4.1 22.0 - - + -
174A ALA 3.1 13.2 + - - +
175A HIS* 3.5 15.7 - - + +
176A LYS 3.2 0.4 - - - -
177A VAL* 1.3 77.3 - - - +
179A LYS* 1.3 62.7 + - + +
181A ALA* 3.6 14.8 + - - +
186A ILE* 4.1 31.2 - - + +
188A MET* 5.1 4.5 - - - -
1275A ACT 5.6 5.4 - - + +
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Residues in contact with LYS 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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119A LYS* 4.5 8.4 + - - +
123A GLY 5.9 2.2 - - - -
175A HIS* 3.1 45.8 + - + +
176A LYS* 3.5 14.1 - - + +
178A LEU* 1.3 79.6 - - + +
180A GLN* 1.3 59.4 + - + +
181A ALA 3.7 0.5 + - - +
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Residues in contact with GLN 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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176A LYS* 2.9 42.6 + - - +
177A VAL* 4.0 6.8 - - - +
179A LYS* 1.3 78.5 - - + +
181A ALA* 1.3 65.5 + - - +
182A PHE* 3.2 4.5 + - - +
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Residues in contact with ALA 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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119A LYS* 2.9 26.1 + - - +
161A ILE* 6.0 0.2 - - + -
162A ASN* 3.8 24.2 - - - +
177A VAL* 3.0 15.7 + - + +
178A LEU* 3.7 10.1 - - - +
179A LYS 3.4 2.4 - - - +
180A GLN* 1.3 77.4 - - - +
182A PHE* 1.3 64.2 + - - +
183A GLY 3.5 0.7 + - - -
185A LYS 5.1 0.2 - - - +
186A ILE* 3.9 22.2 - - + -
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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