Contacts of the helix formed by residues 169 - 178 (chain A) in PDB entry 1DT0
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 LEU 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A TYR* 4.6 0.2 - - - -
166A TYR* 2.8 37.8 + - + +
167A ARG* 4.5 1.1 - - + -
168A ASN* 1.3 95.7 - - - +
170A ARG* 1.3 65.2 + - - +
171A PRO* 3.3 7.6 - - + -
172A LYS* 3.3 34.2 + - + -
173A TYR* 3.4 1.4 + - - +
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Residues in contact with ARG 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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114A SER 3.7 5.1 + - - -
115A VAL* 3.0 40.9 + - + +
117A THR* 2.6 25.8 + - - +
119A GLY* 2.8 29.5 + - - +
157A VAL* 2.9 39.4 + - + +
159A GLU* 4.9 4.2 - - - +
162A TYR* 3.1 43.9 + - + +
168A ASN 2.9 10.7 + - - +
169A LEU* 1.3 70.8 - - - +
171A PRO* 1.3 66.8 - - + +
173A TYR* 2.9 20.0 + - + +
174A VAL* 3.1 13.3 + - + +
158B TRP* 5.8 2.4 - - - -
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Residues in contact with PRO 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A THR* 5.5 5.8 - - + +
112A LYS* 6.1 2.2 - - - +
115A VAL* 4.0 30.7 - - + -
168A ASN 4.5 2.0 - - - +
169A LEU* 3.4 8.3 - - + -
170A ARG* 1.3 95.5 - - + +
172A LYS* 1.3 63.2 + - + +
173A TYR 3.0 0.4 + - - -
174A VAL* 3.2 3.1 + - + +
175A GLU* 3.0 25.2 + - - +
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Residues in contact with LYS 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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166A TYR* 3.6 20.7 - - + -
169A LEU* 3.3 31.8 + - + +
170A ARG 3.3 1.0 - - - -
171A PRO* 1.3 79.3 - - + +
173A TYR* 1.3 59.9 + - - +
175A GLU* 4.0 31.1 + - - +
176A ALA* 3.4 21.0 + - - +
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Residues in contact with TYR 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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17A HIS 5.3 0.2 - - - -
18A ILE* 4.0 22.0 - - + -
76A TYR* 2.8 27.8 + - - -
155A CYS* 3.6 19.8 - - - -
156A ASP 2.8 30.5 + - - -
157A VAL* 4.4 2.7 - - + -
161A ALA* 3.8 19.4 - - + +
162A TYR* 3.5 40.8 - + + -
166A TYR* 3.8 22.0 - + + -
169A LEU 3.4 5.4 + - - +
170A ARG* 2.9 12.5 + - + +
172A LYS* 1.3 77.7 - - - +
174A VAL* 1.3 68.9 + - + +
176A ALA* 3.1 3.3 + - - +
177A PHE* 2.9 30.6 + - + +
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Residues in contact with VAL 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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110A PHE* 5.0 1.8 - - + -
111A THR* 3.7 37.0 - - + +
114A SER* 4.4 15.5 - - - +
115A VAL* 3.9 18.4 - - + -
155A CYS* 4.4 8.1 - - - -
157A VAL* 4.7 1.3 - - + -
170A ARG* 3.1 17.2 + - + +
171A PRO 3.7 4.9 - - - +
173A TYR* 1.3 89.1 - - + +
175A GLU* 1.3 62.6 + - - +
177A PHE* 3.0 30.8 + - + +
178A TRP* 3.3 17.7 + - + +
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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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111A THR* 5.8 1.3 - - + +
171A PRO 3.0 16.2 + - - +
172A LYS* 4.0 33.2 + - - +
174A VAL* 1.3 79.2 - - - +
176A ALA* 1.3 59.6 + - - +
178A TRP* 3.5 25.4 + - + +
179A ASN* 3.9 9.6 + - - +
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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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17A HIS* 3.5 33.5 - - + +
166A TYR* 3.3 27.8 - - + +
172A LYS 3.4 12.4 + - - +
173A TYR 3.1 5.1 + - - +
175A GLU* 1.3 79.1 - - - +
177A PHE* 1.3 64.1 + - - +
178A TRP 3.2 0.4 - - - -
179A ASN* 3.3 20.5 + - - +
180A LEU* 3.8 1.9 - - - +
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Residues in contact with PHE 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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18A ILE* 5.5 2.7 - - + -
76A TYR* 5.0 4.3 - + - -
80A LEU* 3.7 26.5 - - + -
110A PHE* 3.8 17.0 - + - -
153A LEU* 4.0 19.7 - - + -
154A THR 3.5 22.0 - - - -
155A CYS* 3.8 30.1 - - + -
173A TYR* 2.9 20.8 + + + +
174A VAL* 3.0 18.6 + - + +
176A ALA* 1.3 75.1 - - - +
178A TRP* 1.3 87.3 + + - +
179A ASN 3.0 1.8 - - - -
180A LEU* 2.7 34.4 + - - +
181A VAL* 3.3 14.1 + - + +
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Residues in contact with TRP 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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85A GLY* 3.4 16.8 - - - -
86A GLY 4.5 2.4 + - - +
103A PHE* 5.0 0.7 - + - -
106A PHE* 3.7 22.2 - + - -
107A LYS* 3.7 50.4 - - + +
110A PHE* 3.3 42.6 - + + -
111A THR* 3.3 17.7 + - - -
153A LEU* 3.9 15.0 - - + -
174A VAL* 3.3 19.8 + - + +
175A GLU* 3.5 18.8 - - + +
177A PHE* 1.3 92.3 - + - +
179A ASN* 1.3 62.8 + - - +
180A LEU 3.0 4.0 + - - -
181A VAL* 3.5 18.6 - - + +
183A TRP* 4.1 12.8 + + - -
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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