Contacts of the helix formed by residues 159 - 171 (chain A) in PDB entry 1D02
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 ASP 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLY* 3.5 4.9 - - - -
105A TRP* 2.7 43.2 + - - +
114A GLY* 3.6 7.6 - - - +
155A ASP 3.3 7.7 + - - +
156A ILE* 3.2 16.0 + - - +
158A ARG* 1.3 76.4 - - - +
160A PRO* 1.3 63.6 - - - +
161A LYS* 2.8 35.3 + - - +
162A ARG* 2.9 26.4 + - + +
163A VAL* 2.9 33.5 + - - +
66B ILE* 5.2 0.2 - - - -
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Residues in contact with PRO 160 (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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105A TRP* 3.4 36.1 - - + +
158A ARG 3.5 1.7 - - - +
159A ASP* 1.3 85.2 - - - +
161A LYS* 1.3 58.7 + - - +
163A VAL* 4.3 0.4 - - - +
164A ARG* 2.9 51.8 + - - +
66B ILE* 4.2 7.2 - - + -
67B PHE* 3.4 28.9 - - + +
68B ASN* 5.1 0.4 - - - -
69B PRO* 3.5 25.1 - - + -
73B LEU* 5.9 0.7 - - + -
78B TRP* 3.8 6.9 - - + -
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Residues in contact with LYS 161 (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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105A TRP* 4.4 12.1 - - + -
111A PRO* 5.0 13.7 + - - +
114A GLY 5.7 1.1 - - - +
159A ASP* 2.8 14.5 + - - +
160A PRO* 1.3 75.4 - - - +
162A ARG* 1.3 83.6 + - + +
164A ARG* 3.3 2.9 + - - +
165A GLU* 2.8 29.5 + - - +
53B TYR* 4.8 6.8 - - + +
78B TRP* 3.5 55.7 - - + +
1C G 3.9 14.5 + - - -
2C C 2.7 29.4 + - - +
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Residues in contact with ARG 162 (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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102A GLN* 4.5 2.2 - - - +
103A ASP 5.4 1.6 - - - +
114A GLY 2.9 26.5 + - - +
115A ARG* 3.9 9.5 + - - +
116A GLY 3.2 20.4 + - - -
117A ASN* 5.3 2.0 - - - +
119A HIS* 3.5 26.0 - - - -
156A ILE* 3.5 33.0 - - + +
159A ASP* 2.9 31.1 + - + +
161A LYS* 1.3 95.9 - - + +
163A VAL* 1.3 65.8 - - - +
165A GLU* 3.0 33.1 + - - +
166A ILE* 2.9 30.9 + - + +
53B TYR* 5.9 0.6 - - - -
2C C 6.1 3.6 - - - +
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Residues in contact with VAL 163 (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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156A ILE 3.8 3.6 - - - +
157A THR 3.4 32.8 - - - +
159A ASP 2.9 23.2 + - - +
160A PRO* 4.6 3.1 - - + +
162A ARG* 1.3 76.5 - - - +
164A ARG* 1.3 59.5 + - - +
166A ILE* 4.0 1.7 - - - +
167A THR* 2.7 34.6 + - - +
177A TYR* 6.4 0.2 - - + -
179A MET* 4.2 17.9 - - + +
181A ARG* 4.0 16.6 - - - +
58B LEU* 4.0 28.9 - - + -
62B VAL* 4.4 4.7 - - + -
66B ILE* 4.3 6.7 - - + -
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Residues in contact with ARG 164 (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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160A PRO* 2.9 46.9 + - - +
161A LYS* 3.3 4.1 + - - +
162A ARG 3.3 0.2 - - - -
163A VAL* 1.3 75.5 - - - +
165A GLU* 1.3 61.2 + - - +
167A THR* 3.5 7.0 - - - -
168A PHE* 2.8 31.4 + - - +
53B TYR* 3.4 30.7 - - + +
54B ALA* 3.6 17.0 + - - +
56B VAL* 3.4 26.7 + - + +
58B LEU* 3.7 22.8 - - + +
63B ILE* 3.8 26.1 - - - +
66B ILE* 4.2 2.6 - - - +
68B ASN* 4.5 6.3 + - - -
73B LEU* 3.4 27.6 - - - +
78B TRP* 4.6 2.6 - - - -
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Residues in contact with GLU 165 (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 HIS* 2.8 26.8 + - - -
120A GLU* 4.3 6.9 - - - +
161A LYS* 2.8 19.2 + - + +
162A ARG* 3.0 33.0 + - - +
164A ARG* 1.3 76.6 - - - +
166A ILE* 1.3 57.9 + - - +
168A PHE* 3.3 2.6 + - - +
169A TRP* 2.9 70.8 + - + +
53B TYR* 3.7 36.6 + - + -
124B LYS* 4.4 3.3 + - - -
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Residues in contact with ILE 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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119A HIS* 4.2 3.1 - - + -
152A PHE* 3.7 47.1 - - + -
156A ILE* 4.2 18.4 - - + +
162A ARG* 2.9 23.5 + - + +
165A GLU* 1.3 78.4 - - - +
167A THR* 1.3 68.0 + - - +
169A TRP* 3.3 21.4 + - + -
170A TYR* 3.1 39.5 + - + +
177A TYR* 4.1 8.7 - - + -
179A MET* 3.7 28.7 - - + -
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Residues in contact with THR 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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163A VAL* 2.7 25.0 + - - +
164A ARG* 3.5 5.2 - - - -
166A ILE* 1.3 79.4 - - - +
168A PHE* 1.3 61.2 + - - +
171A ASP* 3.2 5.9 + - - -
174A GLN* 3.0 41.1 + - - +
177A TYR* 3.5 18.5 + - - -
56B VAL* 3.7 21.8 - - + -
57B VAL 4.4 4.9 - - - +
58B LEU* 3.7 17.4 - - + +
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Residues in contact with PHE 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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164A ARG 2.8 17.6 + - - +
165A GLU 3.4 5.6 - - - +
167A THR* 1.3 77.4 - - - +
169A TRP* 1.3 64.4 + - - +
171A ASP* 3.3 12.7 + - - +
52B LEU* 3.6 36.1 - - + -
53B TYR* 3.7 21.3 - + + -
56B VAL* 3.8 15.9 - - + +
129B GLY* 3.3 46.0 - - - -
130B LEU* 4.1 16.2 - - + -
133B ALA* 4.0 14.6 - - + -
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Residues in contact with TRP 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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119A HIS* 3.7 28.7 - + - -
120A GLU* 3.7 33.4 - - + -
122A SER* 5.0 2.7 - - - -
123A CYS* 3.5 27.1 - - - -
126A PHE* 5.3 0.2 - - - -
152A PHE* 5.4 2.5 - + - -
165A GLU* 2.9 46.4 + - + +
166A ILE* 3.6 20.4 - - + +
168A PHE* 1.3 77.0 - - - +
170A TYR* 1.3 73.3 + + + +
53B TYR* 3.2 25.2 + + - -
124B LYS* 4.1 12.1 - - + +
127B THR* 3.5 25.6 - - + -
128B PRO* 3.2 11.6 - - - +
129B GLY* 3.0 23.8 + - - -
130B LEU* 3.9 16.4 - - + +
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Residues in contact with TYR 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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122A SER* 4.9 4.2 + - - -
123A CYS* 5.8 0.6 - - - -
126A PHE* 3.6 32.1 - + - -
148A PHE* 3.7 7.8 - + - -
150A VAL* 3.3 31.2 - - - +
152A PHE* 4.7 4.4 - + - -
166A ILE* 3.1 31.7 + - + +
169A TRP* 1.3 90.8 - + + +
171A ASP* 1.3 71.5 - - - +
172A HIS 3.1 0.9 + - - -
173A TYR* 2.8 44.1 + - + +
174A GLN* 3.7 14.4 - - - +
176A ASN* 3.9 26.7 - - + -
177A TYR* 3.5 23.6 - + + -
128B PRO* 3.7 8.4 - - - +
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Residues in contact with ASP 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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167A THR 3.2 10.5 + - - -
168A PHE 3.3 7.9 + - - +
169A TRP 3.2 1.2 - - - -
170A TYR* 1.3 76.6 - - - +
172A HIS* 1.3 76.0 + - - +
173A TYR 3.1 2.8 + - - -
174A GLN* 2.8 29.0 + - - +
128B PRO* 3.9 16.3 - - + +
129B GLY* 4.0 12.3 - - - +
132B LYS* 2.7 44.7 + - - +
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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