Contacts of the helix formed by residues 152 - 164 (chain A) in PDB entry 2DSA
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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLN 5.2 0.4 - - - -
82A LEU* 3.2 16.2 - - - +
83A ALA* 4.7 2.2 - - - -
84A PRO* 4.9 1.1 - - - -
94A LEU* 3.3 18.7 - - - +
147A LEU* 3.9 18.5 - - - +
150A GLN* 3.5 4.5 + - - -
151A LEU* 1.3 81.6 - - - +
153A VAL* 1.3 63.1 + - - +
154A ALA* 3.3 16.3 + - - +
155A ASP* 2.9 27.6 + - - +
156A ILE* 3.4 13.6 + - - +
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Residues in contact with VAL 153 (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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13A SER* 4.7 0.7 + - - -
17A ALA* 4.1 17.7 - - + -
70A VAL* 3.5 52.3 - - + +
71A GLN 4.7 0.4 - - - +
74A ALA* 4.1 8.5 - - + -
82A LEU* 2.8 30.8 + - + +
83A ALA* 4.6 3.1 - - + -
94A LEU* 4.0 23.8 - - + -
98A LEU* 4.0 5.4 - - + +
152A SER* 1.3 72.0 - - - +
154A ALA* 1.3 57.2 - - - +
155A ASP 3.3 0.2 - - - -
156A ILE* 3.4 13.1 + - + +
157A TYR* 3.0 27.2 + - - +
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Residues in contact with ALA 154 (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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94A LEU* 3.7 14.1 - - + +
97A TRP* 4.1 17.0 - - + -
98A LEU* 3.6 17.0 - - + -
101A ILE* 3.2 13.4 - - + +
146A LEU* 3.8 19.7 - - + -
147A LEU* 5.4 1.3 - - + -
152A SER* 3.1 13.0 + - - +
153A VAL* 1.3 78.0 - - - +
155A ASP* 1.3 61.3 + - - +
157A TYR 3.4 0.7 + - - -
158A LEU* 2.9 24.3 + - - +
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Residues in contact with ASP 155 (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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145A TYR* 3.3 23.6 - - - +
146A LEU* 2.9 33.7 + - - +
147A LEU 4.9 0.7 + - - -
150A GLN 3.9 0.9 - - - +
151A LEU* 3.6 15.1 - - + -
152A SER* 2.9 34.6 + - - +
154A ALA* 1.3 73.9 - - - +
156A ILE* 1.3 61.0 + - - +
159A PHE* 2.9 27.3 + - - +
181A PHE* 3.2 34.9 - - + -
185A VAL* 4.7 2.0 - - + -
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Residues in contact with ILE 156 (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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13A SER* 3.4 30.7 - - - +
16A ILE* 3.5 34.3 - - + -
17A ALA* 4.1 17.0 - - + -
20A GLU* 4.2 14.6 - - + -
70A VAL* 6.1 0.4 - - + -
82A LEU* 4.8 2.5 - - + -
151A LEU* 4.3 18.6 - - + -
152A SER 3.4 13.4 + - - +
153A VAL* 3.7 20.4 - - + +
154A ALA 3.3 0.2 - - - -
155A ASP* 1.3 74.9 - - - +
157A TYR* 1.3 64.6 - - - +
159A PHE* 3.4 7.0 + - - +
160A VAL* 3.2 22.7 + - - +
185A VAL* 5.0 5.8 - - + -
188A ARG* 6.4 0.4 - - - -
191A VAL* 5.7 0.4 - - + -
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Residues in contact with TYR 157 (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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10A CYS* 4.7 11.9 - - + -
13A SER* 3.5 24.4 + - - +
66A GLY* 5.5 5.8 - - - -
67A PRO* 4.0 15.9 - - + -
70A VAL* 5.6 2.2 - - + -
98A LEU* 3.8 26.2 - - + -
101A ILE* 3.5 26.5 - - + -
102A SER* 3.4 28.6 + - - -
106A HIS* 2.8 29.1 + - + -
153A VAL 3.0 17.0 + - - +
154A ALA 3.7 4.7 - - - +
156A ILE* 1.3 75.5 - - - +
158A LEU* 1.3 63.0 + - - +
160A VAL* 3.1 12.5 + - + +
161A VAL* 3.2 27.3 + - + +
1224A GSH 4.3 5.9 + - - -
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Residues in contact with LEU 158 (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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101A ILE* 3.9 15.5 - - + +
105A LEU* 3.6 30.7 - - + -
133A LEU* 5.6 0.2 - - + -
136A VAL* 3.6 29.8 - - + -
140A LEU* 3.7 19.7 - - + -
146A LEU* 3.8 16.6 - - + -
154A ALA 2.9 17.4 + - - +
155A ASP 3.8 3.8 - - - +
156A ILE 3.3 0.2 - - - -
157A TYR* 1.3 75.9 - - - +
159A PHE* 1.3 58.1 + - - +
160A VAL 3.2 0.2 + - - -
161A VAL* 3.3 2.6 + - + -
162A LEU* 2.8 53.5 + - + +
181A PHE* 3.9 13.9 - - + -
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Residues in contact with PHE 159 (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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12A LEU* 5.4 2.0 - - + -
16A ILE* 4.2 17.5 - - + -
155A ASP 2.9 18.3 + - - +
156A ILE* 3.6 4.0 - - - +
158A LEU* 1.3 75.7 - - - +
160A VAL* 1.3 64.6 - - + +
162A LEU* 3.9 4.4 - - - +
163A GLY* 3.1 25.1 + - - -
181A PHE* 3.7 11.1 - + + -
182A GLN* 3.4 39.3 - - + +
185A VAL* 3.7 26.5 - - + -
186A GLY* 3.4 11.7 - - - -
191A VAL* 3.5 29.8 - - + -
195A LEU* 5.0 14.6 - - + -
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Residues in contact with VAL 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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9A ALA 3.9 20.9 - - - +
10A CYS* 4.1 14.1 - - + +
12A LEU* 3.8 27.3 - - + +
13A SER* 3.7 25.8 - - - +
16A ILE* 3.9 12.1 - - + -
156A ILE 3.2 14.0 + - - +
157A TYR* 3.1 10.5 + - + +
159A PHE* 1.3 76.9 - - + +
161A VAL* 1.3 66.5 + - + +
163A GLY* 3.2 11.5 + - - -
164A TRP* 3.5 24.1 + - + +
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Residues in contact with VAL 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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101A ILE* 3.9 12.6 - - + -
105A LEU* 4.1 21.1 - - + -
106A HIS* 4.1 14.4 - - + +
109A PHE* 3.5 36.3 - - + -
157A TYR* 3.2 33.3 + - + +
158A LEU* 3.8 5.8 - - + +
160A VAL* 1.3 75.1 - - + +
162A LEU* 1.3 65.5 + - + +
164A TRP* 3.0 39.2 + - + +
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Residues in contact with LEU 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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105A LEU* 5.6 0.4 - - + -
109A PHE* 5.1 2.9 - - + -
133A LEU* 3.7 31.0 - - + -
158A LEU* 2.8 41.1 + - + +
159A PHE 3.9 4.5 - - - +
161A VAL* 1.3 74.0 - - + +
163A GLY* 1.3 57.6 + - - +
165A SER* 2.7 32.6 + - - -
172A LEU* 4.3 11.8 - - + +
178A LEU* 4.2 33.9 - - + +
181A PHE* 3.9 28.5 - - + -
182A GLN* 3.8 20.7 - - + +
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Residues in contact with GLY 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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159A PHE* 3.1 16.3 + - - -
160A VAL* 3.2 8.2 + - - -
162A LEU* 1.3 74.4 - - - +
164A TRP* 1.3 63.0 - - - +
165A SER* 3.2 1.2 + - - -
166A ALA* 4.0 6.9 + - - +
167A TYR* 3.6 20.3 - - - -
182A GLN* 4.2 6.8 + - - -
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Residues in contact with TRP 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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8A GLY 2.9 21.4 + - - -
10A CYS* 3.5 33.0 - - + -
106A HIS* 3.7 42.6 - + - -
109A PHE* 3.7 35.4 - + + -
113A PHE* 3.6 18.9 - + + -
160A VAL* 3.6 17.5 + - + +
161A VAL* 3.0 31.3 + - + +
163A GLY* 1.3 78.6 - - - +
165A SER* 1.3 63.7 + - - +
166A ALA 3.3 0.2 - - - -
167A TYR* 3.1 20.7 + + - +
168A VAL* 3.4 12.3 + - - +
1224A GSH 3.8 5.8 - - - -
1225A HPX 3.5 35.4 - + + -
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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