Contacts of the helix formed by residues 152 - 163 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C GLN 5.2 0.7 - - - -
82C LEU* 3.2 15.9 - - - +
83C ALA* 4.7 2.2 - - - -
84C PRO* 4.9 1.3 - - - -
94C LEU* 3.2 26.6 - - - +
147C LEU* 4.0 17.5 - - - +
150C GLN* 3.4 4.2 + - - -
151C LEU* 1.3 80.9 - - - +
153C VAL* 1.3 63.5 + - - +
154C ALA* 3.3 10.0 + - - +
155C ASP* 2.9 27.2 + - - +
156C ILE* 3.4 12.9 + - - +
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 4.6 0.9 + - - -
17C ALA* 4.0 22.7 - - + -
70C VAL* 3.6 47.3 - - + +
71C GLN 4.7 0.4 - - - +
74C ALA* 4.1 8.3 - - + -
82C LEU* 2.9 30.8 + - + +
83C ALA* 4.6 3.4 - - + -
94C LEU* 4.0 22.9 - - + -
98C LEU* 4.0 4.6 - - + +
152C SER* 1.3 71.4 - - - +
154C ALA* 1.3 58.7 + - - +
156C ILE* 3.4 13.7 + - + +
157C TYR* 3.0 27.7 + - - +
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LEU* 3.7 13.7 - - + +
97C TRP* 4.1 17.0 - - + -
98C LEU* 3.6 18.2 - - + -
101C ILE* 3.2 13.8 - - + +
146C LEU* 3.9 18.8 - - + -
147C LEU* 5.5 1.3 - - + -
152C SER* 3.1 13.2 + - - +
153C VAL* 1.3 81.3 - - - +
155C ASP* 1.3 57.7 + - - +
157C TYR* 3.4 0.5 + - - +
158C LEU* 2.9 24.3 + - - +
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Residues in contact with ASP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C TYR* 3.3 21.8 - - - +
146C LEU* 2.8 35.5 + - - +
147C LEU 4.9 0.3 + - - -
150C GLN 3.9 1.0 - - - +
151C LEU* 3.5 14.9 - - + -
152C SER* 2.9 34.4 + - - +
154C ALA* 1.3 73.3 - - - +
156C ILE* 1.3 60.4 + - - +
158C LEU 3.3 0.3 + - - -
159C PHE* 2.8 28.0 + - - +
181C PHE* 3.2 33.6 - - + -
185C VAL* 4.7 2.0 - - + -
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Residues in contact with ILE 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C SER* 3.4 30.7 - - - +
16C ILE* 3.6 31.2 - - + -
17C ALA* 4.1 23.6 - - + -
20C GLU* 4.2 12.6 - - + -
70C VAL* 6.1 0.4 - - + -
82C LEU* 4.5 4.5 - - + -
151C LEU* 4.3 17.7 - - + -
152C SER 3.4 7.1 + - - +
153C VAL* 3.6 25.4 - - + +
154C ALA 3.3 0.4 - - - -
155C ASP* 1.3 77.5 - - - +
157C TYR* 1.3 62.3 + - - +
159C PHE* 3.3 7.1 + - - +
160C VAL* 3.1 22.5 + - - +
185C VAL* 5.0 6.3 - - + -
188C ARG* 6.4 0.4 - - - -
191C VAL* 5.8 0.2 - - + -
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Residues in contact with TYR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C CYS* 4.7 11.4 - - + -
13C SER* 3.5 24.7 - - - +
66C GLY* 5.5 5.4 - - - -
67C PRO* 4.1 15.7 - - + +
70C VAL* 5.6 1.8 - - + -
98C LEU* 3.7 34.5 - - + -
101C ILE* 3.6 26.5 - - + -
102C SER* 3.4 21.0 + - - -
106C HIS* 2.8 28.4 + - + -
153C VAL 3.0 17.4 + - - +
154C ALA 3.6 4.9 - - - +
156C ILE* 1.3 75.7 - - - +
158C LEU* 1.3 61.4 + - - +
160C VAL* 3.1 12.1 + - + +
161C VAL* 3.2 27.1 + - + +
3224C GSH 4.3 5.9 + - - -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ILE* 3.9 15.4 - - + +
105C LEU* 3.6 30.7 - - + -
136C VAL* 3.5 30.7 - - + -
140C LEU* 3.7 13.0 - - + -
146C LEU* 3.9 13.7 - - + -
154C ALA 2.9 17.8 + - - +
155C ASP 3.3 4.2 + - - +
157C TYR* 1.3 74.5 - - - +
159C PHE* 1.3 58.3 + - - +
160C VAL 3.2 0.3 + - - -
161C VAL* 3.3 2.9 + - + -
162C LEU* 2.9 52.2 + - + +
181C PHE* 3.7 22.7 - - + -
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Residues in contact with PHE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 5.3 2.2 - - + -
16C ILE* 4.3 11.7 - - + -
155C ASP 2.8 16.6 + - - +
156C ILE* 3.6 4.5 - - - +
158C LEU* 1.3 76.8 - - - +
160C VAL* 1.3 74.5 + - + +
162C LEU* 4.0 3.9 - - - +
163C GLY* 3.1 20.5 + - - -
181C PHE* 3.7 10.7 - + + -
182C GLN* 3.4 39.6 - - + +
185C VAL* 3.7 28.3 - - + -
186C GLY* 3.5 20.9 - - - -
191C VAL* 3.5 19.7 - - + -
195C LEU* 5.0 15.0 - - + -
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLY 4.8 0.2 - - - +
9C ALA 3.8 22.2 - - - +
10C CYS* 4.2 13.5 - - + +
12C LEU* 3.9 27.1 - - + -
13C SER* 3.7 27.1 - - - +
16C ILE* 4.0 12.1 - - + -
156C ILE 3.1 14.3 + - - +
157C TYR* 3.1 9.6 + - + +
159C PHE* 1.3 77.1 - - + +
161C VAL* 1.3 66.5 + - + +
163C GLY* 3.2 14.3 + - - -
164C TRP* 3.6 19.2 - - + +
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ILE* 3.8 21.1 - - + -
105C LEU* 4.1 20.2 - - + -
106C HIS* 4.1 13.7 - - + +
109C PHE* 3.6 34.0 - - + -
133C LEU* 6.3 0.4 - - + -
157C TYR* 3.2 27.9 + - + +
158C LEU* 3.8 6.3 - - + +
160C VAL* 1.3 75.7 - - + +
162C LEU* 1.3 62.9 + - + +
164C TRP* 3.0 39.6 + - + +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LEU* 5.7 0.4 - - + -
109C PHE* 5.1 3.4 - - + -
133C LEU* 3.7 30.1 - - + -
158C LEU* 2.9 41.9 + - + +
159C PHE 4.0 3.1 - - - +
161C VAL* 1.3 74.7 - - + +
163C GLY* 1.3 58.0 + - - +
164C TRP 3.0 0.9 + - - -
165C SER* 2.7 31.4 + - - -
172C LEU* 4.3 11.4 - - + +
178C LEU* 4.2 34.5 - - + +
181C PHE* 3.9 28.9 - - + -
182C GLN* 3.8 21.2 - - + +
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Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C PHE* 3.1 16.9 + - - -
160C VAL* 3.6 7.9 - - - -
161C VAL 3.2 0.8 - - - -
162C LEU* 1.3 74.5 - - - +
164C TRP* 1.3 62.4 + - - +
165C SER* 3.2 1.0 + - - -
166C ALA* 4.2 5.0 + - - +
167C TYR* 3.6 20.4 - - - -
182C GLN* 4.2 6.2 + - - -
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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