Contacts of the helix formed by residues 95 - 107 (chain B) in PDB entry 2DOU
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 GLY 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B LEU* 2.9 21.5 + - - +
94B ILE* 1.3 81.0 - - - +
96B SER* 1.3 63.6 + - - -
97B GLN 3.4 2.5 - - - -
98B GLU* 3.5 10.3 - - - +
238B ARG* 3.6 12.9 - - - -
239B LEU 4.0 12.1 - - - -
240B GLY 3.6 4.4 - - - +
504B SO4 3.6 15.5 - - - -
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 4.0 9.9 - - - -
95B GLY* 1.3 67.1 - - - -
97B GLN* 1.3 65.0 + - - +
98B GLU 3.0 2.5 - - - -
99B GLY* 2.9 3.1 + - - -
100B LEU* 2.9 23.8 + - - +
197B ASP* 4.1 12.0 + - - -
199B PRO* 4.8 4.7 - - - +
225B LEU* 4.3 20.4 - - - +
226B PHE 3.8 20.0 - - - -
227B SER* 3.8 7.2 - - - -
240B GLY* 4.5 0.8 - - - -
504B SO4 2.8 31.6 + - - -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLY 4.0 5.5 + - - +
258A VAL 3.5 17.3 - - - +
259A ILE 3.3 9.7 - - - +
260A ASP 3.4 17.8 + - - +
261A PHE* 3.0 35.1 - - + -
96B SER* 1.3 78.9 + - - +
98B GLU* 1.3 60.2 + - - +
100B LEU* 3.5 8.5 + - + +
101B ALA* 3.2 23.0 + - - +
121B TYR* 3.1 19.0 + - + -
123B SER* 2.5 34.2 + - - +
197B ASP* 5.9 1.8 - - - -
238B ARG* 4.8 0.9 - - - +
504B SO4 3.1 17.6 + - - +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ILE* 3.1 23.0 + - + +
260A ASP* 5.2 5.2 - - + -
93B LEU* 3.8 2.8 - - - -
94B ILE* 3.0 37.1 + - + +
95B GLY 3.5 8.5 + - - +
97B GLN* 1.3 75.2 - - - +
99B GLY* 1.3 67.7 + - - +
101B ALA* 3.5 0.7 + - - +
102B HIS* 2.5 67.5 + - + +
238B ARG* 5.5 0.6 - - - +
256B LYS* 2.8 43.3 + - - +
260B ASP* 4.0 2.0 - - - +
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 3.9 29.6 - - - -
95B GLY 3.7 1.4 + - - -
96B SER 2.9 8.6 + - - -
98B GLU* 1.3 85.4 + - - +
100B LEU* 1.3 53.2 + - - +
102B HIS* 4.0 1.7 - - - +
103B LEU* 2.7 40.8 + - - +
225B LEU* 4.5 4.7 - - - -
252B LEU* 4.3 5.3 - - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A VAL 5.8 1.1 - - - +
96B SER 2.9 11.8 + - - +
97B GLN* 3.6 13.2 - - + +
99B GLY* 1.3 76.0 - - - +
101B ALA* 1.3 66.7 + - + +
103B LEU* 3.1 3.6 + - - +
104B LEU* 3.0 32.2 + - + +
123B SER 5.1 0.7 - - - +
124B TYR* 4.4 25.8 - - + -
127B ALA* 3.5 26.0 - - + -
163B LEU* 3.8 33.9 - - + -
195B ILE* 4.2 8.3 - - + -
197B ASP* 4.7 4.7 - - - +
225B LEU* 3.8 23.3 - - + +
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A VAL 4.4 3.4 - - - +
259A ILE* 3.5 35.4 - - + -
97B GLN 3.2 13.7 + - - +
98B GLU 4.1 2.5 - - - +
100B LEU* 1.3 84.3 - - - +
102B HIS* 1.3 63.6 + - - +
104B LEU* 3.3 12.2 + - - +
105B LEU* 3.3 18.1 + - + +
127B ALA* 3.9 23.1 - - + +
130B VAL* 6.0 1.8 - - + -
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Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A HIS* 2.8 38.9 + + - -
259A ILE* 3.9 12.3 - - + +
98B GLU* 2.5 53.8 + - + +
101B ALA* 1.3 75.6 - - - +
103B LEU* 1.3 60.9 + - - +
105B LEU* 3.3 19.4 + - + +
106B ALA* 2.9 29.5 + - - +
252B LEU* 3.8 17.3 - - + -
255B VAL* 4.1 11.8 - - + +
256B LYS* 4.1 4.2 - - + +
259B ILE* 3.5 31.0 - - + +
260B ASP* 5.1 0.9 - - - -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY 2.7 22.6 + - - +
100B LEU 3.5 4.7 - - - +
102B HIS* 1.3 72.4 - - - +
104B LEU* 1.3 63.3 + - - +
106B ALA* 3.3 1.2 + - - +
107B LEU* 3.0 56.6 + - + +
195B ILE* 3.7 38.1 - - + -
223B VAL* 3.8 31.6 - - + -
225B LEU* 4.4 9.6 - - + -
248B ALA 4.4 4.5 - - - +
249B LEU* 5.2 0.4 - - + -
252B LEU* 3.7 31.6 - - + +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 3.0 23.8 + - + +
101B ALA 3.5 7.0 - - - +
102B HIS 3.2 0.2 - - - -
103B LEU* 1.3 77.9 - - - +
105B LEU* 1.3 55.7 + - - +
107B LEU* 5.2 0.7 - - - -
108B THR* 2.6 38.3 + - - +
114B LEU* 4.3 20.9 - - + -
124B TYR 4.8 1.6 - - - +
127B ALA* 3.8 37.0 - - + +
128B ALA* 4.1 5.2 - - - +
131B ALA* 4.4 11.0 - - + -
133B LEU* 4.3 13.5 - - + -
161B VAL* 4.3 16.8 - - + -
163B LEU* 5.0 4.0 - - + -
195B ILE* 3.9 23.6 - - + -
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Residues in contact with LEU 105 (chain B).
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* 4.4 18.2 - - + -
130A VAL* 3.8 40.6 - - + +
259A ILE* 5.5 1.8 - - + -
101B ALA 3.3 16.3 + - - +
102B HIS* 3.3 27.0 + - + +
103B LEU 3.3 0.4 - - - -
104B LEU* 1.3 77.8 - - - +
106B ALA* 1.3 65.2 + - - +
108B THR* 3.3 21.2 - - - +
130B VAL* 4.2 14.8 - - + +
131B ALA* 3.8 28.5 - - + +
255B VAL* 4.7 4.7 - - + -
259B ILE* 5.4 0.2 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B HIS 2.9 16.9 + - - +
103B LEU* 3.5 6.3 - - - +
105B LEU* 1.3 79.3 - - - +
107B LEU* 1.3 62.3 + - + +
108B THR 3.7 0.9 + - - +
251B ARG* 3.1 60.6 + - + +
252B LEU* 3.7 7.6 - - - +
255B VAL* 3.6 14.1 - - + +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 3.0 40.0 + - + +
104B LEU* 5.2 0.7 - - - -
106B ALA* 1.3 79.7 - - + +
108B THR* 1.3 68.7 + - + +
112B ASP* 4.7 1.2 - - - +
160B LYS* 5.6 2.1 - - - +
161B VAL* 4.7 3.3 - - + +
193B TRP* 3.8 47.8 + - + -
195B ILE* 4.5 12.1 - - + -
223B VAL* 5.3 1.6 - - + -
248B ALA* 3.9 37.7 - - + +
251B ARG* 3.9 29.6 + - + +
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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