Contacts of the helix formed by residues 95 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.0 22.2 + - - +
94A ILE* 1.3 79.2 - - - +
96A SER* 1.3 65.0 + - - +
97A GLN 3.4 2.2 - - - -
98A GLU* 3.5 9.1 - - - +
99A GLY 3.7 0.2 + - - -
238A ARG* 3.5 22.2 - - - -
239A LEU 3.8 17.7 - - - -
240A GLY 4.5 0.7 - - - -
503A SO4 3.7 4.5 - - - -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 4.2 9.4 - - - -
95A GLY* 1.3 67.3 - - - -
97A GLN* 1.3 65.6 + - - +
98A GLU 3.1 2.5 - - - -
99A GLY* 2.7 12.8 + - - -
100A LEU* 2.9 14.4 + - - +
197A ASP* 4.0 20.5 + - - -
199A PRO* 4.7 5.4 - - - +
225A LEU* 4.4 12.3 - - - +
226A PHE 4.1 17.7 - - - -
227A SER* 3.9 7.4 - - - -
240A GLY* 4.7 1.4 - - - -
501A EPE 4.9 2.4 - - - -
503A SO4 2.6 34.9 + - - -
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Residues in contact with GLN 97 (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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95A GLY 3.4 0.2 - - - -
96A SER* 1.3 80.2 + - - +
98A GLU* 1.3 62.1 + - - +
100A LEU* 3.3 9.4 + - - +
101A ALA* 3.3 21.3 + - - +
121A TYR* 3.1 22.9 + - - -
123A SER* 2.8 34.9 + - - -
124A TYR* 4.9 5.4 - - - -
197A ASP* 5.4 0.9 - - - +
238A ARG* 4.4 1.6 - - - +
501A EPE 4.5 8.6 - - - -
503A SO4 3.0 16.9 + - - +
257B GLY 5.0 2.8 + - - -
258B VAL 3.8 8.7 + - - +
259B ILE 3.2 24.1 - - - +
260B ASP 4.3 0.4 - - - +
261B PHE* 3.4 29.6 - - + -
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Residues in contact with GLU 98 (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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93A LEU* 3.7 4.7 - - - +
94A ILE* 3.0 39.8 + - + +
95A GLY 3.5 8.0 + - - +
97A GLN* 1.3 80.0 - - - +
99A GLY* 1.3 64.2 + - - +
101A ALA* 3.6 0.5 + - - +
102A HIS* 2.7 65.2 + - + +
256A LYS* 2.7 43.4 + - - +
260A ASP* 4.1 2.0 - - - +
259B ILE* 3.0 19.0 + - + +
260B ASP* 5.3 5.6 - - + -
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Residues in contact with GLY 99 (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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93A LEU* 4.1 28.7 - - - -
95A GLY 3.7 1.4 + - - -
96A SER 2.7 15.1 + - - -
98A GLU* 1.3 81.2 + - - +
100A LEU* 1.3 55.6 + - - -
102A HIS 3.8 0.2 - - - -
103A LEU* 2.8 35.1 + - - +
225A LEU* 4.3 5.4 - - - -
252A LEU* 4.1 7.4 - - - +
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Residues in contact with LEU 100 (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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96A SER 2.9 9.8 + - - +
97A GLN* 3.7 14.6 - - - +
99A GLY* 1.3 74.9 - - - +
101A ALA* 1.3 65.6 + - - +
103A LEU* 3.2 2.8 + - - +
104A LEU* 3.0 38.8 + - + +
123A SER* 5.7 0.4 - - - +
124A TYR* 3.3 48.2 - - + -
127A ALA* 5.0 4.3 - - + -
163A LEU* 3.7 29.2 - - + -
195A ILE* 4.0 15.3 - - + -
197A ASP* 4.5 8.3 - - - +
225A LEU* 3.7 16.1 - - + +
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Residues in contact with ALA 101 (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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97A GLN 3.3 12.4 + - - +
98A GLU 4.1 2.9 - - - +
100A LEU* 1.3 79.8 - - - +
102A HIS* 1.3 64.5 + - - +
104A LEU* 3.3 5.0 + - - +
105A LEU* 3.2 25.2 + - + +
127A ALA* 4.1 26.3 - - + +
130A VAL* 6.0 1.6 - - + -
258B VAL 4.4 1.1 - - - +
259B ILE* 3.5 38.4 - - + -
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Residues in contact with HIS 102 (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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98A GLU* 2.7 48.4 + - + +
101A ALA* 1.3 74.7 - - - +
103A LEU* 1.3 60.7 + - - +
105A LEU* 3.3 21.3 + - + +
106A ALA* 2.8 29.3 + - - +
252A LEU* 3.8 18.0 - - + +
255A VAL* 3.9 12.9 - - + +
256A LYS* 4.3 4.5 - - + +
259A ILE* 3.6 28.7 - - + +
260A ASP* 5.1 1.3 - - - -
102B HIS* 2.8 37.8 + + - -
259B ILE* 3.9 12.0 - - + +
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Residues in contact with LEU 103 (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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99A GLY 2.8 23.0 + - - +
100A LEU 3.6 4.5 - - - +
102A HIS* 1.3 69.7 - - - +
104A LEU* 1.3 67.8 + - - +
106A ALA* 3.1 2.5 + - + -
107A LEU* 2.9 62.6 + - + +
195A ILE* 3.8 28.3 - - + -
223A VAL* 3.5 41.3 - - + -
225A LEU* 4.3 9.6 - - + -
248A ALA 4.5 4.5 - - - +
249A LEU* 5.4 0.2 - - + -
252A LEU* 3.7 29.1 - - + +
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Residues in contact with LEU 104 (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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100A LEU* 3.0 27.9 + - + +
101A ALA 3.5 7.0 - - - +
103A LEU* 1.3 77.2 - - - +
105A LEU* 1.3 57.0 + - - +
107A LEU* 5.0 1.1 - - - -
108A THR* 2.7 38.3 + - + +
114A LEU* 4.0 31.6 - - + -
124A TYR* 4.8 2.0 - - - +
127A ALA* 3.8 29.6 - - + +
128A ALA* 4.0 16.6 - - - +
131A ALA* 4.4 11.4 - - + -
133A LEU* 4.2 9.0 - - + -
161A VAL* 4.4 6.5 - - + -
163A LEU* 5.3 4.0 - - + -
195A ILE* 3.9 21.1 - - + -
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Residues in contact with LEU 105 (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 ALA* 3.2 14.7 + - + +
102A HIS* 3.5 28.3 - - + +
103A LEU 3.2 0.2 - - - -
104A LEU* 1.3 79.5 - - - +
106A ALA* 1.3 63.2 + - - +
108A THR* 3.3 22.1 - - - +
130A VAL* 4.1 15.3 - - + +
131A ALA* 3.7 29.8 - - + +
255A VAL* 4.7 4.9 - - + -
105B LEU* 4.4 17.7 - - + -
130B VAL* 4.2 37.5 - - + +
259B ILE* 5.5 1.3 - - + -
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Residues in contact with ALA 106 (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 HIS 2.8 19.7 + - - +
103A LEU* 3.1 5.4 + - - +
105A LEU* 1.3 74.5 - - - +
107A LEU* 1.3 63.6 + - + +
108A THR 3.6 1.2 + - - +
251A ARG* 3.5 54.2 + - + +
252A LEU* 3.6 8.1 - - + +
255A VAL* 3.6 13.8 - - + +
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Residues in contact with LEU 107 (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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103A LEU* 2.9 45.7 + - + +
104A LEU* 4.3 2.9 - - - +
106A ALA* 1.3 76.3 - - - +
108A THR* 1.3 67.3 + - + +
112A ASP* 4.7 0.9 - - - +
160A LYS* 5.6 1.9 - - - +
161A VAL* 4.7 3.1 - - + +
193A TRP* 3.9 55.4 + - + -
195A ILE* 4.5 9.6 - - + -
223A VAL* 5.1 2.0 - - + -
248A ALA* 3.9 29.4 - - + +
251A ARG* 3.7 31.7 + - + +
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Residues in contact with THR 108 (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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104A LEU* 2.7 25.0 + - + +
105A LEU* 3.3 16.4 + - - +
106A ALA 3.4 1.8 - - - +
107A LEU* 1.3 87.1 - - + +
109A GLU* 1.3 73.5 + - - +
110A PRO* 4.8 0.3 - - - +
112A ASP* 3.3 15.5 - - + +
131A ALA* 4.3 3.1 + - - +
133A LEU* 3.3 34.8 - - + +
160A LYS* 5.3 0.9 - - + -
161A VAL* 3.9 24.5 - - + -
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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