Contacts of the helix formed by residues 78 - 89 (chain A) in PDB entry 2DVL
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.2 13.2 - - + +
26A ALA* 3.5 29.5 + - + +
29A TYR* 5.2 3.8 - - - +
36A PRO* 5.5 0.2 - - - +
39A GLN* 4.5 6.2 + - - -
74A LEU 2.9 12.7 + - - +
75A ALA 3.3 3.3 + - - -
77A ALA* 1.3 80.2 - - - +
79A PRO* 1.3 68.2 - - - +
80A SER* 2.9 20.7 + - - -
81A VAL* 3.1 28.3 + - + +
82A ALA 3.1 17.3 + - - -
199A ALA* 5.4 1.9 - - - +
344A ARG* 3.0 13.6 + - - -
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Residues in contact with PRO 79 (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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75A ALA* 3.1 26.4 - - + +
77A ALA 4.3 0.4 - - - -
78A ASP* 1.3 84.8 - - - +
80A SER* 1.3 59.7 + - - +
82A ALA* 3.3 2.2 + - + +
83A VAL* 3.0 29.7 + - + +
197A LEU* 4.0 9.0 - - + -
242A GLN* 4.5 0.2 - - - +
246A ILE* 3.8 26.2 - - + -
344A ARG* 3.5 20.0 - - - +
345A TYR* 4.1 16.6 - - + -
348A ASP* 3.1 25.8 - - + +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 4.8 0.2 + - - -
78A ASP* 2.9 12.8 + - - -
79A PRO* 1.3 79.5 - - - +
81A VAL* 1.3 62.4 + - - +
83A VAL* 3.4 4.6 + - - +
84A ILE* 3.3 27.1 + - - +
197A LEU* 3.2 35.7 - - - +
198A HIS 3.7 0.2 + - - -
199A ALA* 3.6 17.9 + - - +
200A ALA* 3.8 21.5 - - - +
344A ARG* 3.3 8.3 + - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 16.8 - - + -
36A PRO* 3.8 28.9 - - + -
39A GLN* 4.0 17.5 - - + -
40A LEU* 4.4 7.6 - - + -
43A LEU* 3.5 30.7 - - + -
74A LEU* 5.7 0.2 - - + -
78A ASP* 3.1 29.9 + - + +
80A SER* 1.3 76.7 - - - +
82A ALA* 1.3 63.0 + - - +
84A ILE* 3.2 6.8 + - - +
85A VAL* 3.0 29.6 + - + +
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Residues in contact with ALA 82 (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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71A LEU* 4.2 4.6 - - + +
74A LEU* 4.0 10.0 + - + -
75A ALA* 3.6 40.8 - - + +
78A ASP 3.1 6.0 + - - +
79A PRO* 3.6 7.0 - - + +
81A VAL* 1.3 76.7 - - - +
83A VAL* 1.3 56.5 + - - +
85A VAL* 3.3 8.7 + - - +
86A SER* 2.9 26.9 + - - -
242A GLN* 3.2 19.4 - - + +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 3.0 16.2 + - + +
80A SER 3.7 7.0 - - - +
81A VAL 3.2 0.4 - - - -
82A ALA* 1.3 76.6 - - - +
84A ILE* 1.3 58.3 + - - +
86A SER* 2.8 19.0 + - - +
87A VAL* 2.9 22.3 + - + +
156A THR* 4.3 21.5 - - + +
197A LEU* 3.9 30.1 - - + -
200A ALA* 4.7 5.4 - - + -
242A GLN* 3.1 14.3 + - - +
355A TYR* 3.6 26.9 - - + +
1001A FAD 5.8 3.6 - - + -
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Residues in contact with ILE 84 (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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35A TYR* 3.6 42.6 - - + +
36A PRO* 3.6 29.2 - - + -
40A LEU* 3.9 19.5 - - + -
80A SER 3.3 12.1 + - - +
81A VAL* 3.2 6.6 + - - +
83A VAL* 1.3 76.2 - - - +
85A VAL* 1.3 58.7 + - - +
87A VAL* 3.7 0.7 - - - +
88A THR* 2.8 30.2 + - + +
118A ILE* 4.4 10.5 - - + -
156A THR* 4.5 12.1 - - + -
157A SER* 3.6 13.0 + - - +
200A ALA* 4.1 17.9 - - + -
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Residues in contact with VAL 85 (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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40A LEU* 4.5 3.6 - - + -
43A LEU* 3.7 29.4 - - + -
48A LEU 3.9 20.6 - - - +
49A LEU* 3.9 13.7 - - + -
51A MET* 3.9 18.4 - - + -
71A LEU* 4.1 7.4 - - + -
74A LEU* 4.3 8.7 - - + -
81A VAL* 3.0 21.4 + - + +
82A ALA* 3.5 8.5 - - - +
83A VAL 3.2 0.2 - - - -
84A ILE* 1.3 76.4 - - - +
86A SER* 1.3 62.9 + - - +
87A VAL 3.1 0.3 + - - -
88A THR* 3.2 8.5 + - - +
89A SER* 2.8 33.4 + - - +
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Residues in contact with SER 86 (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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67A TRP* 6.1 2.7 - - - +
71A LEU* 4.3 14.8 - - - -
82A ALA 2.9 12.6 + - - -
83A VAL* 2.8 22.0 + - - +
85A VAL* 1.3 75.5 - - - +
87A VAL* 1.3 59.2 + - - +
89A SER* 3.6 5.5 - - - -
90A GLY* 2.8 27.5 + - - -
235A GLY 6.1 0.7 - - - -
238A GLY* 5.4 1.8 - - - -
239A VAL* 5.4 2.5 - - - +
242A GLN* 3.1 33.5 + - - -
355A TYR* 5.3 1.9 + - - -
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Residues in contact with VAL 87 (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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83A VAL* 2.9 25.2 + - + +
84A ILE 3.8 2.2 - - - +
86A SER* 1.3 77.9 + - - +
88A THR* 1.3 65.9 + - - +
89A SER 3.2 1.6 - - - -
90A GLY* 3.0 9.8 + - - -
91A LEU 4.3 0.4 + - - +
92A PRO* 3.2 17.4 - - + +
119A GLY 4.0 13.9 - - - +
120A ALA* 4.5 8.1 - - - -
121A PHE* 4.6 7.6 - - + +
156A THR* 4.2 38.6 - - + +
157A SER* 5.4 0.9 - - - +
355A TYR* 6.0 4.0 - - + -
356A GLU* 5.7 5.2 - - - +
1001A FAD 4.8 6.7 - - - +
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Residues in contact with THR 88 (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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49A LEU* 4.4 24.0 - - + +
84A ILE* 2.8 19.4 + - + +
85A VAL* 3.3 16.8 - - - +
87A VAL* 1.3 75.0 - - - +
89A SER* 1.3 66.8 + - - +
90A GLY 3.3 0.4 + - - -
92A PRO* 4.1 9.0 - - - +
93A GLN* 3.0 21.3 + - - +
112A LEU* 4.2 4.2 + - - +
117A TRP 3.9 4.3 + - - -
118A ILE* 3.3 21.5 - - + -
119A GLY* 2.6 39.9 + - - +
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 5.3 0.4 + - - -
49A LEU 3.5 26.9 - - - -
50A GLY* 4.7 2.0 - - - -
51A MET* 4.9 5.8 + - - +
52A THR* 2.9 38.1 + - - +
67A TRP* 5.2 2.8 + - - -
85A VAL* 2.8 30.5 + - - +
86A SER* 3.6 4.4 + - - -
88A THR* 1.3 75.9 - - - +
90A GLY* 1.3 63.4 + - - +
93A GLN* 3.2 14.4 - - - +
94A TYR* 5.0 0.3 + - - +
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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