Contacts of the strand formed by residues 39 - 46 (chain B) in PDB entry 2ODY
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 GLU 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 3.5 9.5 - - - -
35B ARG* 2.8 66.0 + - + -
37B PRO* 2.9 20.2 + - - +
38B GLN* 1.3 75.4 - - - +
40B LEU* 1.3 66.1 + - - +
41B LEU* 3.3 9.3 + - + +
76E ARG* 2.9 45.2 + - + +
77E VAL 3.9 11.4 - - - +
80E PHE* 3.6 10.5 - - - -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B MET* 3.5 35.4 - - + -
33B LEU 3.9 2.9 - - - -
34B PHE* 4.7 3.4 - - - -
39B GLU* 1.3 71.4 - - - +
41B LEU* 1.3 61.7 + - - +
42B CYS 3.7 21.8 - - - +
43B GLY* 5.4 0.2 - - - -
73B ARG* 5.3 3.6 - - + -
141B TRP* 3.8 39.0 - - + +
142B GLY* 4.4 0.9 - - - -
151B GLN* 6.1 0.4 - - - +
193B GLY* 3.6 28.1 - - - +
76E ARG* 3.4 26.0 + - - +
77E VAL 5.0 0.2 + - - -
80E PHE* 3.6 23.0 - - + -
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Residues in contact with LEU 41 (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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33B LEU* 2.9 22.9 + - + +
34B PHE 4.3 1.6 - - - -
35B ARG* 3.7 32.8 - - + +
39B GLU* 3.3 24.1 + - + +
40B LEU* 1.3 75.4 - - - +
42B CYS* 1.3 73.5 + - + +
58B CYS 5.0 2.0 - - - +
60B LYS* 3.7 37.8 + - + +
64B LEU* 3.3 35.0 - - + -
193B GLY* 4.6 8.9 - - - -
16E GLN* 4.8 2.1 - - - +
76E ARG* 4.3 21.6 + - - +
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Residues in contact with CYS 42 (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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32B MET 3.8 0.2 - - - -
33B LEU* 2.8 39.6 + - + +
40B LEU* 3.6 11.4 - - - +
41B LEU* 1.3 88.6 - - - +
43B GLY* 1.3 61.5 + - - +
57B HIS* 5.1 0.9 - - - -
58B CYS* 2.0 57.9 - - + -
60B LYS* 5.6 2.2 - - - -
193B GLY 4.0 10.3 - - - -
195B SER* 3.3 16.6 - - - +
16E GLN* 5.0 5.4 - - - -
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Residues in contact with GLY 43 (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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30B GLN* 4.4 7.2 - - - -
31B VAL 3.4 9.0 - - - -
32B MET* 4.9 0.2 - - - -
33B LEU* 4.7 0.5 - - - +
40B LEU* 5.4 1.1 - - - -
42B CYS* 1.3 76.9 - - - +
44B ALA* 1.3 61.0 + - - +
54B THR* 3.0 18.7 + - - -
140B GLY* 6.2 1.3 - - - -
141B TRP* 5.6 3.4 - - - -
193B GLY 3.8 7.1 + - - -
194B ASP* 4.5 2.2 - - - -
195B SER 2.8 12.3 + - - +
196B GLY* 3.2 15.1 - - - -
197B GLY* 4.0 8.5 - - - -
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Residues in contact with ALA 44 (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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30B GLN* 3.9 2.3 + - - +
31B VAL* 2.8 35.8 + - + +
33B LEU* 5.1 7.2 - - + -
43B GLY* 1.3 75.3 - - - +
45B SER* 1.3 64.1 + - - +
52B VAL* 3.6 19.3 - - + -
53B LEU 3.3 10.3 - - - +
54B THR* 3.9 8.1 - - - -
106B LEU* 5.2 1.6 - - + -
196B GLY 3.3 14.3 + - - -
197B GLY* 4.0 1.2 - - - -
198B PRO* 3.7 12.7 - - - +
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Residues in contact with SER 45 (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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29B TRP* 3.1 10.8 - - - -
31B VAL* 3.7 6.3 - - - -
44B ALA* 1.3 77.5 - - - +
46B LEU* 1.3 60.2 + - - +
47B ILE* 3.7 1.2 + - - +
52B VAL* 3.2 5.2 - - - -
53B LEU* 2.8 44.5 + - - +
121B VAL* 4.5 8.5 - - - -
196B GLY 5.3 0.2 + - - -
198B PRO* 4.1 16.4 - - - -
209B GLN* 2.5 36.3 + - - -
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Residues in contact with LEU 46 (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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28B PRO 5.1 0.2 - - - +
29B TRP* 2.8 25.6 + - - +
31B VAL* 3.6 5.7 - - + +
45B SER* 1.3 70.3 - - - +
47B ILE* 1.3 61.2 + - - +
48B SER 2.7 30.3 - - - +
49B ASP 4.7 0.4 - - - -
51B TRP 3.6 12.6 - - - +
52B VAL* 4.0 13.0 - - + -
68B ILE* 4.4 13.9 - - + -
108B LEU* 4.5 14.4 - - + -
112B ILE* 4.3 6.5 - - + -
114B LEU* 4.2 9.0 - - + -
118B ILE* 4.0 24.9 - - + -
119B HIS 4.2 1.8 - - - +
120B PRO* 3.3 20.7 - - - +
121B VAL* 3.1 26.0 + - - +
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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