Contacts of the strand formed by residues 30 - 37 (chain B) in PDB entry 3OEE
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 THR 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ALA* 4.5 10.5 - - + -
26B ASN* 2.7 24.6 - - - +
27B LEU* 3.4 13.0 - - + +
28B ASN 3.4 1.4 + - - -
29B GLU* 1.3 83.8 + - - +
31B GLY* 1.3 64.6 + - - +
32B ARG* 5.9 0.7 - - + -
45B GLY 3.8 0.2 - - - -
46B LEU* 2.8 25.4 + - - +
89B LEU* 3.3 34.5 - - + +
90B VAL 3.2 9.0 + - - -
91B LYS* 4.6 10.7 - - - +
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Residues in contact with GLY 31 (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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27B LEU* 4.9 2.7 - - - -
30B THR* 1.3 79.0 - - - +
32B ARG* 1.3 63.2 + - - +
43B VAL* 3.9 3.4 - - - -
44B PHE 3.2 12.3 - - - -
45B GLY* 4.6 0.2 - - - -
46B LEU* 3.8 12.3 - - - -
89B LEU* 3.3 10.9 - - - +
90B VAL* 2.7 36.3 + - - -
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Residues in contact with ARG 32 (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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27B LEU* 5.0 7.6 - - + +
30B THR* 5.9 0.7 - - + -
31B GLY* 1.3 76.4 - - - +
33B VAL* 1.3 64.2 + - - +
34B LEU* 3.4 2.0 + - + +
43B VAL* 3.6 3.1 - - - +
44B PHE* 2.8 50.0 + - + +
87B GLY* 2.9 33.1 + - - -
88B GLU* 3.3 2.9 - - - +
89B LEU* 3.6 36.1 - - + +
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Residues in contact with VAL 33 (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 ARG* 1.3 72.3 - - - +
34B LEU* 1.3 65.0 + - - +
35B ALA 3.6 25.4 - - - +
36B VAL* 4.6 0.9 - - + -
41B ALA* 4.6 5.2 - - + -
42B ARG 3.7 6.5 - - - +
43B VAL* 4.2 2.9 - - + -
57B PHE* 4.2 14.8 - - + -
84B VAL* 4.2 11.4 - - + -
85B LYS 3.3 27.8 - - - +
86B GLU* 3.5 5.9 - - - +
87B GLY* 2.9 23.9 + - - +
88B GLU* 2.9 24.4 + - + +
90B VAL* 3.8 17.7 - - + -
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Residues in contact with LEU 34 (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 ARG* 4.7 1.6 - - + +
33B VAL* 1.3 74.8 - - - +
35B ALA* 1.3 59.6 + - - +
42B ARG* 2.7 31.6 + - - +
43B VAL 4.3 0.9 - - - -
44B PHE* 3.8 41.7 - - + +
71B GLY 4.7 2.7 - - - +
72B GLN* 3.6 29.2 - - + +
86B GLU* 3.0 25.1 - - - +
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Residues in contact with ALA 35 (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 VAL* 3.5 7.8 - - - +
34B LEU* 1.3 82.8 - - - +
36B VAL* 1.3 66.1 + - - +
41B ALA* 3.4 1.4 - - - -
42B ARG* 2.8 62.0 + - + +
86B GLU* 4.4 7.9 - - - +
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Residues in contact with VAL 36 (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 VAL* 4.6 1.1 - - + -
35B ALA* 1.3 78.8 - - - +
37B GLY* 1.3 63.3 + - - +
40B ILE 3.4 13.7 - - - +
41B ALA* 4.3 7.2 - - + -
77B LEU* 4.2 22.9 - - + -
81B ASP* 4.2 16.8 - - + +
84B VAL* 3.3 34.8 - - + +
85B LYS* 4.3 12.3 - - - -
86B GLU* 4.5 2.7 - - + +
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Residues in contact with GLY 37 (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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36B VAL* 1.3 76.3 - - - +
38B ASP* 1.3 74.9 + - - +
39B GLY 3.2 3.6 - - - -
40B ILE* 3.0 21.2 + - - +
81B ASP* 3.7 8.1 - - - -
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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