Contacts of the strand formed by residues 30 - 37 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C ASN 3.4 17.8 + - - -
27C LEU* 3.2 13.8 - - - +
29C GLU* 1.3 84.5 + - + +
31C GLY* 1.3 58.8 + - - +
46C LEU* 2.8 24.1 + - - -
89C LEU* 4.0 26.0 - - + -
90C VAL 3.2 11.9 - - - +
91C LYS* 4.8 7.4 - - + -
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 5.3 3.6 - - - -
30C THR* 1.3 75.9 - - - +
32C ARG* 1.3 63.5 + - - +
43C VAL* 3.6 11.2 - - - -
44C PHE 2.8 17.5 - - - -
45C GLY* 4.5 0.4 - - - -
46C LEU* 3.7 4.1 - - - +
89C LEU* 3.4 8.2 - - - +
90C VAL 2.9 31.7 + - - -
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Residues in contact with ARG 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 3.8 28.1 - - - +
31C GLY* 1.3 77.7 - - - +
33C VAL* 1.3 64.9 + - - +
34C LEU* 3.1 1.2 + - - +
43C VAL* 3.7 3.4 - - - -
44C PHE* 2.7 54.2 + - + +
87C GLY* 3.4 27.6 - - - +
88C GLU 3.4 2.7 - - - +
89C LEU* 5.1 5.2 - - + -
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ARG* 1.3 69.4 - - - +
34C LEU* 1.3 62.0 + - - +
35C ALA 3.7 25.1 - - - +
36C VAL* 4.0 12.6 - - + -
41C ALA* 4.7 1.8 - - + -
42C ARG 3.8 4.9 - - - +
43C VAL* 4.1 4.2 - - + +
57C PHE* 3.5 35.2 - - + -
84C VAL* 4.0 7.2 - - + -
85C LYS 3.5 21.8 - - - +
86C GLU* 3.6 8.9 - - - +
87C GLY* 2.8 25.5 + - - +
88C GLU* 2.9 20.9 + - + +
90C VAL* 3.8 5.6 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ARG 3.1 1.8 + - - -
33C VAL* 1.3 74.4 - - - +
35C ALA* 1.3 59.7 + - - +
42C ARG* 2.7 31.9 + - + +
43C VAL 4.6 0.2 - - - -
44C PHE* 4.0 35.0 - - + +
71C GLY 4.6 1.1 - - - +
72C GLN* 4.2 33.4 - - + +
86C GLU* 3.8 19.0 - - - +
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.5 5.2 - - - +
34C LEU* 1.3 80.2 - - - +
36C VAL* 1.3 66.4 + - - +
40C ILE 4.2 0.2 - - - +
41C ALA* 3.6 0.5 - - - -
42C ARG* 3.1 57.9 + - + +
86C GLU* 5.3 3.8 - - - -
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 4.0 12.8 - - + -
35C ALA* 1.3 77.5 - - - +
37C GLY* 1.3 63.7 + - - +
40C ILE 3.3 15.3 - - - +
41C ALA* 4.1 7.4 - - + -
77C LEU* 4.9 1.1 - - + -
81C ASP* 4.2 16.2 - - + +
84C VAL* 3.9 45.3 - - + +
85C LYS* 4.6 5.4 - - - -
86C GLU* 4.6 3.1 - - + +
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 1.3 75.8 - - - +
38C ASP* 1.3 74.2 + - - +
39C GLY 3.2 3.1 - - - -
40C ILE* 3.0 28.0 + - - +
81C ASP* 3.2 11.0 - - - -
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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