Contacts of the strand formed by residues 36 - 46 (chain B) in PDB entry 1OCU
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 LEU 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B PHE* 1.3 79.8 - - - +
37B GLU* 1.3 77.1 + - - +
38B ILE* 4.0 14.8 - - + -
64B CYS* 4.0 12.6 - - - -
65B ARG 3.4 5.8 - - - -
66B THR* 3.8 6.7 - - - +
68B LEU* 3.5 26.5 - - + -
71B PHE* 3.8 24.0 - - + -
139B ALA* 3.9 33.2 - - + +
140B GLY* 5.6 0.9 - - - -
145B GLN* 4.2 10.2 + - + +
151B LEU* 5.9 0.7 - - + -
155B ILE* 6.3 0.2 - - + -
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Residues in contact with GLU 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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35B PHE* 4.2 22.2 - - + +
36B LEU* 1.3 77.1 - - - +
38B ILE* 1.3 63.2 + - - +
64B CYS* 3.2 5.9 - - - -
65B ARG* 2.9 54.6 + - + +
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Residues in contact with ILE 38 (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 LEU* 4.0 14.3 + - + -
37B GLU* 1.3 76.6 - - - +
39B GLU* 1.3 61.8 + - - +
62B ILE* 3.8 10.3 - - + -
63B ILE 3.3 11.0 - - - +
64B CYS* 3.8 11.7 - - + -
132B ASN 5.6 0.2 - - - +
135B MET* 3.6 25.6 - - + +
136B GLN* 2.7 65.7 + - + +
139B ALA* 4.2 7.0 - - + -
155B ILE* 3.2 37.2 - - + -
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Residues in contact with GLU 39 (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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38B ILE* 1.3 80.3 - - - +
40B VAL* 1.3 75.9 + - - +
41B HIS* 3.9 25.0 + - + +
61B GLU 3.5 0.7 - - - +
62B ILE* 3.2 5.7 - - - +
63B ILE* 2.9 49.9 + - + +
128B ARG* 4.8 4.3 + - - -
132B ASN* 3.3 18.8 + - - +
135B MET* 6.2 0.2 - - - -
136B GLN* 4.6 2.5 - - - +
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Residues in contact with VAL 40 (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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39B GLU* 1.3 78.8 - - - +
41B HIS* 1.3 63.9 + - - +
60B TYR* 3.7 30.3 - - + -
61B GLU 3.3 5.8 - - - +
62B ILE* 4.1 16.2 - - + -
85B PHE* 4.4 9.0 - - + -
128B ARG* 3.0 27.6 + - + +
131B LEU* 3.8 35.7 - - + +
132B ASN* 3.0 22.0 + - - +
135B MET* 3.9 16.8 - - + -
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Residues in contact with HIS 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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39B GLU* 3.9 22.8 + - + +
40B VAL* 1.3 76.8 - - - +
42B ASN* 1.3 83.9 + - + +
43B PRO* 3.5 3.8 - - - -
60B TYR* 3.9 2.3 - - - -
61B GLU* 2.9 63.6 + - - +
63B ILE* 4.0 20.7 - - + +
128B ARG* 3.8 18.4 - - - +
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Residues in contact with ASN 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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51A MET* 5.9 3.2 - - - +
41B HIS* 1.3 94.6 + - + +
43B PRO* 1.3 71.1 + - - +
44B LYS* 3.9 22.0 + - - +
61B GLU* 3.3 17.8 + - - +
79B ARG* 2.4 47.7 + - - +
128B ARG* 4.6 0.4 - - - +
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Residues in contact with PRO 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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51A MET* 3.5 39.7 - - + +
42B ASN* 1.3 93.4 + - - +
44B LYS* 1.3 65.9 + - - +
58B THR* 5.2 1.1 - - - +
59B ASP 3.5 9.0 - - - +
60B TYR* 4.0 17.0 - - + -
124B ILE* 3.6 30.7 - - + -
125B GLU* 5.5 2.0 - - - +
128B ARG* 3.7 24.9 - - + -
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Residues in contact with LYS 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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50A GLY 3.5 14.4 - - - +
51A MET* 4.1 2.2 - - + +
42B ASN* 3.8 24.5 + - - +
43B PRO* 1.3 81.4 - - - +
45B THR* 1.3 62.2 + - - +
46B HIS* 3.4 28.1 + - + +
58B THR* 3.0 3.4 - - - -
59B ASP 3.0 31.3 + - - -
79B ARG* 3.7 27.6 - - - +
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Residues in contact with THR 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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47A ILE* 3.8 25.5 - - + +
50A GLY* 3.3 13.8 + - - +
51A MET 2.5 28.7 + - - -
52A ASP* 4.1 4.1 - - - -
53A SER 5.2 1.3 - - - +
44B LYS* 1.3 71.5 - - - +
46B HIS* 1.3 64.5 + - - +
56B MET* 3.7 34.1 - - + -
57B PHE 3.4 9.4 - - - +
58B THR* 3.1 18.6 - - - +
119B PHE* 3.9 12.3 - - + -
124B ILE* 4.7 0.5 - - - +
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Residues in contact with HIS 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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44B LYS* 3.4 36.1 + - + -
45B THR* 1.3 75.4 + - - +
47B ILE* 1.3 64.7 + - - +
48B PRO* 3.4 8.2 - - + +
56B MET* 3.5 10.3 - - - +
57B PHE* 2.7 69.6 + + + +
59B ASP* 2.9 27.5 + - - -
79B ARG* 5.1 3.4 - - - -
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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