Contacts of the strand formed by residues 137 - 142 (chain J) in PDB entry 1OQE
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 PHE 137 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7J GLN* 5.0 10.3 - - + -
8J LEU 3.3 14.4 - - - +
9J ILE* 4.1 11.0 - - + -
27J TRP* 3.7 7.1 - - - -
55J TYR* 4.2 20.9 - + - -
56J GLY* 3.3 2.3 - - - -
57J GLN* 2.9 69.8 + - + +
105J TYR* 4.3 19.7 - + - -
120J LEU* 5.0 0.9 - - - +
133J GLY 4.0 6.5 - - - -
134J ASP* 3.6 21.3 - - - -
135J VAL 4.0 0.2 - - - -
136J THR* 1.3 82.2 - - - +
138J PHE* 1.3 63.3 + - - +
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Residues in contact with PHE 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU 4.2 0.2 - - - +
7J GLN* 4.6 0.7 - - - -
8J LEU* 2.6 49.4 + - + +
27J TRP* 3.5 39.0 - + + -
43J LYS* 5.6 1.3 - - - -
44J ILE* 3.7 27.4 - - + -
54J ILE* 4.2 7.9 - - + -
55J TYR* 3.2 23.1 - - - -
71J ILE* 4.1 24.0 - - + -
118J LEU* 4.0 13.2 - - + -
119J GLN* 3.7 30.5 - - - -
120J LEU* 3.9 25.4 - - + -
137J PHE* 1.3 76.8 - - - +
139J GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU 3.3 11.4 - - - -
7J GLN* 4.2 0.4 - - - -
44J ILE* 4.4 7.0 - - - -
54J ILE* 3.6 5.4 - - - +
55J TYR* 3.0 56.7 + - - +
138J PHE* 1.3 77.4 - - - +
140J ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J CYS* 3.2 5.2 - - - +
6J LEU 3.0 31.6 + - - +
37J LEU* 3.2 21.1 - - + +
44J ILE* 4.5 8.1 - - + -
52J PHE* 5.0 3.8 - - + -
53J PHE 3.3 9.0 - - - +
54J ILE* 4.5 4.5 - - + -
55J TYR* 3.8 4.0 + - - -
118J LEU* 4.2 25.1 - - + -
139J GLY* 1.3 75.7 - - - +
141J LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J GLN* 3.5 26.0 - - + +
4J ASP 3.6 10.1 - - - +
5J CYS* 3.9 13.7 - - + -
52J PHE* 3.2 5.6 - - - -
53J PHE* 2.8 54.9 + - + +
55J TYR* 5.1 5.6 - - + -
140J ALA* 1.3 76.4 - - - +
142J LYS* 1.3 79.5 + - - +
143J LEU* 3.5 14.3 + - + -
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Residues in contact with LYS 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J GLN* 3.5 18.1 - - - +
4J ASP* 2.8 29.0 + - + +
36J ALA* 3.8 19.1 - - + -
37J LEU* 4.6 1.0 - - - +
48J GLU* 3.3 30.0 + - - +
49J THR 3.3 24.9 + - - -
50J GLY* 4.5 7.2 - - - -
51J TYR 4.1 3.1 - - - +
52J PHE* 3.5 30.1 - - + -
141J LEU* 1.3 83.2 - - - +
143J LEU* 1.3 73.4 + - - +
144J LEU* 5.3 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