Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 1OWH
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 ALA 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.3 8.2 - - - +
51A SER 3.0 32.3 + - - +
52A ALA 3.9 5.6 - - - +
53A THR* 3.7 23.3 - - - +
56A PHE* 4.2 11.0 - - + -
94A ILE 3.3 12.8 - - - +
95A LEU* 4.0 9.4 - - + -
110A ILE* 1.3 76.6 - - - +
112A LEU* 1.3 64.8 + - - +
113A LEU* 4.4 5.1 - - + +
253A TRP* 4.2 2.9 - - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A MET* 5.6 2.9 - - + -
48A TRP* 3.8 22.9 - - + -
49A VAL 3.6 7.4 - - - +
50A ILE* 4.0 25.6 - - + -
92A ASN 3.7 1.0 - - - +
93A LEU* 3.7 3.1 - - - +
94A ILE* 2.8 41.4 + - + +
111A ALA* 1.3 77.2 - - - +
113A LEU* 1.3 60.7 + - - +
114A LYS 4.2 0.4 - - - -
253A TRP* 3.6 29.3 - - + -
254A ILE* 4.4 8.7 - - + +
257A HIS* 3.8 28.5 - - + +
258A THR* 4.0 28.3 - - + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.5 10.1 - - + -
48A TRP* 3.7 3.1 - - - -
49A VAL* 2.9 46.4 + - + +
51A SER* 4.3 13.0 - - - -
56A PHE* 3.9 39.0 - - + -
67A TYR* 5.4 2.0 - - + -
69A VAL* 4.4 11.7 - - + -
90A VAL* 3.9 26.5 - - + -
92A ASN 3.6 4.3 - - - -
93A LEU* 3.7 19.3 - - + -
111A ALA* 4.4 3.6 - - + -
112A LEU* 1.3 78.2 - - - +
114A LYS* 1.3 64.2 - - - +
115A ILE* 3.5 8.6 + - + +
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A CYS* 3.2 38.6 - - + +
48A TRP* 3.7 38.6 - - + +
90A VAL* 3.5 4.9 - - - -
91A GLU* 2.8 67.4 + - + +
92A ASN* 2.9 27.3 + - + +
113A LEU* 1.3 72.2 - - - +
115A ILE* 1.3 55.5 + - - +
122A CYS* 4.7 7.3 - - - -
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.1 8.1 - - + -
44A PRO 3.7 15.7 - - - +
46A CYS* 3.0 25.0 + - - +
48A TRP 4.4 0.7 - - - +
49A VAL* 4.3 13.0 - - + -
69A VAL* 4.2 24.5 - - + -
71A LEU* 3.9 26.7 - - + -
88A PHE* 3.9 30.7 - - + -
89A GLU 3.5 9.4 - - - +
90A VAL* 5.0 1.1 - - + -
91A GLU* 4.6 4.1 - - - +
113A LEU* 3.9 13.2 - - + +
114A LYS* 1.3 75.1 + - - +
116A ARG* 1.3 64.3 + - - +
121A ARG 4.1 0.2 - - - +
122A CYS* 3.8 20.3 - - - -
123A ALA 5.1 0.2 - - - +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LYS* 5.4 5.7 - - - +
88A PHE* 3.7 5.8 - - - -
89A GLU* 3.0 39.1 + - + +
90A VAL 5.4 1.2 + - - -
91A GLU* 3.8 52.4 + - + +
114A LYS 4.4 0.2 + - - -
115A ILE* 1.3 78.6 - - - +
117A SER* 1.3 69.1 + - - +
120A GLY* 4.4 18.4 - - - +
121A ARG 3.2 9.9 - - - +
122A CYS* 5.8 0.9 - - - -
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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