Contacts of the strand formed by residues 86 - 95 (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 MET 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A TYR* 3.3 8.8 - - - -
71A LEU 2.9 29.8 + - - +
84A GLY 4.0 3.6 - - - +
85A GLU* 1.3 86.3 - - - +
87A LYS* 1.3 61.0 + - - +
88A PHE* 3.8 25.2 - - + -
117A SER* 6.3 3.1 - - - -
121A ARG* 6.0 4.9 - - - +
124A GLN* 5.4 17.5 - - + +
129A ILE* 3.7 21.8 - - + -
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Residues in contact with LYS 87 (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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21A ARG* 5.5 5.0 - - - +
68A ILE* 3.8 34.4 - - + +
69A VAL 3.7 3.4 - - - -
70A TYR* 3.8 34.7 + - + +
85A GLU* 6.2 0.2 - - + -
86A MET* 1.3 75.5 - - - +
88A PHE* 1.3 70.2 + - - +
117A SER* 4.3 11.3 - - - -
118A LYS* 5.3 11.1 + - - +
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Residues in contact with PHE 88 (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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68A ILE* 3.6 9.7 - - - +
69A VAL* 2.8 41.4 + - + +
71A LEU* 3.7 25.8 - - + -
86A MET* 3.8 32.5 - - + -
87A LYS* 1.3 78.8 - - - +
89A GLU* 1.3 70.9 + - - +
115A ILE* 3.9 28.3 - - + -
116A ARG 3.7 7.9 - - - -
117A SER* 3.7 23.6 - - - +
121A ARG 3.8 4.5 - - - -
122A CYS* 3.8 9.0 - - - -
123A ALA* 3.6 39.5 - - + -
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Residues in contact with GLU 89 (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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21A ARG* 4.0 22.8 + - - +
63A GLU 5.8 0.9 - - - -
67A TYR 4.2 12.1 - - - +
68A ILE* 6.2 0.9 - - + -
88A PHE* 1.3 76.9 - - - +
90A VAL* 1.3 66.4 + - - +
91A GLU 4.0 0.2 - - - -
115A ILE* 3.5 4.3 - - - +
116A ARG* 3.0 41.9 + - + +
117A SER* 5.0 0.6 - - - +
118A LYS* 3.5 36.8 - - + +
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Residues in contact with VAL 90 (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* 3.4 39.4 + - + +
63A GLU* 5.5 0.5 - - - -
67A TYR* 3.9 26.4 + - + +
69A VAL* 4.1 13.2 - - + -
89A GLU* 1.3 77.9 - - - +
91A GLU* 1.3 59.6 + - - +
92A ASN 3.4 28.7 - - - +
93A LEU* 4.0 10.3 - - + +
113A LEU* 3.9 31.6 - - + -
114A LYS 3.5 7.2 - - - +
115A ILE* 5.0 1.3 - - + -
116A ARG* 5.3 1.8 + - - -
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Residues in contact with GLU 91 (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* 3.0 20.9 + - - +
89A GLU 3.9 2.6 + - - -
90A VAL* 1.3 73.0 - - - +
92A ASN* 1.3 62.0 + - + +
114A LYS* 2.8 51.3 + - + +
115A ILE 4.6 0.3 - - - +
116A ARG* 3.8 57.1 + - + +
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A TRP* 4.5 6.5 - - + -
62A LYS* 4.3 2.9 - - - -
90A VAL* 3.4 6.3 - - - +
91A GLU* 1.3 84.1 - - + +
93A LEU* 1.3 65.5 + - - +
94A ILE* 3.4 33.6 - - + +
112A LEU 3.7 1.4 - - - +
113A LEU* 3.6 2.1 - - - -
114A LYS* 2.9 44.7 + - + +
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Residues in contact with LEU 93 (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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56A PHE* 4.3 20.9 - - + -
60A PRO* 4.1 32.8 - - + +
62A LYS* 4.0 28.3 - - + +
67A TYR* 4.6 8.7 - - + -
90A VAL* 4.0 3.8 - - + +
92A ASN* 1.3 77.9 + - - +
94A ILE* 1.3 60.0 + - - +
95A LEU* 3.9 27.6 + - + +
112A LEU 3.7 0.9 - - - +
113A LEU* 3.7 34.8 - - + -
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Residues in contact with ILE 94 (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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48A TRP* 4.0 14.4 - - + -
92A ASN* 3.4 35.9 - - - +
93A LEU* 1.3 72.4 - - - +
95A LEU* 1.3 66.2 + - - +
111A ALA* 3.3 6.2 - - - +
112A LEU* 2.8 47.3 + - + +
253A TRP* 4.1 18.0 - - + -
257A HIS* 3.6 52.7 - - + +
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Residues in contact with LEU 95 (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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53A THR* 3.7 22.0 - - + +
56A PHE* 4.0 18.4 - - + +
57A ILE* 4.2 30.7 - - + -
60A PRO* 4.4 21.1 - - + -
93A LEU* 3.9 27.0 + - + +
94A ILE* 1.3 80.9 - - - +
96A HIS* 1.3 67.8 + - - +
97A LYS* 3.2 5.0 + - - +
111A ALA* 4.0 14.1 - - + -
253A TRP* 4.3 3.7 + - - -
257A HIS* 6.0 0.7 - - - -
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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