Contacts of the strand formed by residues 105 - 111 (chain A) in PDB entry 1OXC
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ALA* 5.9 0.2 - - + -
19A PHE 3.3 8.1 - - - +
26A GLN* 3.2 27.6 - - + +
28A VAL* 4.3 9.4 - - + -
50A ILE* 5.5 0.9 - - + -
67A VAL* 3.6 18.1 - - + +
92A VAL* 4.0 0.7 - - - +
93A GLY* 3.8 1.9 - - - -
94A SER* 2.8 43.1 + - - +
103A ASN 4.3 0.2 - - - -
104A ASP* 1.3 73.5 - - - +
106A VAL* 1.3 62.8 + - - +
107A VAL* 4.1 4.0 + - + +
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Residues in contact with VAL 106 (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 ALA* 3.2 4.0 - - - -
19A PHE* 2.8 52.5 + - + +
21A ASN* 4.4 2.9 - - - +
92A VAL 3.4 4.0 - - - +
102A TYR 4.5 3.1 - - - +
103A ASN* 3.5 37.9 - - + +
105A ALA* 1.3 73.0 - - - +
107A VAL* 1.3 65.1 + - - +
108A VAL* 4.6 2.2 - - + -
87B LEU* 4.5 7.4 - - + -
89B PHE* 3.5 34.1 - - + -
110B ASN* 4.4 19.3 - - + +
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Residues in contact with VAL 107 (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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16A VAL* 3.7 25.1 - - + -
17A THR 3.3 9.4 - - - +
18A ALA* 4.2 6.3 - - + -
28A VAL* 3.9 30.1 - - + -
65A VAL* 4.1 24.7 - - + -
67A VAL* 4.7 7.0 - - + -
90A ALA 3.8 0.9 - - - +
91A LEU* 3.6 3.8 - - - +
92A VAL* 2.8 50.1 + - + +
105A ALA 4.7 1.1 - - - +
106A VAL* 1.3 83.5 - - - +
108A VAL* 1.3 68.4 + - - +
109A ILE* 4.2 2.5 - - + -
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Residues in contact with VAL 108 (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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15A GLY 3.7 1.4 - - - +
16A VAL* 3.4 2.1 - - - -
17A THR* 2.8 40.7 + - - +
19A PHE* 4.0 22.2 - - + -
89A PHE* 4.6 7.6 - - + -
90A ALA 3.8 2.0 - - - -
91A LEU* 4.2 23.6 - - + -
106A VAL* 4.6 1.8 - - + -
107A VAL* 1.3 77.9 - - - +
109A ILE* 1.3 70.9 + - - +
110A ASN* 4.2 8.3 + - + +
19B PHE* 5.1 7.0 - - + -
89B PHE* 4.3 9.2 - - + -
108B VAL* 4.2 33.0 - - + -
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Residues in contact with ILE 109 (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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6A PHE* 4.2 16.6 - - + -
8A LEU* 4.5 3.8 - - + -
14A PHE* 3.6 24.0 - - + -
15A GLY 3.1 4.7 - - - +
16A VAL* 3.9 19.5 - - + -
30A VAL* 5.4 0.2 - - + -
63A VAL* 4.0 22.2 - - + -
65A VAL* 3.8 26.9 - - + -
88A ASN 3.9 0.2 - - - +
89A PHE* 3.4 4.7 - - - -
90A ALA* 2.8 45.2 + - + +
92A VAL* 5.7 0.4 - - + -
107A VAL* 4.6 3.8 - - + -
108A VAL* 1.3 76.3 - - - +
110A ASN* 1.3 64.5 + - - +
111A TRP* 3.9 20.6 - - + -
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Residues in contact with ASN 110 (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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14A PHE* 3.5 1.4 - - - -
15A GLY* 2.9 39.0 + - - +
17A THR* 5.2 0.3 + - - -
87A LEU* 6.2 2.8 - - + +
88A ASN 3.4 10.1 - - - +
89A PHE* 4.5 15.9 - - + -
108A VAL* 4.7 9.6 - - + +
109A ILE* 1.3 76.8 - - - +
111A TRP* 1.3 66.2 + - - +
112A PRO 4.7 2.8 + - - -
113A LEU* 3.5 11.1 - - - +
19B PHE* 4.8 8.8 - - - +
21B ASN* 4.4 4.6 - - - +
47B ASN* 2.9 40.9 + - - -
103B ASN* 5.7 0.2 - - - +
106B VAL* 4.6 17.4 - - + +
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Residues in contact with TRP 111 (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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6A PHE* 5.3 0.2 - - + -
7A THR 4.7 1.3 - - - -
8A LEU* 3.5 45.3 - - + -
9A PRO* 3.4 35.2 - - + +
12A THR* 4.8 4.0 - - + -
13A ARG 3.8 16.2 - - - +
14A PHE* 4.0 3.8 - - + -
80A GLN* 3.6 27.1 - - + -
87A LEU* 3.9 4.6 - - - +
88A ASN* 2.9 72.8 + - + +
90A ALA* 4.0 14.8 - - + -
109A ILE* 3.9 20.0 - - + -
110A ASN* 1.3 77.2 - - - +
112A PRO* 1.3 83.1 - - + +
113A LEU 4.2 0.2 - - - +
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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