Contacts of the strand formed by residues 103 - 112 (chain A) in PDB entry 1X0O
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 ILE 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.8 14.8 - - + +
65A VAL* 4.5 12.3 - - + -
68A LYS* 4.3 21.3 - - + -
94A THR* 3.4 32.5 - - + +
95A PHE 3.2 8.7 - - - +
96A GLN* 3.5 24.7 - - + +
101A ASP 5.0 1.1 - - - +
102A GLU* 1.3 81.1 - - - +
104A GLU* 1.3 65.9 + - - +
105A TYR* 3.3 29.6 - - - +
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Residues in contact with GLU 104 (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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17A ASN* 5.7 2.1 - - - -
18A ILE* 5.9 1.0 - - - +
95A PHE* 3.1 37.0 + - + +
97A ASN* 2.7 26.6 + - - +
102A GLU* 3.7 10.1 + - - +
103A ILE* 1.3 76.2 - - - +
105A TYR* 1.3 100.9 + - + +
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Residues in contact with TYR 105 (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 ARG* 2.9 54.2 + - + -
16A HIS 3.5 18.8 - - - +
17A ASN* 4.9 2.9 - - - +
18A ILE* 5.3 3.1 - - - -
23A THR* 5.6 2.5 - - - +
95A PHE* 3.1 47.0 + + + -
103A ILE* 3.3 7.3 - - - +
104A GLU* 1.3 112.8 + - + +
106A ILE* 1.3 74.4 + - - +
107A ILE* 3.5 24.7 - - + +
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Residues in contact with ILE 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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15A ARG* 3.6 3.1 - - - -
16A HIS* 2.8 62.5 + - + +
18A ILE* 3.5 46.9 - - + +
61A PHE* 5.0 11.7 - - + +
64A VAL* 4.7 13.2 - - + -
65A VAL* 4.5 14.8 - - + -
92A SER* 5.1 3.8 - - - -
93A PHE 3.3 19.7 - - - +
94A THR* 4.4 10.1 - - + -
103A ILE* 5.1 0.4 - - + -
105A TYR* 1.3 77.6 - - - +
107A ILE* 1.3 69.7 + - - +
108A CYS* 5.1 1.1 - - - -
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Residues in contact with ILE 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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13A ILE* 4.0 26.0 - - + -
14A SER 3.5 4.0 - - - +
15A ARG* 4.7 6.5 - - + +
91A SER 3.3 16.3 - - - +
92A SER* 4.1 1.6 - - - -
93A PHE* 2.8 53.2 + - + +
95A PHE* 3.8 13.0 - - + -
105A TYR* 3.5 32.8 - - + +
106A ILE* 1.3 72.4 - - - +
108A CYS* 1.3 61.1 + - - +
109A THR* 3.4 12.9 + - - +
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Residues in contact with CYS 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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12A PHE* 3.5 2.9 - - - +
13A ILE* 3.4 6.6 - - - -
14A SER* 2.8 43.8 + - - +
16A HIS* 3.1 44.4 - - - -
22A PHE* 4.5 5.6 - - + -
45A ILE* 4.4 14.8 - - - -
61A PHE* 4.6 2.9 - - - -
90A THR* 4.2 15.7 - - - -
106A ILE* 3.9 1.1 + - - -
107A ILE* 1.3 71.2 - - - +
109A THR* 1.3 61.3 + - - +
110A ASN* 3.4 16.7 + - - +
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Residues in contact with THR 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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11A GLU* 4.3 18.2 - - - +
13A ILE* 3.7 26.0 - - + +
89A ARG 3.5 2.6 - - - +
90A THR* 3.2 3.5 - - - -
91A SER* 2.8 57.8 + - - +
93A PHE* 5.8 1.6 - - - +
107A ILE* 4.2 10.9 + - - +
108A CYS* 1.3 72.0 - - - +
110A ASN* 1.3 59.5 + - - +
111A THR* 3.8 5.5 + - - +
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Residues in contact with ASN 110 (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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11A GLU* 3.1 19.7 - - - +
12A PHE* 2.9 58.3 + - + +
22A PHE* 5.5 0.6 - - - -
45A ILE* 4.3 5.3 - - - +
78A PHE* 3.7 20.0 - - - -
88A MET* 3.4 19.8 - - - +
89A ARG 3.8 2.5 - - - -
90A THR* 2.8 31.5 + - - +
108A CYS* 3.4 12.5 - - - +
109A THR* 1.3 75.8 - - - +
111A THR* 1.3 62.2 + - - +
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Residues in contact with THR 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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10A THR 5.3 0.4 - - - +
11A GLU* 2.6 34.8 + - + +
88A MET* 3.7 2.2 - - - -
89A ARG* 2.8 60.4 + - - +
91A SER* 5.2 0.9 + - - -
109A THR* 4.4 8.1 + - - +
110A ASN* 1.3 72.9 - - - +
112A ASN* 1.3 69.9 + - - +
113A VAL* 3.6 8.2 + - + +
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Residues in contact with ASN 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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10A THR* 3.5 40.8 + - + +
32A THR* 3.6 19.7 - - + -
86A LEU* 3.4 33.0 - - - +
87A TRP 3.3 17.3 + - - -
88A MET* 3.7 5.7 - - - -
111A THR* 1.3 78.0 - - - +
113A VAL* 1.3 68.3 + - - +
114A LYS 3.5 10.1 + - - +
115A ASN* 5.4 2.5 + - - +
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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