Contacts of the strand formed by residues 113 - 123 (chain A) in PDB entry 5EXU
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 CYS 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A MET* 3.8 5.7 - - - +
9A LYS* 3.3 26.0 - - + -
10A ILE 3.7 4.3 - - - -
11A LYS* 3.9 8.7 - - - -
109A MET* 3.7 1.4 - - - +
110A GLU 3.1 14.6 + - - +
111A GLY 3.3 3.6 + - - -
112A ASP* 1.3 88.8 - - - +
114A PHE* 1.3 74.6 + - - +
115A PHE* 3.0 46.3 - - + -
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Residues in contact with PHE 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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4A ILE* 3.8 27.1 - - + -
8A MET* 3.5 26.9 - - + -
9A LYS 2.7 13.1 + - - +
10A ILE* 3.3 2.6 - - - -
11A LYS 2.9 26.6 + - - +
33A PRO* 4.5 4.3 - - + -
65A ASN* 3.5 15.3 - - - -
67A ALA* 3.8 16.6 - - + -
68A PHE* 3.7 27.1 - + - -
83A PHE* 3.5 42.0 - + - -
107A ILE* 4.4 0.4 - - + -
108A THR 3.5 4.7 - - - +
109A MET* 3.8 10.8 - - + -
113A CYS* 1.3 75.7 - - - +
115A PHE* 1.3 60.4 + - - +
116A TYR* 3.7 18.4 - - + +
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Residues in contact with PHE 115 (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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11A LYS* 3.2 37.2 - - + +
106A ASP 3.5 1.6 - - - +
107A ILE* 3.3 4.3 - - - -
108A THR* 2.9 50.9 + - - +
109A MET* 4.2 0.7 - - - -
110A GLU* 3.1 37.0 - - + -
113A CYS* 3.0 46.2 - - + -
114A PHE* 1.3 74.3 - - - +
116A TYR* 1.3 63.4 + - - +
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Residues in contact with TYR 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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10A ILE* 3.5 24.8 - - + +
11A LYS* 2.9 27.1 + - - -
12A LEU* 3.3 26.4 - - + -
13A ARG 3.1 16.8 + - - -
38A GLN* 4.6 1.6 + - - -
40A LEU* 5.1 1.1 - - + -
60A ALA 5.2 0.2 - - - -
61A PHE 3.5 22.4 - - - -
62A CRQ 4.5 4.9 - - - -
65A ASN* 2.7 48.2 + - + +
68A PHE* 3.5 13.5 - - - -
105A SER* 3.7 13.2 - - - +
106A ASP 3.4 4.0 - - - -
107A ILE* 3.7 15.7 - - + -
114A PHE* 3.7 15.5 - - + -
115A PHE* 1.3 81.4 - - - +
117A GLU* 1.3 57.7 - - - +
118A ILE* 3.9 10.1 - - + -
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Residues in contact with GLU 117 (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 LYS* 3.7 12.3 + - - +
13A ARG* 3.2 49.5 + - - +
15A GLU* 4.8 4.2 + - - +
104A THR* 3.7 2.1 + - - +
105A SER* 3.3 1.9 - - - -
106A ASP* 2.9 43.1 + - + +
116A TYR* 1.3 72.0 - - - +
118A ILE* 1.3 66.4 + - - +
119A ARG 4.3 0.3 + - - -
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Residues in contact with ILE 118 (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 LEU* 4.0 41.3 - - + -
13A ARG 2.9 12.2 + - - +
14A MET* 3.2 25.1 - - + -
15A GLU* 3.1 25.5 + - - +
60A ALA* 3.7 28.5 - - + +
61A PHE* 4.2 7.0 - - + -
89A TRP* 4.9 1.8 - - + -
103A ALA* 5.3 0.4 - - + -
104A THR 3.1 11.0 - - - +
105A SER* 3.6 18.6 - - - +
116A TYR* 3.9 11.4 - - + -
117A GLU* 1.3 78.7 + - - +
119A ARG* 1.3 69.0 + - - +
120A PHE* 4.8 0.9 - - + +
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Residues in contact with ARG 119 (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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15A GLU* 3.4 42.9 + - - +
16A GLY* 4.1 12.6 - - - -
17A ALA* 4.2 4.6 - - - +
102A ILE 4.6 0.2 - - - -
103A ALA* 3.1 7.0 - - - +
104A THR* 2.8 56.0 + - + +
117A GLU 4.3 0.4 + - - -
118A ILE* 1.3 75.3 - - - +
120A PHE* 1.3 59.8 + - - +
121A ASP* 2.7 39.8 + - - +
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Residues in contact with PHE 120 (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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14A MET* 3.9 23.1 - - + -
15A GLU 3.1 7.0 + - - +
16A GLY* 2.9 30.3 - - - -
17A ALA 3.1 4.0 + - - -
18A VAL* 4.0 18.6 - - + -
23A PHE* 4.2 2.7 - + + -
56A ILE* 3.6 28.7 - - + -
57A LEU* 3.7 29.2 - - + -
60A ALA* 4.0 16.4 - - + -
93A MET* 3.8 16.8 - - + -
101A CYS* 3.7 35.4 - - + -
102A ILE 3.7 2.0 - - - -
103A ALA* 4.0 13.5 - - + -
118A ILE* 4.2 0.6 - - + -
119A ARG* 1.3 74.6 - - - +
121A ASP* 1.3 67.1 + - - +
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Residues in contact with ASP 121 (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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17A ALA* 3.2 13.4 + - - +
100A ILE* 5.0 0.4 - - - +
101A CYS* 3.1 3.6 - - - +
102A ILE* 2.7 55.7 + - + +
119A ARG* 2.7 54.0 + - - +
120A PHE* 1.3 80.8 - - - +
122A GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 122 (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 ALA 2.9 10.1 + - - +
18A VAL* 3.2 14.5 - - - +
19A ASN* 2.9 23.5 + - - -
20A GLY 4.6 0.9 + - - -
100A ILE 3.2 10.8 - - - -
101A CYS* 3.9 13.2 - - - -
121A ASP* 1.3 76.6 - - - +
123A THR* 1.3 65.0 + - - -
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Residues in contact with THR 123 (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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19A ASN* 3.4 11.0 + - - +
99A GLY* 3.9 0.2 - - - -
100A ILE* 2.9 40.9 + - + +
122A GLY* 1.3 78.5 - - - -
124A ASN* 1.3 107.9 + - - +
125A PHE* 3.3 6.8 + - - -
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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