Contacts of the strand formed by residues 10 - 24 (chain A) in PDB entry 5JTP
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 THR 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLU 3.3 9.3 + - - -
9A MET* 1.3 78.0 + - - +
11A PHE* 1.3 68.5 + - - +
12A GLN* 4.2 6.3 - - + +
85A SER 4.2 12.6 - - - +
86A ILE* 3.3 24.1 - - - +
87A ALA* 3.0 17.1 + - - +
89A ILE* 4.4 4.8 - - - +
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Residues in contact with PHE 11 (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* 1.3 77.0 - - - +
12A GLN* 1.3 65.6 + - - +
13A ILE* 3.8 21.8 - - + -
84A PHE* 3.9 27.6 - + - -
86A ILE* 3.6 16.6 - - + -
97A CYS* 5.7 6.1 - - + -
101A TYR* 3.7 37.0 - + - -
102A CYS* 3.5 28.5 - - - -
105A ILE* 4.3 7.4 - - + -
132C ASN* 6.2 0.2 - - - -
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Residues in contact with GLN 12 (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* 4.8 7.0 - - + -
11A PHE* 1.3 79.9 - - - +
13A ILE* 1.3 83.6 + - - +
14A GLN* 4.7 1.8 - - - +
84A PHE* 3.5 6.2 - - - +
85A SER* 2.8 50.8 + - - +
86A ILE* 4.3 0.4 - - - +
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Residues in contact with ILE 13 (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 PHE* 3.8 19.1 - - + -
12A GLN* 1.3 89.6 + - - +
14A GLN* 1.3 64.1 + - - +
15A ARG 3.8 11.4 - - - +
16A ILE* 3.6 27.4 - - + -
83A ILE 3.9 4.7 - - - +
84A PHE* 3.8 15.9 - - + -
105A ILE* 3.3 35.2 - - + -
130C PRO* 3.8 33.5 - - + +
132C ASN* 6.5 0.2 - - + -
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Residues in contact with GLN 14 (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 GLN* 3.5 5.8 + - - -
13A ILE* 1.3 73.8 - - - +
15A ARG* 1.4 73.2 + - - +
55A VAL* 5.4 3.4 - - + -
83A ILE* 2.9 52.2 + - + +
85A SER* 3.3 24.9 - - - +
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Residues in contact with ARG 15 (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* 3.4 4.0 - - - +
14A GLN* 1.4 96.5 - - - +
16A ILE* 1.3 67.7 + - - +
17A TYR* 3.7 15.5 - - + -
82A GLY* 3.2 3.1 - - - -
83A ILE* 2.8 36.6 + - + +
32B PHE* 3.5 53.9 + - - +
122B THR* 2.9 51.7 + - + +
130C PRO* 6.0 2.5 - - - -
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Residues in contact with ILE 16 (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* 3.6 22.4 - - + +
15A ARG* 1.3 78.0 - - - +
17A TYR* 1.3 69.1 + - - +
80A GLN* 3.6 15.3 - - - +
81A GLY 3.6 4.0 - - - -
82A GLY* 4.5 0.4 - - - -
84A PHE* 5.1 0.2 - - + -
105A ILE* 3.9 17.9 - - + -
106A LEU* 3.9 21.8 - - + -
109A TYR* 3.6 50.3 - - + -
120B ARG 4.4 0.5 - - - +
122B THR* 3.3 15.4 - - - +
111C ARG* 4.5 10.6 + - - +
130C PRO* 3.8 22.1 - - + +
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Residues in contact with TYR 17 (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* 3.7 16.4 - - + -
16A ILE* 1.3 82.5 - - - +
18A THR* 1.3 65.1 + - - +
19A LYS* 3.3 18.4 + - + -
57A GLU* 2.9 23.2 + - - -
80A GLN* 3.1 8.5 - - - -
81A GLY* 2.8 35.6 + - - +
83A ILE* 3.5 25.6 - - + +
25B ALA* 5.5 0.2 - - + -
28B ALA* 3.5 24.5 - - + -
29B PRO* 3.2 24.6 - - - +
32B PHE* 3.5 22.0 - + - -
120B ARG 3.1 18.4 - - - +
121B GLY* 3.7 5.8 - - - -
122B THR* 3.5 16.4 - - + +
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Residues in contact with THR 18 (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 TYR* 1.3 72.0 - - - +
19A LYS* 1.3 61.2 + - - +
20A ASP 3.3 3.1 - - - -
21A ILE* 3.3 23.2 - - - +
78A VAL* 3.8 15.0 - - + -
79A GLN 3.6 6.3 - - - -
80A GLN* 3.3 28.9 - - - +
113A CYS* 3.8 14.6 - - + -
23B PHE* 3.1 22.3 - - - -
120B ARG* 3.0 33.0 + - + +
121B GLY* 3.5 4.9 + - - -
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Residues in contact with LYS 19 (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 TYR* 3.5 17.9 - - + +
18A THR* 1.3 72.1 - - - +
20A ASP* 1.3 62.1 + - + +
49A SER* 4.7 3.8 + - - -
57A GLU* 2.9 39.9 + - - +
59A VAL* 3.8 24.4 - - + +
79A GLN* 3.0 10.7 + - + +
81A GLY* 3.9 13.9 - - - +
23B PHE 3.8 1.5 - - - +
24B GLU* 3.8 0.7 - - - -
25B ALA* 2.9 46.7 + - - +
26B PRO 5.9 0.7 - - - -
29B PRO* 3.3 26.6 - - - +
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Residues in contact with ASP 20 (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 THR* 4.3 0.3 - - - -
19A LYS* 1.3 81.3 - - + +
21A ILE* 1.3 83.2 + - - +
22A SER* 4.7 4.9 - - - -
77A GLU* 4.0 14.2 - - - +
78A VAL* 3.6 1.6 - - - +
79A GLN* 2.9 68.8 + - + +
23B PHE 3.1 9.2 - - - +
24B GLU* 4.0 16.0 - - - +
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Residues in contact with ILE 21 (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 THR* 3.3 30.1 - - - +
20A ASP* 1.3 87.9 - - - +
22A SER* 1.3 65.7 + - - +
77A GLU 3.6 4.9 - - - -
78A VAL* 4.2 2.9 - - + -
113A CYS* 3.7 13.5 - - - -
117A MET* 3.6 27.4 - - + -
21B ILE* 3.6 20.0 - - + -
22B SER* 3.4 6.4 + - - -
23B PHE* 2.8 37.2 + - + +
24B GLU* 5.3 0.2 - - - +
117B MET* 3.4 34.5 - - + -
120B ARG* 3.8 3.8 - - - -
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Residues in contact with SER 22 (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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20A ASP* 4.7 8.7 - - - -
21A ILE* 1.3 75.7 - - - +
23A PHE* 1.3 62.7 + - - +
24A GLU* 4.3 18.0 + - - +
75A LEU* 4.4 3.0 - - - +
76A CYS* 3.7 0.2 - - - -
77A GLU* 2.8 52.2 + - - +
117A MET* 3.6 7.0 - - - +
21B ILE 3.3 6.0 + - - -
22B SER* 4.8 0.7 - - - +
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Residues in contact with PHE 23 (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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22A SER* 1.3 71.4 + - - +
24A GLU* 1.3 61.2 + - - +
25A ALA* 3.7 6.5 - - + -
74A PHE* 3.8 14.6 - - + -
75A LEU 3.2 22.7 - - - -
76A CYS* 3.3 27.6 - - - -
117A MET* 3.3 27.4 - - + -
118A VAL* 4.8 0.7 - - - -
121A GLY* 4.2 6.7 - - - -
123A PHE* 3.6 29.6 - + - -
18B THR* 3.2 26.0 - - + -
19B LYS 3.4 26.7 - - - -
20B ASP* 3.0 36.0 - - - +
21B ILE* 2.8 30.1 + - + +
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Residues in contact with GLU 24 (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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22A SER* 4.3 14.3 + - - +
23A PHE* 1.3 78.6 - - - +
25A ALA* 1.3 58.2 + - - +
26A PRO* 3.5 15.2 - - + +
72A THR* 4.9 1.2 - - - +
74A PHE* 3.5 2.4 - - - -
75A LEU* 2.9 64.9 + - + +
19B LYS 4.0 0.9 - - - -
20B ASP* 4.2 9.2 - - - +
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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