Contacts of the strand formed by residues 12 - 23 (chain A) in PDB entry 3CJE
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ARG* 1.3 71.0 - - - +
13A GLU* 1.3 58.1 - - - +
100A ASP* 3.1 7.2 - - - +
101A TRP* 3.0 74.4 + - + +
173A GOL 3.7 14.6 - - - +
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Residues in contact with GLU 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 ARG* 3.5 11.2 + - + +
12A ALA* 1.3 77.5 - - - +
14A VAL* 1.3 63.6 + - - +
15A VAL* 3.8 18.3 - - + +
36A LYS* 3.2 45.2 + - + +
37A PRO* 4.1 2.8 - - - +
96A ARG* 4.9 4.7 + - - -
98A VAL* 3.6 14.6 - - + +
99A TRP 3.2 7.2 - - - +
100A ASP* 4.8 0.7 - - + -
101A TRP* 3.6 12.0 - - - -
113A LYS* 2.6 39.6 + - + +
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Residues in contact with VAL 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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13A GLU* 1.3 78.6 - - - +
15A VAL* 1.3 61.9 + - - +
16A PHE* 3.7 27.6 - - + -
34A MSE 5.1 1.1 - - - -
36A LYS 3.4 10.5 - - - +
37A PRO* 4.1 13.0 - - + -
62A LEU* 3.9 17.3 - - + -
98A VAL* 3.4 2.8 - - - -
99A TRP* 2.9 47.8 + - + +
100A ASP* 6.0 0.4 - - - -
101A TRP* 4.0 21.8 - - + -
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Residues in contact with VAL 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 GLU* 3.8 15.5 - - + +
14A VAL* 1.3 78.2 - - - +
16A PHE* 1.3 69.3 + - - +
17A THR* 4.7 0.2 - - + -
35A VAL* 2.8 47.0 + - + -
36A LYS* 2.9 46.8 + - + +
96A ARG* 3.8 31.2 - - + +
97A VAL 3.4 9.0 - - - +
98A VAL* 4.0 12.6 - - + -
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Residues in contact with PHE 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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14A VAL* 3.7 20.4 - - + -
15A VAL* 1.3 77.8 - - - +
17A THR* 1.3 65.6 + - - +
32A VAL* 3.9 15.9 - - + -
33A ALA 3.2 14.4 - - - -
34A MSE 3.7 40.8 - - + -
42A PHE* 4.4 1.3 - + - -
60A PRO* 4.2 15.5 - - + -
62A LEU* 3.7 22.9 - - + -
63A ALA* 3.8 26.2 - - + -
66A ILE* 3.4 17.9 - - + +
96A ARG* 3.4 3.8 - - - +
97A VAL 2.9 32.4 + - - +
99A TRP* 4.0 17.0 - + + -
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Residues in contact with THR 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 VAL* 4.7 1.6 - - + -
16A PHE* 1.3 79.7 - - - +
18A CYS* 1.3 63.1 + - - +
31A ASP 4.5 0.6 + - - -
32A VAL* 3.3 7.3 - - - +
33A ALA* 2.9 49.1 + - - +
35A VAL* 4.0 18.4 - - + +
41A ARG* 5.2 3.8 + - - -
66A ILE* 3.8 3.1 - - - -
95A CYS 3.1 7.2 - - - -
96A ARG* 3.9 26.0 - - + +
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Residues in contact with CYS 18 (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 THR* 1.3 78.6 - - - +
19A ASN* 1.3 62.2 + - - +
30A LEU* 3.8 31.2 - - - -
31A ASP 3.3 4.9 - - - +
32A VAL* 3.8 14.8 - - + -
66A ILE* 4.0 12.8 - - + -
67A ALA* 4.3 3.8 - - - -
70A THR* 3.5 36.0 - - - +
93A VAL 3.6 1.4 - - - +
94A GLU* 3.3 4.7 - - - +
95A CYS* 2.8 32.4 + - - +
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Residues in contact with ASN 19 (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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18A CYS* 1.3 72.5 - - - +
20A GLY* 1.3 57.6 + - - +
21A LYS* 3.8 15.7 - - - +
29A GLU 3.6 2.8 - - - +
31A ASP* 2.9 46.6 + - + +
41A ARG* 6.1 0.7 - - - +
92A ASP* 2.5 40.5 + - - +
93A VAL 3.6 0.7 - - - -
94A GLU* 3.1 20.6 - - + +
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Residues in contact with GLY 20 (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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18A CYS 3.9 1.0 - - - -
19A ASN* 1.3 73.2 - - - +
21A LYS* 1.3 62.6 - - - -
29A GLU 3.4 6.7 - - - -
30A LEU* 3.8 9.6 - - - -
70A THR* 4.3 1.4 - - - +
74A MSE 3.6 20.8 - - - +
92A ASP* 3.2 11.3 - - - -
93A VAL 2.8 38.0 + - - -
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Residues in contact with LYS 21 (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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19A ASN* 3.8 12.1 - - - +
20A GLY* 1.3 74.6 - - - -
22A ALA* 1.3 64.8 + - - +
23A VAL* 3.6 7.4 + - + +
28A ASN* 3.6 0.5 - - - -
29A GLU* 2.9 42.9 + - + +
74A MSE 3.5 4.2 - - - +
91A LEU 3.6 4.9 - - - +
92A ASP* 3.5 23.1 - - + +
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Residues in contact with ALA 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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21A LYS* 1.3 71.4 - - - +
23A VAL* 1.3 65.2 + - - +
27A ARG 3.8 1.3 - - - -
74A MSE 3.4 7.4 - - + +
78A ARG* 3.4 33.2 - - - +
90A ASP* 5.0 8.3 - - - +
91A LEU* 3.1 22.5 + - + +
169A GOL 3.5 26.1 + - - +
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Residues in contact with VAL 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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21A LYS* 3.6 10.1 + - + +
22A ALA* 1.3 79.7 - - - +
24A GLY* 1.3 74.2 + - - +
27A ARG* 2.9 54.8 + - + +
29A GLU* 3.7 36.3 - - + +
78A ARG* 3.1 7.1 + - - -
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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