Contacts of the strand formed by residues 21 - 37 (chain A) in PDB entry 3KJO
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LYS* 2.6 32.3 + - + +
19A GLY 3.8 8.7 - - - +
20A GLY* 1.3 85.8 - - - +
22A ILE* 1.3 62.6 + - - +
23A VAL* 4.1 14.8 - - - +
85A LYS* 3.5 3.3 - - - +
86A ILE* 2.7 38.3 + - - +
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Residues in contact with ILE 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 THR* 1.3 76.7 - - - +
23A VAL* 1.3 69.4 + - - +
24A ASN* 6.0 0.2 - - - +
83A ARG* 3.8 34.1 - - + -
84A LEU 3.3 6.3 - - - +
85A LYS* 4.2 14.8 - - + -
98A SER* 3.2 24.9 - - - +
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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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12A THR* 4.0 22.0 - - + +
17A LEU* 4.0 17.5 - - + -
21A THR* 4.1 18.8 - - - +
22A ILE* 1.3 80.7 - - - +
24A ASN* 1.3 73.1 + - - +
25A VAL* 4.0 11.9 - - + -
83A ARG* 3.2 1.8 + - - -
84A LEU* 2.7 45.2 + - + +
86A ILE* 3.8 20.0 - - + -
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Residues in contact with ASN 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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9A TYR* 3.6 21.1 - - - -
10A ILE 3.2 26.7 + - - +
11A TYR* 3.4 18.3 - - + -
12A THR 3.0 25.5 + - - -
23A VAL* 1.3 86.1 + - - +
25A VAL* 1.3 68.0 + - - +
81A PHE 3.2 7.0 - - - +
82A HIS* 3.3 16.5 - - - +
83A ARG* 3.2 20.6 - - - +
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Residues in contact with VAL 25 (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 TYR* 3.9 7.1 - - - -
12A THR 3.5 19.3 - - - +
14A LEU* 4.1 17.7 - - + -
17A LEU* 4.2 7.9 - - + -
23A VAL* 4.0 17.3 - - + -
24A ASN* 1.3 81.3 - - - +
26A TYR* 1.3 61.7 + - - +
49A ILE* 4.1 11.7 - - + -
57A LEU* 5.2 0.7 - - + -
79A VAL* 4.0 0.6 - - - +
80A ARG* 3.4 4.5 - - - +
81A PHE* 2.7 64.9 + - + +
84A LEU* 3.8 20.2 - - + -
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Residues in contact with TYR 26 (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 TYR* 3.7 23.8 - + - +
12A THR 5.3 1.2 + - - -
14A LEU* 4.3 11.6 - - - +
25A VAL* 1.3 74.0 - - - +
27A GLY* 1.3 57.6 + - - +
49A ILE* 4.7 2.7 - - - -
51A ASP* 4.1 15.1 - - - +
78A ILE* 4.3 2.5 - - + -
79A VAL* 3.4 14.4 - - - -
80A ARG* 3.5 30.8 + - + +
106A PHE* 4.2 11.0 - + - -
129A ASP* 2.6 42.7 + - - +
132A MET* 3.6 50.0 - - + -
133A VAL* 4.1 19.5 - - + -
136A LEU* 4.0 22.0 - - + -
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Residues in contact with GLY 27 (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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26A TYR* 1.3 76.0 - - - +
28A VAL* 1.3 64.1 + - - -
49A ILE* 4.3 14.8 - - - +
50A VAL 3.4 11.9 - - - -
78A ILE* 3.4 5.7 - - - +
79A VAL* 2.9 36.3 + - - +
136A LEU* 3.6 11.8 - - - +
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Residues in contact with VAL 28 (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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27A GLY* 1.3 76.8 - - - -
29A VAL* 1.3 67.1 + - - +
30A LYS 3.4 0.7 + - - -
49A ILE* 3.1 5.9 - - - -
50A VAL* 2.8 37.5 + - + +
76A GLY* 3.6 26.0 - - - +
77A ASP 3.6 2.9 - - - +
78A ILE* 4.4 5.6 - - + +
136A LEU* 4.2 26.0 - - + +
139A TRP* 4.0 24.9 - - + -
140A ALA* 4.2 6.3 - - + -
144A MET* 3.5 30.3 - - - -
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Residues in contact with VAL 29 (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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28A VAL* 1.3 72.5 - - - +
30A LYS* 1.3 61.5 + - - +
31A PHE 3.6 22.7 - - - +
32A PHE* 3.8 25.8 - - + -
47A VAL* 4.0 9.2 - - + -
48A THR 3.7 3.6 - - - -
49A ILE* 4.5 2.5 - - + -
72A ILE* 3.9 18.4 - - + -
74A LYS 4.6 0.9 - - - +
75A ASN* 3.6 5.1 - - - +
76A GLY* 2.8 31.3 + - - +
77A ASP 2.8 25.4 + - - +
79A VAL* 3.8 25.8 - - + -
144A MET* 3.9 4.0 - - - +
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Residues in contact with LYS 30 (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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28A VAL 3.4 1.6 + - - -
29A VAL* 1.3 74.8 - - - +
31A PHE* 1.3 61.0 + - - +
48A THR* 2.9 19.7 + - + +
50A VAL* 4.2 17.1 - - + +
56A LYS* 3.4 40.1 - - + +
75A ASN* 3.4 19.7 + - - +
139A TRP* 6.2 0.4 - - - -
143A HIS 5.6 1.4 + - - -
144A MET* 4.5 25.8 - - + +
7B G 4.2 17.7 - - - +
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Residues in contact with PHE 31 (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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29A VAL* 3.6 5.9 - - - +
30A LYS* 1.3 82.2 - - - +
32A PHE* 1.3 75.7 + - - +
33A LYS* 3.6 33.0 - - + -
46A VAL* 4.4 6.5 - - + -
47A VAL* 3.5 0.5 - - - -
48A THR* 2.9 32.7 + - - +
75A ASN* 3.6 8.5 - - - -
271A TYR* 3.6 26.2 - + - -
272A GLY 3.7 7.6 - - - -
7B G 3.2 86.8 - + + +
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Residues in contact with PHE 32 (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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29A VAL* 3.8 9.9 - - + -
31A PHE* 1.3 87.9 - - - +
33A LYS* 1.3 65.3 + - - +
34A PRO* 3.8 24.3 - - + +
45A SER* 5.6 0.7 - - - -
46A VAL 3.1 11.7 - - - +
47A VAL* 4.3 10.8 - - + -
72A ILE* 3.7 35.2 - - + -
74A LYS* 3.7 27.8 - - - -
75A ASN* 3.4 21.9 + - - -
242A TYR* 3.5 40.3 - + - -
272A GLY* 3.7 14.2 - - - -
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Residues in contact with LYS 33 (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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31A PHE* 3.6 26.5 - - + -
32A PHE* 1.3 75.0 - - - +
34A PRO* 1.3 67.4 - - + +
36A TYR* 4.1 15.6 + - + -
45A SER* 2.8 23.4 + - - -
46A VAL* 2.8 31.3 + - + +
269A THR* 3.1 46.7 + - - +
270A SER* 4.4 1.8 - - - +
272A GLY* 4.0 3.1 - - - -
273A ARG 6.1 0.2 - - - +
6B G 2.7 27.3 + - - -
7B G 3.6 14.1 - - - -
8B G 3.0 21.7 + - - -
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Residues in contact with PRO 34 (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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32A PHE* 3.8 23.3 - - + +
33A LYS* 1.3 87.8 - - + +
35A PRO* 1.3 79.8 - - + +
36A TYR* 3.3 15.9 + - - +
66A TYR* 5.3 0.2 - - - +
242A TYR* 4.0 25.4 - - + -
272A GLY 3.4 24.7 - - - +
273A ARG 4.8 0.9 - - - +
274A GLY* 4.1 16.8 - - - -
275A ILE 4.4 4.5 - - - +
276A ARG* 4.6 12.3 - - + -
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Residues in contact with PRO 35 (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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33A LYS 3.7 0.4 - - - -
34A PRO* 1.3 89.9 - - + +
36A TYR* 1.3 59.4 + - - +
43A TYR* 5.0 1.1 - - + -
44A CYS 3.2 9.6 - - - +
45A SER* 4.1 8.1 - - - +
66A TYR* 3.4 45.7 + - + +
69A LEU* 3.8 35.4 - - + -
70A PRO 4.6 2.9 - - - +
275A ILE 5.1 3.6 - - - +
276A ARG* 3.4 30.1 - - - +
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Residues in contact with TYR 36 (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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33A LYS* 4.1 21.5 - - + +
34A PRO 3.3 14.1 - - - +
35A PRO* 1.3 74.3 - - - +
37A LEU* 1.3 72.4 + - - +
38A SER* 3.1 6.6 + - - -
43A TYR* 3.3 7.5 - - - -
44A CYS* 2.7 73.4 + - + +
45A SER* 4.6 0.7 - - - -
46A VAL* 4.6 0.7 - - + +
225A ASN* 5.9 2.9 - - - +
229A VAL* 6.2 2.7 - - - -
269A THR* 3.9 41.7 + - + -
5B A 3.2 43.6 + - - -
6B G 4.2 2.4 + - - -
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Residues in contact with LEU 37 (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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36A TYR* 1.3 75.7 - - - +
38A SER* 1.3 72.7 + - - +
39A LYS* 5.3 2.1 - - - +
40A GLY 5.4 2.7 - - - +
41A THR 4.7 10.3 - - - +
42A ASP 4.6 5.8 - - - +
43A TYR* 3.6 41.5 - - + +
225A ASN* 5.9 3.5 - - - +
228A HIS* 3.9 38.9 + - + +
229A VAL* 6.1 1.2 - - - +
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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