Contacts of the helix formed by residues 25 - 43 (chain A) in PDB entry 3JRV
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 SER 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PHE* 3.9 21.2 - - - -
20A ILE* 3.9 11.7 - - - -
22A SER* 3.1 23.0 + - - -
23A ARG 3.0 1.2 - - - -
24A ASP* 1.3 78.7 + - - +
26A ILE* 1.3 57.3 + - - +
27A ILE 3.4 1.8 - - - -
28A ASP* 3.4 12.5 + - - +
29A LEU* 2.9 28.6 + - - +
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Residues in contact with ILE 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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20A ILE* 4.0 17.9 - - + -
22A SER 4.0 8.1 - - - +
23A ARG* 3.2 19.1 + - - +
24A ASP 3.5 0.4 - - - -
25A SER* 1.3 78.2 - - - +
27A ILE* 1.3 64.4 + - - +
29A LEU* 3.2 7.4 + - + +
30A ILE* 3.0 22.7 + - + +
132A MSE 3.8 19.1 - - + -
137A ILE* 3.9 17.5 - - + -
140A LEU* 3.7 29.8 - - + -
141A ILE* 3.8 35.7 - - + +
144A LEU* 4.4 9.6 - - + -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG 4.8 0.8 + - - -
24A ASP 5.1 2.8 + - - +
25A SER 3.4 0.4 - - - -
26A ILE* 1.3 75.9 - - - +
28A ASP* 1.3 63.8 + - - +
30A ILE* 3.3 2.3 + - - +
31A ASP* 2.9 23.4 + - - +
128A ILE* 3.7 28.4 - - + +
129A THR* 4.6 17.7 - - + -
132A MSE 3.7 34.5 - - + +
137A ILE* 4.0 20.0 - - + -
88C ARG* 3.6 25.4 - - - +
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Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.1 15.7 - - + -
24A ASP 4.2 14.1 + - - +
25A SER* 3.4 11.7 + - - +
26A ILE 3.3 0.4 - - - -
27A ILE* 1.3 77.7 - - - +
29A LEU* 1.3 57.7 + - - +
31A ASP* 3.5 1.6 + - - +
32A GLU* 2.9 31.4 + - - +
88C ARG* 2.7 37.5 + - - +
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Residues in contact with LEU 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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14A PHE* 3.7 39.4 - - + -
20A ILE* 3.9 22.2 - - + -
25A SER 2.9 14.3 + - - +
26A ILE* 3.4 13.7 - - + +
27A ILE 3.2 0.2 - - - -
28A ASP* 1.3 77.2 - - - +
30A ILE* 1.3 62.8 + - + +
32A GLU* 3.4 0.9 + - - +
33A TYR* 2.9 32.2 + - - +
53A LEU* 3.8 30.7 - - + -
54A TYR* 4.0 9.2 - - + -
57A LEU* 3.9 23.3 - - + -
144A LEU* 4.2 12.1 - - + -
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Residues in contact with ILE 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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26A ILE* 3.0 18.6 + - + +
27A ILE* 4.0 3.8 - - - +
29A LEU* 1.3 77.4 - - + +
31A ASP* 1.3 64.0 + - - +
33A TYR* 3.8 3.0 - - + +
34A ILE* 2.9 37.3 + - + +
57A LEU* 4.0 27.6 - - + -
102A ILE* 4.1 30.5 - - + -
128A ILE* 4.1 16.2 - - + -
131A LEU* 5.5 2.5 - - + -
132A MSE 4.7 10.3 - - - -
140A LEU* 3.6 30.5 - - + -
85C PHE* 4.7 4.5 - - + -
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Residues in contact with ASP 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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27A ILE 2.9 18.6 + - - +
28A ASP 3.6 4.0 - - - +
30A ILE* 1.3 78.3 - - - +
32A GLU* 1.3 63.9 + - - +
34A ILE* 3.4 2.4 + - - +
35A THR* 3.1 20.8 + - - -
128A ILE* 3.8 11.8 - - + +
81C LYS* 6.0 1.2 - - - +
82C SER 4.9 3.4 - - - +
83C SER* 2.6 35.4 + - - -
84C PHE 4.5 0.3 + - - -
85C PHE* 3.8 11.3 - - - -
88C ARG* 2.8 38.3 + - - +
89C GLY 5.2 0.2 + - - -
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Residues in contact with GLU 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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11A VAL 4.1 3.2 - - - +
12A PHE* 3.4 17.9 - - + -
13A TYR* 2.8 36.3 + - - +
14A PHE* 2.7 40.3 + - - +
28A ASP 2.9 17.4 + - - +
29A LEU 3.9 2.7 - - - +
31A ASP* 1.3 80.3 - - - +
33A TYR* 1.3 51.2 + - - +
35A THR* 3.2 8.1 + - - -
36A TRP* 2.8 32.1 + - - +
54A TYR* 2.7 23.3 + - - +
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Residues in contact with TYR 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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29A LEU 2.9 19.3 + - - +
30A ILE* 3.8 3.8 - - + +
32A GLU* 1.3 76.8 - - - +
34A ILE* 1.3 85.6 + - + +
36A TRP* 3.1 8.3 + + - +
37A ARG* 2.7 68.8 + - + +
54A TYR* 4.0 32.0 + + + -
57A LEU* 3.6 46.4 + - + -
58A MSE 3.3 29.1 - - + -
61A ASP* 4.2 0.5 + - - -
102A ILE* 4.4 11.4 - - + -
106A ALA* 4.0 7.7 - - + +
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Residues in contact with ILE 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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30A ILE* 2.9 27.6 + - + +
31A ASP 3.9 1.3 - - - +
33A TYR* 1.3 89.7 - - + +
35A THR* 1.3 65.0 + - - +
37A ARG* 3.4 5.3 + - - +
102A ILE* 3.6 17.9 - - + +
105A CYS* 3.7 5.4 - - + +
106A ALA* 3.5 29.2 - - - +
109A THR* 2.8 50.0 + - + +
125A LEU* 3.9 17.9 - - + -
84C PHE* 4.4 5.2 - - + +
85C PHE* 3.9 24.9 - - + -
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Residues in contact with THR 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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7A TYR* 3.6 29.8 - - + +
10A ALA* 5.4 1.8 - - + -
12A PHE* 3.9 16.2 - - + -
31A ASP* 3.1 14.2 + - - -
32A GLU* 3.4 10.5 - - - -
34A ILE* 1.3 78.0 - - - +
36A TRP* 1.3 63.0 + - - +
38A ASN* 3.0 6.6 + - - +
39A HIS 2.9 18.7 + - - -
122A PHE* 5.6 0.2 - - + -
82C SER* 4.1 11.0 + - - +
83C SER* 4.1 15.8 - - - -
84C PHE* 3.8 21.7 + - + -
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Residues in contact with TRP 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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12A PHE* 3.5 38.1 - + + -
15A VAL* 3.7 13.9 - - + +
32A GLU 2.8 19.9 + - - +
33A TYR* 3.1 8.0 + + - +
35A THR* 1.3 73.6 - - - +
37A ARG* 1.3 88.7 - - + +
39A HIS* 4.1 2.5 - - + -
40A VAL* 2.9 58.7 + - + +
45A LYS* 5.8 2.0 - - - +
46A ASP 4.4 4.7 + - - -
47A ILE* 3.6 35.7 - - + -
49A SER 4.7 1.1 + - - -
50A CYS* 4.0 23.1 - - + -
54A TYR* 3.5 32.5 - + + -
58A MSE 4.0 13.7 - - + -
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Residues in contact with ARG 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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33A TYR* 2.7 60.8 + - + +
34A ILE 3.9 1.8 - - - +
35A THR 3.3 0.4 - - - -
36A TRP* 1.3 100.7 - - - +
38A ASN* 1.3 58.6 + - - +
40A VAL* 3.7 5.2 - - - +
41A ILE* 3.6 14.6 - - - +
47A ILE* 4.6 6.6 - - - +
58A MSE 4.1 19.4 - - - +
61A ASP* 2.9 38.7 + - - -
106A ALA* 3.6 21.9 + - + +
107A LYS* 5.1 0.8 - - - +
109A THR* 3.8 14.6 - - - +
110A GLU* 3.0 54.4 + - - +
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Residues in contact with ASN 38 (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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7A TYR* 2.6 21.4 + - - +
34A ILE 3.7 2.2 + - - -
35A THR 3.0 8.3 + - - +
37A ARG* 1.3 79.0 - - - +
39A HIS* 1.3 65.2 + - - +
40A VAL 3.3 0.2 - - - -
41A ILE* 3.1 7.3 + - - +
42A VAL* 3.0 28.3 + - - +
109A THR* 3.0 29.4 + - - +
110A GLU* 4.6 0.4 - - - +
112A TRP* 3.9 4.6 - - - +
113A GLY* 3.4 8.6 - - - +
117A ILE 3.0 24.6 + - - -
118A SER* 3.4 17.0 - - - -
84C PHE* 3.5 24.4 - - + -
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Residues in contact with HIS 39 (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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7A TYR* 3.0 49.0 + + - +
8A GLU 3.3 15.9 + - - -
10A ALA* 4.0 3.6 - - + +
12A PHE* 3.7 36.0 - + + -
35A THR 2.9 15.1 + - - +
36A TRP* 3.9 4.6 - - + +
38A ASN* 1.3 78.7 - - - +
40A VAL* 1.3 58.0 + - - +
42A VAL* 4.3 3.6 - - - -
43A PHE* 3.0 58.2 + + + +
45A LYS* 4.4 18.1 - - + +
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Residues in contact with VAL 40 (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 TRP* 2.9 41.8 + - + +
37A ARG* 3.7 14.8 - - - +
39A HIS* 1.3 77.7 + - - +
41A ILE* 1.3 72.4 + - + +
44A ASN* 3.3 5.5 + - - -
45A LYS* 2.9 65.0 + - + +
46A ASP 3.9 1.6 - - - +
47A ILE* 3.7 37.5 - - + -
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Residues in contact with ILE 41 (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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37A ARG 3.6 17.9 - - - +
38A ASN 3.1 5.7 + - - +
40A VAL* 1.3 89.5 - - + +
42A VAL* 1.3 64.8 + - - +
43A PHE 3.2 0.2 - - - -
44A ASN* 3.2 13.0 + - - +
47A ILE* 4.9 7.9 - - + -
110A GLU* 4.4 11.7 - - + +
113A GLY* 3.5 31.0 - - - +
114A TYR* 3.7 29.4 - - + +
46B ASP* 4.7 9.2 - - - +
47B ILE* 4.5 12.6 - - + -
48B THR* 3.6 23.4 + - + +
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Residues in contact with VAL 42 (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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7A TYR* 4.5 0.2 - - + -
38A ASN* 3.0 40.2 + - - +
39A HIS* 3.9 3.8 - - - +
41A ILE* 1.3 77.2 - - - +
43A PHE* 1.3 92.2 + - + +
44A ASN 3.9 0.2 + - - -
113A GLY* 3.9 18.4 - - - +
116A LYS* 5.7 2.9 - - - -
117A ILE 4.2 2.9 - - - +
118A SER* 3.9 21.1 - - - +
46B ASP* 5.6 1.0 - - - +
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Residues in contact with PHE 43 (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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7A TYR* 3.5 21.3 - + + -
8A GLU* 3.5 50.0 - - + +
39A HIS* 3.0 53.4 + + + +
42A VAL* 1.3 96.2 - - + +
44A ASN* 1.3 72.2 + - - +
45A LYS* 3.3 24.0 + - + +
119A GLU* 5.8 0.9 - - - -
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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