Contacts of the helix formed by residues 23 - 43 (chain A) in PDB entry 4JUY
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 GLU 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET* 2.9 39.4 + - + +
21A PRO* 4.2 7.1 - - - +
22A GLY* 1.3 85.3 - - - +
24A GLU* 1.3 59.2 + - - +
25A GLU 3.4 2.7 - - - -
26A GLU* 3.0 29.6 + - + +
27A ARG* 3.0 27.5 + - - +
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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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20A MET 3.7 4.4 + - - +
22A GLY* 3.8 2.8 - - - +
23A GLU* 1.3 77.2 - - - +
25A GLU* 1.3 57.0 + - - +
27A ARG* 3.5 7.0 + - - +
28A ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 3.4 0.6 - - - -
24A GLU* 1.3 75.2 - - - +
26A GLU* 1.3 60.5 + - - +
28A ALA* 3.4 6.9 + - - +
29A PHE* 2.9 29.3 + - - +
59A SER* 5.7 5.8 - - - -
60A SER 6.4 0.2 - - - +
61A LEU* 4.5 10.7 - - + +
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Residues in contact with GLU 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 MET* 3.7 19.8 - - + +
23A GLU* 3.0 36.5 + - + +
25A GLU* 1.3 76.5 - - - +
27A ARG* 1.3 61.3 + - - +
29A PHE* 3.1 4.3 + - - +
30A LEU* 2.8 35.6 + - + +
61A LEU* 3.8 29.4 - - + +
65A ALA* 4.2 20.5 - - + +
207A UNX 3.9 18.7 + - - -
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Residues in contact with ARG 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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14A ASN* 2.7 46.3 + - - +
17A PHE* 2.7 32.8 + - + +
18A GLN 2.7 22.5 + - - +
19A GLY* 3.8 4.1 - - - +
20A MET* 3.7 39.9 - - + +
23A GLU 3.0 15.0 + - - +
24A GLU* 3.7 8.1 - - - +
26A GLU* 1.3 74.9 - - - +
28A ALA* 1.3 59.5 + - - +
30A LEU* 3.2 5.1 + - + +
31A VAL* 2.9 39.7 + - + +
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Residues in contact with ALA 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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14A ASN* 6.1 0.4 - - - -
24A GLU 3.0 18.1 + - - +
25A GLU* 3.6 8.1 - - - +
27A ARG* 1.3 77.5 - - - +
29A PHE* 1.3 61.8 + - - +
31A VAL* 4.0 6.1 - - - +
32A ALA* 3.1 24.4 + - - +
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Residues in contact with PHE 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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25A GLU 2.9 14.5 + - - +
26A GLU* 3.1 8.0 + - + +
28A ALA* 1.3 73.7 - - - +
30A LEU* 1.3 71.3 + - + +
32A ALA* 3.2 6.3 + - - +
33A ARG* 2.8 49.6 + - - +
55A PRO 5.0 1.1 - - - +
56A LEU* 3.3 56.4 - - + +
57A LEU* 6.4 0.2 - - + -
59A SER* 4.4 5.6 - - - +
61A LEU* 3.7 22.4 - - + -
65A ALA 3.9 5.2 - - - -
66A ARG* 3.5 48.5 - - + -
68A LEU* 6.3 0.2 - - + -
174A LEU* 4.9 8.1 - - + -
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Residues in contact with LEU 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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17A PHE* 3.9 29.8 - - + -
20A MET* 4.0 27.6 - - + -
26A GLU* 2.8 24.5 + - + +
27A ARG* 3.6 5.8 - - - +
29A PHE* 1.3 93.7 - - + +
31A VAL* 1.3 56.5 + - - +
33A ARG* 3.3 12.7 + - - +
34A GLU* 3.0 31.0 + - - +
65A ALA 4.5 3.6 - - - +
68A LEU* 4.0 15.3 - - + -
207A UNX 3.4 31.9 - - - +
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Residues in contact with VAL 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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13A GLU* 4.4 4.4 - - + +
14A ASN* 3.7 50.0 - - + +
17A PHE* 3.9 28.7 - - + -
27A ARG* 2.9 30.7 + - - +
28A ALA* 4.0 5.8 - - - +
30A LEU* 1.3 74.2 - - - +
32A ALA* 1.3 65.7 + - - +
34A GLU* 3.3 5.6 + - - +
35A GLU* 3.1 27.3 + - + +
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Residues in contact with ALA 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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28A ALA 3.1 18.8 + - - +
29A PHE* 3.7 4.7 - - - +
31A VAL* 1.3 77.7 - - - +
33A ARG* 1.3 61.6 + - - +
35A GLU* 3.3 8.5 + - - +
36A LEU* 3.2 27.8 + - + +
55A PRO* 6.3 0.9 - - + -
56A LEU* 4.0 24.5 - - + -
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Residues in contact with ARG 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 PHE* 2.8 39.4 + - + +
30A LEU* 3.3 15.6 + - - +
32A ALA* 1.3 77.3 - - - +
34A GLU* 1.3 84.1 + - - +
36A LEU 3.2 2.8 + - - -
37A ALA* 3.0 21.1 + - - +
56A LEU* 4.1 15.9 - - + +
66A ARG 4.4 4.4 + - - -
68A LEU* 4.0 27.0 - - - +
69A GLN* 4.9 0.2 - - - +
167A THR* 3.3 36.7 + - - +
170A LEU* 3.2 24.8 - - + +
171A GLU* 2.7 33.5 + - - +
174A LEU* 5.5 2.7 - - + +
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Residues in contact with GLU 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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13A GLU* 4.0 25.4 - - + +
17A PHE* 4.1 23.7 - - + -
30A LEU 3.0 17.1 + - - +
31A VAL 3.3 6.9 + - - +
33A ARG* 1.3 93.9 + - - +
35A GLU* 1.3 58.8 + - - +
37A ALA* 3.3 10.9 + - - +
38A SER* 2.8 34.6 + - - -
163A HIS* 5.9 1.0 + - - -
167A THR* 5.6 1.7 + - - -
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Residues in contact with GLU 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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11A GLY* 5.0 0.9 - - - -
12A ARG* 3.4 21.3 + - - +
13A GLU* 2.9 39.6 + - + +
14A ASN 4.5 0.5 + - - -
31A VAL* 3.1 19.9 + - + +
32A ALA* 3.7 10.1 - - - +
33A ARG 3.3 0.4 - - - -
34A GLU* 1.3 78.0 - - - +
36A LEU* 1.3 60.7 + - + +
38A SER* 3.4 5.0 + - - -
39A ALA* 2.9 27.8 + - - +
42A ARG* 4.5 15.4 + - - -
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Residues in contact with LEU 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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32A ALA* 3.2 10.1 + - + +
33A ARG 3.2 4.3 + - - +
35A GLU* 1.3 76.5 - - + +
37A ALA* 1.3 65.8 + - - +
39A ALA* 3.1 5.2 + - + +
40A LEU* 3.1 21.1 + - - +
48A PHE* 3.5 40.0 - - + -
52A GLN* 4.1 20.6 - - + +
53A LEU* 4.0 18.8 - - + -
56A LEU* 3.7 40.2 - - + -
170A LEU* 3.7 19.5 - - + -
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Residues in contact with ALA 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 ARG* 3.0 15.7 + - + +
34A GLU* 3.5 19.3 - - - +
36A LEU* 1.3 75.6 - - - +
38A SER* 1.3 62.2 + - - +
40A LEU* 3.2 12.6 + - - +
41A ARG* 3.1 24.9 + - - +
163A HIS 5.6 0.2 - - - +
166A ALA* 3.7 23.5 - - + +
167A THR* 4.5 7.2 - - - +
170A LEU* 3.9 11.9 - - + +
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Residues in contact with SER 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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12A ARG* 5.4 2.0 + - - -
13A GLU* 3.4 18.9 + - - -
34A GLU* 2.8 23.2 + - - -
35A GLU* 3.6 9.4 - - - -
37A ALA* 1.3 72.7 - - - +
39A ALA* 1.3 57.6 + - - +
41A ARG* 3.2 32.4 + - - +
42A ARG* 2.9 48.2 + - - +
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Residues in contact with ALA 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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35A GLU 2.9 14.3 + - - +
36A LEU* 3.1 10.7 + - + +
38A SER* 1.3 77.4 - - - +
40A LEU* 1.3 57.0 + - - +
42A ARG* 3.2 23.2 + - - +
43A ASP* 2.9 28.1 + - - +
46A GLN* 4.2 15.4 - - + +
48A PHE* 4.0 20.0 - - + -
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Residues in contact with LEU 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 LEU 3.1 17.3 + - - +
37A ALA* 3.5 7.0 - - - +
39A ALA* 1.3 73.2 - - - +
41A ARG* 1.3 64.4 + - - +
43A ASP 3.1 22.1 - - - +
44A SER* 3.2 13.3 + - - +
46A GLN* 4.3 1.8 - - + +
48A PHE* 4.0 18.6 - - + -
103A ARG* 3.4 45.3 - - + +
106A LEU* 4.1 17.4 - - + +
166A ALA* 3.7 23.8 - - + +
169A THR* 4.3 10.3 - - + -
170A LEU* 4.0 21.5 - - + +
173A LEU* 5.1 2.0 - - + -
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Residues in contact with ARG 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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13A GLU* 5.1 3.0 + - - -
37A ALA* 3.1 12.2 + - - +
38A SER* 3.2 36.3 + - - +
40A LEU* 1.3 73.5 - - - +
42A ARG* 1.3 66.1 + - - +
44A SER 5.0 0.7 + - - -
106A LEU* 4.6 12.3 - - + +
162A GLU* 3.4 65.6 + - + +
163A HIS* 3.3 33.9 + - - +
166A ALA* 3.6 15.8 - - + +
205A UNX 3.7 18.6 + - - -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 3.8 25.7 - - - +
35A GLU* 4.5 11.3 + - - -
38A SER* 2.9 32.5 + - - +
39A ALA* 3.2 37.0 + - - +
41A ARG* 1.3 77.9 - - - +
43A ASP* 1.3 62.4 + - + +
46A GLN* 6.1 0.2 - - - +
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Residues in contact with ASP 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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39A ALA 2.9 9.7 + - - +
40A LEU* 3.1 9.3 - - - +
41A ARG 3.3 0.2 - - - -
42A ARG* 1.3 81.4 - - + +
44A SER* 1.3 59.8 + - - +
45A GLY* 2.9 15.8 + - - -
46A GLN* 3.0 49.9 + - + +
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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