Contacts of the helix formed by residues 42 - 58 (chain A) in PDB entry 1J1U
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 HIS 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A SER* 5.3 1.1 - - - -
40A LYS* 4.1 7.9 - - + -
41A ILE* 1.3 76.1 - - - +
43A LEU* 1.3 68.4 + - - +
44A GLY* 3.1 32.5 + - - -
45A HIS* 3.0 42.2 + + - +
46A TYR 3.0 9.5 + - - -
212A PHE* 3.6 39.9 - + + +
213A ILE 3.1 17.5 - - - +
214A ALA* 4.1 0.2 - - - +
215A VAL* 3.8 9.1 - - - +
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Residues in contact with LEU 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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42A HIS* 1.3 76.9 + - - +
44A GLY* 1.3 56.6 + - - +
46A TYR* 3.6 5.6 - - + +
47A LEU* 2.8 26.9 + - - +
196A LEU* 3.8 12.6 - - + -
213A ILE* 3.2 38.2 + - + +
215A VAL* 4.6 4.0 - - + -
244A ILE* 3.9 32.5 - - + -
248A PHE* 3.2 32.4 - - + -
295A LEU* 4.1 25.4 - - + -
299A LEU* 4.4 17.5 - - + -
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 3.1 18.8 + - - -
43A LEU* 1.3 80.5 - - - +
45A HIS* 1.3 61.4 + - - +
47A LEU* 3.3 5.6 + - - +
48A GLN* 3.2 29.5 + - - +
196A LEU* 3.7 18.7 - - - +
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Residues in contact with HIS 45 (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 PHE* 3.6 41.1 - + + -
36A GLU 5.1 3.2 + - - -
38A SER* 4.0 14.6 - - - -
40A LYS 3.8 17.3 - - - -
41A ILE* 3.7 32.8 - - + +
42A HIS* 3.0 48.6 + + - +
44A GLY* 1.3 73.7 - - - +
46A TYR* 1.3 60.7 + - - +
48A GLN* 3.1 4.0 + - - +
49A ILE* 2.8 31.6 + - - +
93A PHE* 4.2 9.2 - + + -
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Residues in contact with TYR 46 (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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42A HIS 3.0 10.1 + - - +
43A LEU* 3.1 10.5 + - + +
45A HIS* 1.3 77.5 - - - +
47A LEU* 1.3 65.8 + - - +
49A ILE* 4.8 1.8 - - + -
50A LYS* 2.8 47.9 + - + +
53A ILE* 6.0 0.7 - - + -
96A MET* 3.6 53.5 + - + -
215A VAL* 4.1 5.2 - - + -
248A PHE* 3.7 22.4 - + + -
295A LEU* 6.2 0.2 - - + -
298A ILE* 4.0 31.0 + - + +
299A LEU* 4.0 19.5 - - + -
302A ILE* 3.8 12.7 - - + +
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Residues in contact with LEU 47 (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 ASN* 5.2 9.2 - - + +
43A LEU 2.8 13.9 + - - +
44A GLY* 3.5 11.0 - - - +
45A HIS 3.2 0.2 - - - -
46A TYR* 1.3 78.0 - - - +
48A GLN* 1.3 61.2 + - + +
50A LYS* 3.4 12.1 + - - +
51A LYS* 3.2 19.6 + - - +
193A ASN* 4.8 10.8 - - + +
194A PRO* 4.0 38.8 - - + +
196A LEU* 4.1 20.4 - - + -
247A TYR* 3.8 36.8 - - + +
248A PHE* 3.7 9.3 - - + -
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Residues in contact with GLN 48 (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 ILE* 3.5 25.6 - - + +
35A PHE* 4.1 15.7 - - + -
44A GLY 3.2 16.3 + - - +
45A HIS* 3.1 6.3 + - - +
47A LEU* 1.3 75.1 - - + +
49A ILE* 1.4 68.1 + - - +
51A LYS* 2.9 5.0 + - - +
52A MET* 2.9 26.6 + - - +
169A GLY* 3.0 20.8 - - - -
170A GLY* 3.5 21.0 - - - +
193A ASN* 2.8 39.4 + - + +
194A PRO 6.1 0.2 - - - +
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Residues in contact with ILE 49 (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 PHE* 3.9 20.6 - - + -
45A HIS 2.8 18.8 + - - +
46A TYR* 3.8 2.5 - - + +
48A GLN* 1.4 78.3 - - - +
50A LYS* 1.3 62.7 + - - +
52A MET* 3.1 7.3 + - + +
53A ILE* 3.0 26.3 + - + +
64A ILE* 4.2 8.3 - - + -
93A PHE* 3.6 39.0 - - + +
96A MET* 3.7 31.0 - - + -
98A LEU* 3.9 39.5 - - + -
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Residues in contact with LYS 50 (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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46A TYR* 2.8 55.9 + - + +
47A LEU* 3.5 13.7 - - - +
49A ILE* 1.3 76.2 - - - +
51A LYS* 1.3 58.3 + - - +
53A ILE* 3.2 15.7 + - + +
54A ASP* 2.9 33.7 + - - +
247A TYR 3.1 26.9 + - - -
248A PHE* 4.0 20.6 + - + +
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Residues in contact with LYS 51 (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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6A MET 3.3 7.5 + - - -
7A ILE* 2.7 37.4 + - + +
9A ARG* 2.8 24.2 + - - +
10A ASN* 5.3 2.2 - - - -
11A THR* 3.6 12.1 - - + -
47A LEU* 3.2 12.2 + - - +
48A GLN 2.9 10.8 + - - +
50A LYS* 1.3 77.7 - - - +
52A MET* 1.3 62.2 + - - +
54A ASP* 2.7 27.9 + - + +
55A LEU* 3.0 26.6 + - + +
168A VAL* 4.4 11.9 - - + -
191A ILE* 4.7 5.6 - - + -
193A ASN* 3.9 26.7 - - - +
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Residues in contact with MET 52 (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 ALA* 4.0 9.0 - - + -
32A TYR* 3.6 38.1 - - - +
33A ILE* 3.7 21.5 - - + +
48A GLN 2.9 16.6 + - - +
49A ILE* 3.1 11.9 + - - +
51A LYS* 1.3 77.7 - - - +
53A ILE* 1.3 57.3 + - - +
55A LEU* 3.3 5.1 + - + -
56A GLN* 2.8 24.1 + - - +
62A ILE* 3.4 28.9 - - + +
64A ILE* 4.1 7.2 - - + -
98A LEU* 4.1 15.3 - - + -
168A VAL* 3.5 39.7 - - + -
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Residues in contact with ILE 53 (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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46A TYR* 6.0 0.9 - - + -
49A ILE* 3.0 28.9 + - + +
50A LYS* 3.2 16.6 + - + +
52A MET* 1.3 74.7 - - - +
54A ASP* 1.3 55.6 + - - +
56A GLN* 3.1 11.8 + - - +
57A ASN* 2.7 53.5 + - - +
96A MET 3.8 22.2 - - - +
97A GLY* 4.0 17.0 - - - +
98A LEU* 4.1 17.9 - - + -
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Residues in contact with ASP 54 (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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6A MET* 3.4 39.5 - - + +
7A ILE* 4.6 4.9 - - - -
9A ARG* 5.5 2.1 - - - +
50A LYS* 2.9 20.9 + - - +
51A LYS* 2.7 42.7 + - + +
53A ILE* 1.3 77.4 - - - +
55A LEU* 1.4 60.9 + - - +
57A ASN* 3.2 10.7 + - - -
58A ALA* 3.0 17.5 + - - +
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Residues in contact with LEU 55 (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 ILE* 3.6 31.0 - - + -
20A LEU* 5.4 0.4 - - + -
31A ALA* 4.0 11.9 - - + -
51A LYS* 3.0 22.9 + - + +
52A MET* 3.6 13.5 - - - +
53A ILE 3.2 0.2 - - - -
54A ASP* 1.4 71.8 - - - +
56A GLN* 1.3 67.7 + - - +
58A ALA* 2.9 11.7 + - - +
60A PHE* 3.1 56.5 + - + +
62A ILE* 3.9 9.0 - - + -
166A VAL* 4.6 1.8 - - + -
168A VAL* 3.5 32.8 - - + -
191A ILE* 4.1 11.4 - - + -
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Residues in contact with GLN 56 (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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52A MET 2.8 16.5 + - - +
53A ILE* 3.5 15.7 - - - +
55A LEU* 1.3 76.5 - - - +
57A ASN* 1.3 67.2 + - - +
59A GLY* 2.9 15.8 + - - -
60A PHE 3.5 19.9 + - - +
62A ILE* 3.8 17.5 - - + +
97A GLY 5.1 2.9 - - - +
98A LEU* 4.0 10.0 - - - +
99A LYS* 2.5 37.4 + - - +
100A ALA* 4.6 0.6 - - - +
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Residues in contact with ASN 57 (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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3A GLU* 4.6 2.3 - - - +
6A MET* 4.1 19.0 - - + +
53A ILE* 2.7 42.5 + - - +
54A ASP* 3.2 12.2 + - - +
56A GLN* 1.3 75.6 - - - +
58A ALA* 1.3 58.1 + - - +
59A GLY 3.3 1.8 + - - -
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Residues in contact with ALA 58 (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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3A GLU* 3.6 35.0 - - + +
6A MET* 3.8 17.9 - - + -
7A ILE* 3.8 23.1 - - + -
24A LEU* 4.5 1.3 - - + -
29A LYS* 3.5 17.8 + - - -
54A ASP 3.0 3.3 + - - +
55A LEU 2.9 9.6 + - - +
57A ASN* 1.3 76.4 - - - +
59A GLY* 1.3 59.7 + - - +
60A PHE* 3.5 4.5 - - + -
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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