Contacts of the helix formed by residues 52 - 68 (chain V) in PDB entry 1J0B
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 GLY 52 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43V ASP 3.2 19.5 + - - +
44V ASP* 4.3 1.8 - - - +
46V THR* 2.8 24.2 + - - +
51V GLY* 1.3 75.4 - - - -
53V ASN* 1.3 65.0 + - - -
54V LYS* 3.2 4.3 + - - -
55V ILE* 3.4 10.5 + - - +
56V ARG 4.2 1.0 + - - -
308V THR 3.8 14.6 - - - -
309V GLY* 4.1 2.7 - - - -
310V GLY 5.1 0.4 - - - -
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Residues in contact with ASN 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43V ASP 3.9 1.2 + - - -
52V GLY* 1.3 71.7 - - - -
54V LYS* 1.3 92.1 + - - +
55V ILE 3.4 0.2 + - - -
56V ARG* 3.4 9.2 + - - +
57V LYS* 3.6 7.4 + - - +
82V ASN* 5.9 0.7 - - - +
167V TYR* 2.9 47.7 - - + +
194V THR* 3.0 18.0 + - - +
308V THR* 3.3 31.0 + - + +
1221V 5PA 3.6 34.5 + - - -
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Residues in contact with LYS 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52V GLY* 3.2 1.4 - - - -
53V ASN* 1.3 101.4 + - - +
55V ILE* 1.3 53.6 + - + +
57V LYS* 2.8 17.3 + - + +
58V LEU* 2.7 43.8 + - + +
82V ASN* 5.1 2.2 - - + -
83V HIS* 3.4 36.1 - - + +
86V VAL* 3.8 20.9 - - + -
157V GLY* 2.7 32.0 + - - +
1221V 5PA 3.5 54.2 + - - +
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Residues in contact with ILE 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V LEU* 3.7 22.2 - - + -
18V ILE* 3.6 24.0 - - + -
46V THR* 4.0 12.3 - - - +
48V LEU* 3.8 29.2 - - + +
51V GLY* 3.4 33.9 - - - +
52V GLY 3.5 9.0 - - - +
53V ASN 3.2 0.6 - - - -
54V LYS* 1.3 73.3 - - + +
56V ARG* 1.3 64.7 + - - +
57V LYS 2.8 6.3 + - - -
58V LEU* 3.2 15.7 + - + +
59V GLU* 3.2 14.0 + - - +
86V VAL* 3.5 24.0 - - + -
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Residues in contact with ARG 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V ILE* 3.2 35.5 - - + +
22V THR* 2.9 19.4 + - - +
41V LYS* 3.3 7.1 - - - +
43V ASP* 2.6 44.6 + - - +
46V THR* 4.5 7.9 - - + -
52V GLY 5.1 0.4 - - - +
53V ASN 3.4 11.1 + - - +
54V LYS 3.3 0.4 - - - -
55V ILE* 1.3 78.6 - - - +
57V LYS* 1.3 58.8 + - - +
59V GLU* 3.9 14.5 - - - +
60V TYR* 4.0 4.2 - - - -
166V GLY* 3.3 40.5 - - - +
167V TYR* 3.9 12.6 - - + +
169V ARG* 5.8 7.9 - - - +
170V ALA* 3.8 15.8 - - - +
173V GLU* 3.1 32.7 + - - -
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Residues in contact with LYS 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53V ASN* 3.6 12.5 + - - +
54V LYS* 2.8 21.2 + - + +
55V ILE 2.8 1.4 - - - -
56V ARG* 1.3 78.7 - - - +
58V LEU* 1.3 63.6 + - + +
59V GLU 3.1 2.7 + - - -
60V TYR* 3.2 6.4 + - - +
61V LEU* 2.9 34.3 + - + +
83V HIS* 6.0 0.4 - - + -
157V GLY 3.6 19.1 - - - +
158V GLY 4.2 9.6 - - - +
163V GLY* 3.5 26.5 - - - +
164V THR* 4.9 2.5 - - - +
167V TYR* 3.8 16.8 - - + -
193V GLY* 3.6 15.0 - - - -
194V THR* 3.0 46.4 + - - +
1221V 5PA 3.8 3.8 + - - -
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Residues in contact with LEU 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V LEU* 4.1 7.0 - - + -
54V LYS* 2.7 43.7 + - + +
55V ILE* 3.2 9.1 + - + +
57V LYS* 1.3 74.2 - - + +
59V GLU* 1.3 60.4 + - - +
61V LEU* 3.9 8.1 - - + -
62V LEU* 2.5 67.1 + - + +
83V HIS* 5.1 2.2 - - + +
86V VAL* 3.7 21.3 - - + -
87V THR* 3.4 39.9 - - + +
90V ALA* 4.4 7.0 - - + -
154V ILE* 4.2 7.4 - - + -
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Residues in contact with GLU 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V ARG* 2.6 39.3 + - - -
15V VAL* 3.0 32.1 + - - +
16V GLU* 3.4 6.1 - - - +
17V LEU* 2.9 35.9 + - + +
18V ILE* 3.2 29.1 + - + +
55V ILE 3.2 16.3 + - - +
56V ARG* 3.9 10.3 - - - +
57V LYS 3.1 0.4 - - - -
58V LEU* 1.3 74.9 - - - +
60V TYR* 1.3 58.9 + - + +
63V GLY* 2.9 22.9 + - - -
169V ARG* 4.3 7.4 - - - -
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Residues in contact with TYR 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V LEU* 4.3 14.8 + - + +
12V PHE* 4.1 21.8 - - + -
13V PRO 3.8 10.6 - - - +
14V ARG* 3.6 33.8 + - + -
56V ARG 4.0 9.0 - - - -
57V LYS 3.2 5.1 + - - +
59V GLU* 1.3 77.7 - - - +
61V LEU* 1.3 55.6 + - - +
63V GLY* 2.7 2.1 + - - -
64V ASP* 2.6 38.3 + - - +
162V ILE* 3.4 35.8 - - + +
163V GLY 4.9 0.4 - - - -
165V LEU* 3.5 40.2 + - + -
166V GLY* 3.9 12.3 - - - -
169V ARG* 3.2 34.2 + - - +
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Residues in contact with LEU 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57V LYS* 2.9 35.0 + - + +
58V LEU* 3.9 9.4 - - + +
60V TYR* 1.3 70.7 - - - +
62V LEU* 1.3 63.6 + - - +
63V GLY 2.8 3.8 - - - -
64V ASP* 3.0 12.7 + - - -
65V ALA 3.2 6.8 + - - -
83V HIS* 5.0 2.0 - - - +
152V TYR* 3.7 25.1 + - - +
154V ILE* 4.0 26.9 - - + -
155V PRO* 5.2 1.8 - - + -
158V GLY* 3.6 33.7 - - - +
160V SER* 3.6 10.5 - - - +
162V ILE* 3.2 28.7 - - + -
163V GLY* 3.8 6.1 - - - +
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Residues in contact with LEU 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V VAL* 4.3 2.7 - - + -
17V LEU* 5.2 6.3 - - + -
58V LEU* 2.5 41.0 + - + +
61V LEU* 1.3 75.3 - - - +
63V GLY* 1.3 54.6 + - - -
64V ASP 3.2 0.2 - - - -
65V ALA* 3.0 27.7 + - + +
66V LEU* 3.5 15.1 - - - +
73V VAL* 3.9 29.4 - - + -
87V THR 4.3 2.0 - - - +
90V ALA* 3.3 36.3 - - + -
91V ALA* 3.7 14.6 - - + +
94V LEU* 4.2 20.0 - - + -
96V LEU* 5.2 2.0 - - + -
154V ILE* 4.2 10.1 - - + -
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Residues in contact with GLY 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V PRO* 4.6 12.4 - - - +
14V ARG* 4.7 0.2 - - - -
15V VAL* 3.5 16.1 - - - +
59V GLU 2.9 20.8 + - - -
60V TYR* 2.7 11.7 + - - -
62V LEU* 1.3 80.2 - - - +
64V ASP* 1.3 56.9 + - - +
65V ALA 3.2 0.6 + - - -
66V LEU* 4.4 3.6 + - - +
67V SER* 3.3 23.6 + - - -
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Residues in contact with ASP 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V PRO* 5.4 6.4 - - + +
60V TYR 2.6 15.7 + - - +
61V LEU* 3.0 6.7 + - - +
63V GLY* 1.3 72.3 - - - +
65V ALA* 1.3 68.2 + - - +
67V SER* 4.0 10.3 - - - -
68V LYS* 3.2 54.7 + - - +
152V TYR* 3.5 20.8 + - - +
162V ILE* 5.0 15.4 - - + +
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Residues in contact with ALA 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61V LEU 3.2 4.5 + - - +
62V LEU* 3.0 27.3 + - + +
64V ASP* 1.3 75.1 - - - +
66V LEU* 1.3 70.0 - - - +
68V LYS* 2.7 18.0 + - - +
69V GLY 3.2 5.7 + - - -
70V ALA* 3.9 8.9 + - + +
73V VAL* 5.1 0.4 - - + -
96V LEU* 3.9 22.9 - - + -
152V TYR* 3.8 27.6 - - + -
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Residues in contact with LEU 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V VAL* 3.5 33.0 - - + -
62V LEU 3.5 10.1 - - - +
63V GLY 4.6 2.2 - - - +
65V ALA* 1.3 71.4 - - + +
67V SER* 1.3 55.7 + - - +
69V GLY* 2.4 31.6 + - - +
70V ALA 4.9 2.7 - - - +
94V LEU* 3.6 29.4 - - + +
96V LEU* 3.7 34.5 - - + +
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Residues in contact with SER 67 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V PRO* 3.7 23.4 - - - +
63V GLY 3.3 19.7 + - - -
64V ASP* 4.0 14.4 - - - -
65V ALA 3.1 0.2 + - - -
66V LEU* 1.3 77.1 - - - +
68V LYS* 1.3 59.6 + - - +
69V GLY 3.3 1.0 + - - -
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Residues in contact with LYS 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64V ASP* 3.2 46.9 + - - +
65V ALA 2.7 8.6 + - - +
67V SER* 1.3 75.8 - - - +
69V GLY* 1.3 70.7 + - - +
70V ALA* 4.9 1.3 - - + +
150V LYS* 4.5 4.0 + - - +
152V TYR* 4.6 13.1 - - + -
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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
------------------------------------------------------------
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