Contacts of the helix formed by residues 5 - 23 (chain A) in PDB entry 1JHH
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 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ALA 5.4 0.4 - - - +
4A LEU* 1.3 77.8 - - - +
6A ALA* 1.3 64.8 + - - +
7A ARG* 3.5 6.6 + - - +
8A GLN* 3.0 45.8 + - - +
9A GLN* 3.0 20.1 + - - +
46A HIS* 5.9 0.2 - - - -
53A LYS* 5.1 3.4 - - - +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU 3.9 0.2 + - - -
5A THR* 1.3 73.2 - - - +
7A ARG* 1.3 62.3 + - - +
9A GLN* 3.4 7.8 + - - +
10A GLU* 3.2 28.2 + - - +
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Residues in contact with ARG 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 3.2 6.2 + - - +
6A ALA* 1.3 78.3 - - - +
8A GLN* 1.3 64.5 + - - +
10A GLU* 3.1 24.4 + - + +
11A VAL* 3.0 21.4 + - - +
35A LEU 5.7 1.8 + - - -
37A PHE* 3.6 31.3 - - + -
38A ARG* 2.9 32.1 - - - +
46A HIS* 3.6 30.3 + - + +
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Residues in contact with GLN 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 6.9 - - + +
5A THR* 3.0 45.0 + - - +
7A ARG* 1.3 76.7 - - - +
9A GLN* 1.3 57.5 + - - +
11A VAL* 3.2 8.4 + - - +
12A PHE* 2.8 30.8 + - - +
46A HIS* 4.3 19.5 + - + +
49A ALA* 3.5 27.7 - - + +
50A LEU* 3.8 23.4 - - + +
52A ARG* 5.2 1.8 - - - +
53A LYS* 3.2 25.2 + - - +
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Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.8 27.9 + - + +
5A THR 3.0 14.6 + - - +
6A ALA* 3.4 12.3 - - - +
8A GLN* 1.3 78.2 - - - +
10A GLU* 1.3 52.6 + - + +
12A PHE* 3.3 4.0 + - - +
13A ASP* 2.7 70.9 + - - +
16A ARG* 3.5 10.7 + - - -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA* 3.2 13.2 + - - +
7A ARG* 3.1 33.4 + - - +
9A GLN* 1.3 76.7 - - + +
11A VAL* 1.3 64.2 + - - +
13A ASP* 3.4 6.5 + - - +
14A LEU* 3.1 23.6 + - - +
35A LEU* 4.2 22.7 - - + +
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG 3.0 15.5 + - - +
8A GLN* 3.2 7.2 + - - +
10A GLU* 1.3 75.3 - - - +
12A PHE* 1.3 63.6 + - - +
14A LEU* 3.2 4.9 + - - +
15A ILE* 3.0 25.5 + - + +
31A ILE* 4.2 14.6 - - + -
35A LEU* 3.7 22.7 - - + -
37A PHE* 3.9 19.7 - - + -
46A HIS* 3.9 20.9 - - + -
47A LEU* 4.0 18.8 - - + -
50A LEU* 3.9 17.7 - - + -
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Residues in contact with PHE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.9 23.8 - - + -
8A GLN 2.8 17.7 + - - +
9A GLN* 3.6 6.3 - - - +
11A VAL* 1.3 77.7 - - - +
13A ASP* 1.3 60.6 - - - +
15A ILE* 3.3 4.9 + - + +
16A ARG* 3.1 68.0 + - + +
50A LEU* 4.0 10.1 - - + +
55A VAL* 3.8 44.2 - - + -
56A ILE* 4.2 8.1 - - + -
68A LEU* 3.9 25.4 - - + -
69A LEU 5.8 1.8 - - - -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 2.7 43.5 + - - +
10A GLU* 3.9 6.9 - - - +
12A PHE* 1.3 73.4 - - - +
14A LEU* 1.3 59.9 + - - +
16A ARG* 2.6 34.5 + - - +
17A ASP* 2.9 38.8 + - - +
91A GLN* 3.5 24.9 + - + +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 3.1 17.2 + - - +
11A VAL* 3.2 4.9 + - - +
13A ASP* 1.3 77.8 - - - +
15A ILE* 1.3 58.2 + - + +
17A ASP* 3.4 8.4 + - + +
18A HIS* 2.9 40.6 + - + +
26A PRO* 5.0 7.4 - - + -
30A GLU 4.6 1.3 - - - +
31A ILE* 3.9 35.9 - - + -
34A ARG* 3.6 50.3 - - + +
35A LEU* 4.3 17.0 - - + -
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.0 22.1 + - + +
12A PHE* 3.6 8.3 - - + +
13A ASP 3.3 0.2 - - - -
14A LEU* 1.3 77.3 - - - +
16A ARG* 1.3 63.3 + - - +
18A HIS* 3.6 1.6 - - - +
19A ILE* 3.0 45.7 + - + +
25A PRO* 4.9 0.2 - - + -
26A PRO* 4.1 29.4 - - + -
31A ILE* 4.3 5.2 - - + -
47A LEU* 3.5 32.1 - - + -
50A LEU* 4.3 10.5 - - + -
56A ILE* 4.7 5.8 - - + -
66A ILE* 4.4 20.6 - - + -
68A LEU* 4.0 15.9 - - + -
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.5 11.7 + - - -
12A PHE* 3.1 56.4 + - + +
13A ASP* 2.6 29.8 + - - +
15A ILE* 1.3 75.8 - - - +
17A ASP* 1.3 57.5 + - - +
19A ILE* 3.2 7.6 + - - +
20A SER* 2.8 36.2 + - - +
68A LEU* 4.2 19.3 - - + -
91A GLN* 2.9 40.7 + - - +
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 2.9 25.3 + - - +
14A LEU* 3.8 10.9 - - + +
16A ARG* 1.3 75.6 - - - +
18A HIS* 1.3 57.4 + - - +
20A SER* 3.3 8.0 + - - -
21A GLN* 3.0 31.7 + - - +
34A ARG* 6.2 0.9 - - - +
86A GLU* 4.6 8.4 - - - +
87A PRO* 3.8 8.7 - - + +
89A LEU 4.5 1.0 - - - +
90A ALA* 3.4 15.5 - - - +
91A GLN* 3.0 36.1 + - - +
92A GLN* 4.8 6.8 + - - +
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Residues in contact with HIS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.9 27.6 + - + +
15A ILE 3.6 4.3 - - - +
17A ASP* 1.3 75.7 - - - +
19A ILE* 1.3 56.9 + - - +
21A GLN* 4.8 6.1 - - - +
22A THR* 2.6 66.0 + - + +
24A MET* 3.0 22.7 + - + -
25A PRO 4.0 2.7 - - - -
26A PRO* 3.7 29.3 - - + -
30A GLU* 3.4 26.2 + - + -
34A ARG* 5.8 7.0 - - - -
64A ARG* 4.0 6.1 - - - -
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.0 28.4 + - + +
16A ARG* 3.7 4.3 - - - +
18A HIS* 1.3 74.6 - - - +
20A SER* 1.3 60.3 + - - +
23A GLY* 2.6 40.9 + - - +
24A MET 3.6 17.5 - - - +
25A PRO* 3.9 22.7 - - + -
66A ILE* 5.3 1.3 - - + +
67A ARG* 6.0 0.2 - - - -
68A LEU* 3.7 39.5 - - + +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 2.8 22.3 + - - +
17A ASP* 3.6 7.1 - - - -
19A ILE* 1.3 78.4 - - - +
21A GLN* 1.3 56.4 + - - +
87A PRO* 4.0 20.8 - - - +
89A LEU* 4.5 21.8 + - - +
135A LYS* 5.5 8.6 + - - +
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 3.0 16.4 + - - +
18A HIS* 4.1 6.1 - - - +
20A SER* 1.3 80.3 - - - +
22A THR* 1.3 72.0 + - + +
23A GLY 3.8 0.2 - - - -
85A GLY 3.1 24.6 + - - +
86A GLU* 4.7 0.7 - - - +
87A PRO* 3.5 26.1 - - + +
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 2.6 41.8 + - + +
21A GLN* 1.3 96.0 - - + +
23A GLY* 1.3 59.9 + - - +
24A MET* 3.0 38.9 + - - +
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 2.6 36.0 + - - +
20A SER 4.7 0.2 - - - -
21A GLN 3.8 0.2 - - - -
22A THR* 1.3 73.0 - - - +
24A MET* 1.3 59.5 + - - +
25A PRO* 4.8 0.2 - - - +
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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
------------------------------------------------------------
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