Contacts of the helix formed by residues 5 - 19 (chain B) in PDB entry 1JAT
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 PRO 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ASN* 4.0 10.3 - - - +
34A TYR* 3.5 57.2 - - + +
57A TYR* 3.6 22.0 - - + -
3B LYS* 3.5 5.6 - - + +
4B VAL* 1.3 91.6 - - + +
6B ARG* 1.3 67.3 + - - +
7B ASN 3.3 1.1 - - - +
8B PHE* 3.0 11.3 + - + -
9B ARG* 2.9 19.9 + - - +
105B ARG* 4.5 2.2 - - - +
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Residues in contact with ARG 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL 3.7 1.2 + - - -
5B PRO* 1.3 69.7 - - - +
7B ASN* 1.3 88.1 + - - +
9B ARG* 3.1 2.5 + - - +
10B LEU* 2.9 45.2 + - + +
37B THR* 2.9 33.6 + - - +
38B MET 3.8 2.0 + - - -
39B THR* 3.5 11.9 + - - -
64B CYS 2.8 24.4 + - - -
65B GLY 2.8 20.7 + - - -
66B PRO* 3.5 25.0 - - - +
68B TYR* 3.3 24.4 + - - +
69B PRO* 4.3 8.1 - - - -
105B ARG* 4.4 4.0 - - - +
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Residues in contact with ASN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.8 8.8 + - - +
55A GLU* 3.0 41.5 + - - +
70A ARG* 3.5 18.2 + - - +
72A LEU* 4.4 5.3 - - - +
5B PRO* 3.3 1.2 - - - +
6B ARG* 1.3 109.3 + - - +
8B PHE* 1.3 58.1 + - + +
10B LEU* 4.7 0.4 - - - -
11B LEU* 3.0 31.7 + - - +
37B THR* 4.7 1.6 - - - +
38B MET* 3.4 10.0 - - - +
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Residues in contact with PHE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.9 17.9 - + - -
55A GLU* 3.5 42.2 - - + -
56A LEU 4.0 0.7 - - - -
57A TYR* 3.6 29.2 - + + -
68A LYS* 3.5 53.2 - - + +
69A VAL* 3.8 7.4 - - - -
70A ARG* 4.4 0.2 - - + -
4B VAL* 3.9 15.0 - - + -
5B PRO* 3.0 12.3 + - + +
7B ASN* 1.3 77.2 - - + +
9B ARG* 1.3 60.4 + - - +
11B LEU* 3.4 26.1 + - + +
12B GLU* 3.0 32.1 + - - +
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Residues in contact with ARG 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 3.6 21.9 - - + +
5B PRO 2.9 15.6 + - - +
6B ARG* 3.6 8.1 - - - +
8B PHE* 1.3 75.8 - - - +
10B LEU* 1.3 64.4 + - + +
12B GLU* 3.2 24.6 + - - +
13B GLU* 3.0 52.2 + - - +
68B TYR* 3.2 10.8 + - + -
69B PRO* 3.5 27.8 - - + +
105B ARG* 2.9 28.0 + - - +
106B ALA* 4.2 7.1 + - - +
107B TYR 2.6 26.2 + - - -
108B THR* 3.6 11.8 - - - +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 2.9 59.5 + - + +
7B ASN 3.8 4.3 - - - +
9B ARG* 1.3 75.9 - - - +
11B LEU* 1.3 59.7 + - - +
13B GLU* 3.2 5.3 + - - +
14B LEU* 2.9 29.1 + - - +
37B THR 4.2 1.8 - - - +
38B MET* 3.6 28.3 - - + +
41B TRP* 3.9 24.3 - - + +
64B CYS* 4.0 15.3 - - + -
68B TYR* 3.5 31.2 - - + -
109B MET* 4.2 5.8 - - + -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL 5.3 0.9 - - - +
70A ARG* 3.6 34.1 - - + +
83A LEU* 5.1 2.2 - - + +
85A ARG* 4.3 28.5 - - + -
7B ASN 3.0 18.7 + - - +
8B PHE* 3.7 34.8 - - + +
10B LEU* 1.3 76.7 - - - +
12B GLU* 1.3 61.1 + - + +
14B LEU* 3.4 8.6 + - + +
15B GLU* 3.0 34.7 + - + +
38B MET* 3.6 24.5 - - + -
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 5.6 1.2 - - - -
68A LYS* 3.7 28.0 + - + +
4B VAL* 3.7 24.5 - - - +
8B PHE* 3.0 22.5 + - - +
9B ARG* 3.2 29.7 - - - +
10B LEU 3.2 0.2 - - - -
11B LEU* 1.3 78.9 - - - +
13B GLU* 1.3 63.6 + - + +
15B GLU* 3.4 7.0 + - - +
16B LYS* 3.2 21.7 + - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 3.0 34.5 + - - +
10B LEU* 3.2 7.6 + - - +
12B GLU* 1.3 74.6 - - + +
14B LEU* 1.3 59.8 + - - +
16B LYS* 3.3 4.3 + - + -
17B GLY 2.8 15.4 + - - -
28B TYR* 2.7 33.1 + - - +
68B TYR* 2.7 30.0 + - - -
108B THR* 3.3 18.1 - - + -
109B MET* 2.9 49.5 + - + +
110B GLU 4.4 0.9 + - - -
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.3 32.8 - - + -
85A ARG* 3.7 20.9 - - - +
10B LEU 2.9 17.1 + - - +
11B LEU* 3.5 15.5 - - + +
12B GLU 3.3 0.2 - - - -
13B GLU* 1.3 77.7 - - - +
15B GLU* 1.3 56.6 + - - +
17B GLY* 3.0 3.2 + - - -
18B GLU* 2.8 51.7 + - + +
28B TYR* 4.8 0.4 - - - -
29B GLY* 5.2 3.6 - - - -
30B LEU* 4.2 18.6 - - + +
38B MET* 4.6 2.9 - - - -
41B TRP* 3.8 26.4 - - + -
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 3.2 30.5 + - - +
11B LEU* 3.0 21.0 + - + +
12B GLU* 3.7 7.4 - - - +
14B LEU* 1.3 75.5 - - - +
16B LYS* 1.3 62.5 + - - +
18B GLU* 3.3 19.3 + - - +
19B LYS* 3.3 39.2 + - - +
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLU 3.2 11.5 + - - +
13B GLU* 3.6 10.3 - - - +
14B LEU 3.2 0.2 - - - -
15B GLU* 1.3 79.9 - - - +
17B GLY* 1.3 61.7 + - - +
19B LYS* 3.6 22.8 - - - +
28B TYR* 4.0 8.3 - - + +
110B GLU* 2.8 34.0 + - - +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU 2.8 15.7 + - - -
14B LEU* 3.0 4.2 + - - -
16B LYS* 1.3 76.5 - - - +
18B GLU* 1.3 63.3 + - - +
19B LYS 3.6 4.7 + - - -
27B SER* 6.0 1.0 - - - -
28B TYR* 3.7 36.3 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 2.9 43.6 + - - -
14B LEU* 2.8 31.6 + - + +
15B GLU* 3.3 16.0 + - - +
17B GLY* 1.3 74.7 - - - +
19B LYS* 1.3 64.7 + - + +
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 3.3 38.4 + - - +
16B LYS* 3.6 18.5 - - - +
17B GLY 3.3 4.9 - - - -
18B GLU* 1.3 82.5 - - + +
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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