Contacts of the helix formed by residues 4 - 24 (chain B) in PDB entry 2JJ7
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 SER 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B MET 3.7 1.8 + - - -
3B ALA* 1.3 76.3 - - - +
5B ARG* 1.3 64.5 - - - +
6B GLU* 3.4 16.8 + - - +
7B GLN* 3.0 25.5 + - - +
8B THR* 3.1 20.8 + - - -
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Residues in contact with ARG 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA 4.0 0.6 + - - -
4B SER* 1.3 72.7 - - - +
6B GLU* 1.3 89.9 + - - +
8B THR* 3.3 4.4 + - - -
9B MET* 3.1 55.5 + - - +
47B TYR* 3.4 40.8 - - + +
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER* 3.2 12.6 - - - +
5B ARG* 1.3 115.1 + - - +
7B GLN* 1.3 56.6 + - - +
9B MET* 3.5 7.1 + - - +
10B GLU* 3.0 29.6 + - - +
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Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 4.6 12.3 - - + -
4B SER* 3.0 25.6 + - - +
6B GLU* 1.3 75.2 - - - +
8B THR* 1.3 59.3 + - - +
10B GLU* 3.3 21.4 + - - +
11B ASN* 2.8 47.9 + - - +
14B LYS* 5.7 1.8 - - - +
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Residues in contact with THR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 3.8 16.1 + - - +
4B SER 3.1 14.4 + - - -
5B ARG* 3.8 8.0 - - - -
7B GLN* 1.3 75.8 - - - +
9B MET* 1.3 57.6 + - - +
11B ASN* 3.3 10.0 + - - +
12B ILE* 2.9 41.6 + - + +
39B VAL* 3.8 25.6 - - + -
43B MET* 4.7 8.1 - - + -
47B TYR* 4.2 16.6 - - + -
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Residues in contact with MET 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 3.1 62.0 + - - +
6B GLU* 3.8 5.8 - - - +
8B THR* 1.3 74.8 - - - +
10B GLU* 1.3 58.7 + - - +
12B ILE* 3.3 3.7 + - - +
13B LEU* 3.0 37.1 + - + +
47B TYR* 3.7 40.4 - - + +
48B PHE* 3.6 34.8 - - + -
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU 3.0 18.7 + - - +
7B GLN* 3.5 19.3 + - - +
9B MET* 1.3 73.8 - - - +
11B ASN* 1.3 60.3 + - - +
13B LEU* 3.1 9.4 + - - +
14B LYS* 2.9 56.0 + - - +
61B LYS* 3.2 33.2 + - - +
62B TYR* 4.4 0.2 + - - -
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Residues in contact with ASN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLN* 2.8 47.2 + - - +
8B THR* 3.4 12.6 - - - +
10B GLU* 1.3 72.4 - - - +
12B ILE* 1.3 58.2 + - - +
14B LYS* 3.5 16.0 + - - +
15B ALA* 3.0 28.1 + - - +
37B ALA* 3.8 21.5 + - + +
39B VAL* 5.3 3.2 - - + +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 2.9 36.6 + - + +
9B MET 3.6 6.3 - - - +
10B GLU 3.2 0.4 - - - -
11B ASN* 1.3 75.3 - - - +
13B LEU* 1.3 59.0 + - - +
15B ALA* 3.4 2.6 + - - +
16B ALA* 2.9 26.2 + - - +
33B ILE* 3.8 13.2 - - + +
37B ALA* 3.8 9.6 - - + -
39B VAL* 3.9 22.2 - - + -
43B MET 4.9 0.4 - - - -
44B ALA* 3.9 30.3 - - + +
47B TYR* 4.3 10.1 - - + -
48B PHE* 3.9 26.5 - - + -
54B LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B MET* 3.0 22.8 + - + +
10B GLU* 3.1 5.4 + - - +
12B ILE* 1.3 74.1 - - - +
14B LYS* 1.3 59.9 + - - +
16B ALA* 3.8 1.4 - - - +
17B LYS* 2.9 31.5 + - - +
48B PHE* 3.8 14.6 - - + -
54B LEU* 3.7 28.5 - - + +
57B GLU* 3.8 33.4 - - + +
58B VAL* 4.2 6.4 - - + +
61B LYS* 3.7 36.8 - - + -
62B TYR* 3.5 6.5 - - + +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLN* 5.7 1.6 - - - +
10B GLU* 2.9 44.5 + - + +
11B ASN* 3.7 15.8 + - - +
13B LEU* 1.3 75.2 - - - +
15B ALA* 1.3 61.7 + - - +
17B LYS* 3.6 4.8 + - - +
18B LYS* 3.1 23.4 + - - +
62B TYR* 3.3 21.7 + - + +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN 3.0 15.0 + - - +
12B ILE 3.5 9.2 - - - +
14B LYS* 1.3 77.1 - - - +
16B ALA* 1.3 57.5 + - - +
18B LYS* 3.2 5.6 + - - +
19B LYS* 2.9 32.8 + - - +
33B ILE* 3.5 25.6 - - - +
36B GLU* 3.7 14.6 - - + -
37B ALA* 3.6 16.6 - - + +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE 2.9 18.1 + - - +
13B LEU* 3.8 1.3 - - - +
15B ALA* 1.3 73.0 - - - +
17B LYS* 1.3 59.7 + - - +
20B PHE* 2.8 40.9 + - + -
33B ILE* 3.8 31.4 - - + +
54B LEU* 3.9 14.4 - - + -
58B VAL* 3.7 18.4 - - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU 2.9 17.6 + - - +
14B LYS* 3.6 6.1 - - - +
16B ALA* 1.3 75.4 - - - +
18B LYS* 1.3 55.7 + - - +
20B PHE* 4.0 1.8 - - - +
21B GLY 3.0 24.3 + - - -
58B VAL* 3.8 15.7 - - + +
62B TYR* 3.5 48.9 - - + -
96B GLU 3.9 5.1 + - - -
97B ASN* 2.8 39.9 + - - +
98B PRO* 5.1 0.4 - - - +
99B GLU* 3.2 45.9 + - + +
100B ILE* 4.8 1.8 - - + -
103B LEU* 5.1 0.4 - - - +
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Residues in contact with LYS 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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14B LYS 3.1 12.0 + - - +
15B ALA* 3.2 8.9 + - - +
17B LYS* 1.3 81.1 - - - +
19B LYS* 1.3 60.1 + - + +
21B GLY* 3.7 1.2 - - - -
22B GLU* 3.0 56.9 + - + +
36B GLU* 3.5 37.6 + - + +
99B GLU* 4.1 15.2 - - - +
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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 ALA 2.9 22.3 + - - +
18B LYS* 1.3 73.1 - - - +
20B PHE* 1.3 65.9 + - - +
22B GLU* 3.2 28.5 + - + +
23B ARG* 3.0 33.2 + - - +
28B THR* 3.3 23.5 + - + +
32B GLU* 4.2 27.9 - - + +
33B ILE* 4.0 9.0 - - + -
36B GLU* 3.9 39.7 + - + -
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Residues in contact with PHE 20 (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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16B ALA* 2.8 38.1 + - + +
17B LYS* 4.1 1.1 - - - +
19B LYS* 1.3 71.3 - - - +
21B GLY* 1.3 56.8 + - - +
24B GLY* 2.7 37.6 + - - -
25B TYR* 3.7 28.0 - + - -
28B THR* 3.6 27.7 + - + +
33B ILE* 3.9 19.7 - - + -
51B LYS* 3.7 29.8 - - + -
54B LEU* 4.3 1.8 - - + -
55B TYR* 3.7 36.3 - + + -
58B VAL* 4.2 7.4 - - + -
102B THR* 5.3 0.2 - - - +
103B LEU* 3.4 23.7 - - + +
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Residues in contact with GLY 21 (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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145A PHE* 3.4 26.3 - - - +
17B LYS 3.0 19.2 + - - -
18B LYS 3.7 0.4 - - - -
20B PHE* 1.3 77.0 - - - +
22B GLU* 1.3 60.9 + - - +
24B GLY 4.7 0.3 + - - -
99B GLU* 3.6 27.3 - - - +
102B THR* 3.9 11.1 - - - +
103B LEU* 4.4 7.2 - - - +
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Residues in contact with GLU 22 (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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144A PHE 5.3 0.5 - - - +
145A PHE* 3.5 41.6 - - + +
18B LYS* 3.0 49.3 + - + +
19B LYS* 3.2 34.1 + - + +
21B GLY* 1.3 79.2 - - - +
23B ARG* 1.3 67.9 + - + +
24B GLY 3.8 0.2 - - - -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE 5.2 2.7 - - - -
19B LYS* 3.0 19.0 + - + +
22B GLU* 1.3 85.5 - - + +
24B GLY* 1.3 65.5 + - - +
27B GLY* 3.3 37.1 + - - +
28B THR* 3.7 8.1 - - - +
32B GLU* 2.8 40.1 + - - +
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE 5.5 0.6 + - - -
20B PHE* 2.7 25.2 + - - -
21B GLY 4.6 1.2 + - - -
22B GLU 3.8 0.8 - - - -
23B ARG* 1.3 74.8 - - - +
25B TYR* 1.3 64.4 + - - -
26B GLU 3.4 1.1 - - - -
27B GLY 4.8 0.2 - - - -
28B THR* 2.5 29.5 + - - -
102B THR* 5.9 3.3 - - - +
103B LEU* 4.5 6.7 - - - -
106B GLU* 6.1 4.9 - - - -
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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
------------------------------------------------------------
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