Contacts of the helix formed by residues 3 - 19 (chain B) in PDB entry 2J3T
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 ASP 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A SER* 5.0 0.2 + - - -
19A PHE* 5.6 0.2 - - - +
62A ARG* 2.8 35.5 + - - -
85A MET 3.4 20.3 + - - +
86A TYR* 2.9 21.7 + - + -
2B ALA* 1.3 79.9 - - - +
4B THR* 1.3 68.9 + - - +
5B VAL* 2.6 43.2 + - - +
6B LEU* 3.4 14.5 + - + +
7B PHE* 4.0 3.5 + - - +
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Residues in contact with THR 4 (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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2B ALA 4.5 0.2 - - - -
3B ASP* 1.3 80.2 + - - +
5B VAL* 1.3 64.4 + - + +
7B PHE* 3.2 21.9 + - + +
8B GLU* 3.2 23.8 + - + +
77B VAL 5.6 1.3 - - - +
79B GLN* 3.4 37.8 + - - +
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Residues in contact with VAL 5 (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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55A LEU* 3.8 7.0 - - + -
58A ASP* 3.6 14.6 - - - +
62A ARG* 4.3 3.6 - - - +
86A TYR* 3.3 31.4 - - + -
3B ASP* 2.6 29.2 + - - +
4B THR* 1.3 73.7 - - - +
6B LEU* 1.3 58.4 + - - +
8B GLU* 3.3 14.0 - - - +
9B PHE* 2.8 44.6 + - + +
111C LYS* 3.8 30.5 - - - +
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Residues in contact with LEU 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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19A PHE* 3.9 19.2 - - + -
51A ILE* 5.2 7.2 - - + +
55A LEU* 4.0 18.2 - - + -
86A TYR* 2.9 60.1 - - + +
87A LEU* 4.0 4.5 - - + -
1068A PLM 3.9 33.2 - - + -
2B ALA* 3.8 12.1 - - + -
3B ASP 3.4 9.2 + - - +
4B THR 3.2 0.6 - - - -
5B VAL* 1.3 82.4 - - - +
7B PHE* 1.3 57.4 + - - +
9B PHE* 4.1 2.7 - - - +
10B LEU* 2.9 30.5 + - - +
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Residues in contact with PHE 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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18A LEU* 3.7 38.4 - - + -
19A PHE* 4.1 17.6 - - + -
22A THR* 3.4 35.2 - - + -
3B ASP 4.0 2.6 + - - +
4B THR* 3.2 16.3 + - + +
6B LEU* 1.3 75.8 - - - +
8B GLU* 1.3 61.2 + - + +
10B LEU* 3.6 1.3 - - - +
11B HIS* 2.7 48.8 + + + +
77B VAL* 4.7 7.4 - - + -
78B PHE* 4.5 15.3 - + - -
102B LEU* 4.3 22.0 - - + -
122B PHE* 3.8 26.7 - + - -
123B THR* 6.0 0.4 - - - -
126B LEU* 5.3 1.6 - - + -
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Residues in contact with GLU 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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4B THR* 3.2 24.5 + - + +
5B VAL* 3.2 17.4 + - - +
7B PHE* 1.3 87.1 - - + +
9B PHE* 1.3 64.7 + - + +
11B HIS* 3.5 5.9 + - - +
12B THR* 3.0 30.5 + - - +
101B PRO* 5.2 12.3 - - - +
102B LEU* 4.4 19.8 - - + +
105B PRO* 4.6 9.2 - - + +
111C LYS* 3.9 32.6 + - - +
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Residues in contact with PHE 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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51A ILE* 3.8 24.9 - - + +
54A ARG* 4.2 16.4 - - + -
55A LEU* 3.6 48.9 - - + -
58A ASP* 4.5 7.2 - - + -
5B VAL* 2.8 29.0 + - + +
6B LEU 4.1 2.0 - - - +
8B GLU* 1.3 81.0 - - + +
10B LEU* 1.3 65.6 + - - +
12B THR* 3.2 12.7 + - + +
13B GLU* 3.0 25.5 + - - +
110C VAL* 4.2 24.0 - - + -
111C LYS* 4.3 30.1 - - + -
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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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19A PHE* 3.4 34.3 - - + +
22A THR* 3.7 24.2 - - + -
23A TYR* 4.0 22.2 - - + +
26A LEU* 3.9 27.8 - - + -
47A MET* 5.4 2.0 - - + -
51A ILE* 3.7 20.3 - - + +
130A LEU* 4.6 6.7 - - + -
6B LEU 2.9 19.5 + - - +
7B PHE* 3.6 4.0 - - - +
9B PHE* 1.3 76.4 - - - +
11B HIS* 1.3 64.5 + - - +
13B GLU* 3.0 5.9 + - - +
14B MET* 2.9 30.6 + - + +
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Residues in contact with HIS 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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7B PHE* 2.7 35.4 + + + +
8B GLU* 3.6 7.0 + - - +
10B LEU* 1.3 73.4 - - - +
12B THR* 1.3 59.4 + - - +
14B MET* 2.9 30.7 + - + +
15B VAL* 2.9 40.6 + - + +
37B LEU* 6.0 0.2 - - + -
102B LEU* 3.4 36.4 - - + +
118B LYS 5.4 0.2 + - - -
119B PHE* 3.8 26.7 + + - -
122B PHE* 3.6 44.7 - + + +
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Residues in contact with THR 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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8B GLU* 3.0 17.0 + - - +
9B PHE* 3.4 17.4 - - + +
11B HIS* 1.3 81.6 + - - +
13B GLU* 1.3 77.0 + - - +
15B VAL* 3.5 7.2 + - - +
16B ALA* 3.1 24.4 + - + +
106B MET* 5.9 0.2 - - - +
119B PHE* 4.1 9.8 - - + -
113C PRO* 3.5 41.8 - - + +
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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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47A MET* 3.3 28.6 - - + +
50A ASN* 3.4 43.6 + - - +
51A ILE* 3.4 31.8 - - + +
54A ARG* 5.6 1.9 - - - +
9B PHE 3.0 6.9 + - - +
10B LEU* 3.0 8.9 + - + +
12B THR* 1.3 90.9 - - - +
14B MET* 1.3 57.5 + - - +
16B ALA* 3.8 11.2 - - - +
17B GLU* 3.1 34.3 + - - +
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Residues in contact with MET 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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22A THR* 3.4 37.2 - - + +
26A LEU* 4.1 24.7 - - + +
47A MET* 4.0 7.4 - - + -
10B LEU* 2.9 26.4 + - + +
11B HIS* 2.9 15.7 + - + +
13B GLU* 1.3 75.8 - - - +
15B VAL* 1.3 65.2 + - + +
17B GLU* 4.0 0.4 - - - -
18B LEU* 3.1 31.6 + - + +
37B LEU* 3.6 10.1 - - + +
40B MET* 3.4 39.3 - - + -
122B PHE* 4.4 15.3 - - + -
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Residues in contact with VAL 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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11B HIS* 2.9 44.1 + - + +
12B THR 3.7 3.6 - - - +
14B MET* 1.3 73.6 - - - +
16B ALA* 1.3 72.4 + - + +
19B TRP* 2.9 32.1 + - + +
37B LEU* 3.6 18.4 - - + -
118B LYS* 3.9 25.6 - - + +
119B PHE* 3.5 36.8 - - + -
122B PHE* 6.0 0.2 - - + -
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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
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12B THR* 3.1 17.5 + - + +
13B GLU* 3.8 15.9 - - - +
14B MET 3.3 0.2 - - - -
15B VAL* 1.3 86.8 - - + +
17B GLU* 1.3 61.0 - - + +
19B TRP* 3.4 18.4 + - - -
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Residues in contact with GLU 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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30A LEU* 5.8 0.7 - - + -
43A GLN* 2.5 33.5 + - - +
46A ARG* 2.4 36.1 + - - -
47A MET* 4.3 18.4 - - + +
50A ASN* 5.2 4.5 + - - -
13B GLU* 3.1 18.9 + - - +
14B MET 4.3 0.9 - - - +
16B ALA* 1.3 84.5 - - - +
18B LEU* 1.3 70.6 + - + +
19B TRP* 3.9 0.7 - - - -
20B ALA 5.5 0.2 + - - -
21B HIS* 4.9 2.8 - - - +
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Residues in contact with LEU 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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26A LEU* 4.2 15.7 - - + -
29A GLN* 4.1 12.8 - - + -
30A LEU* 4.8 12.8 - - + -
33A ASP* 3.8 21.8 - - - +
43A GLN* 6.0 0.4 - - - +
14B MET* 3.1 19.2 + - - +
15B VAL 3.9 0.2 - - - -
17B GLU* 1.3 90.5 - - + +
19B TRP* 1.3 65.0 + - - +
20B ALA 3.2 3.7 + - - -
21B HIS* 3.3 35.6 + - + +
34B LEU* 5.6 0.5 - - - -
36B VAL* 4.2 17.7 + - + +
37B LEU* 4.3 9.2 + - + +
40B MET* 4.1 28.9 - - + -
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Residues in contact with TRP 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 VAL* 2.9 29.7 + - + +
16B ALA* 3.4 18.9 + - - +
17B GLU 3.9 0.6 - - - -
18B LEU* 1.3 76.2 - - - +
20B ALA* 1.3 78.6 + - + +
21B HIS 3.5 1.3 - - - +
34B LEU* 3.1 45.7 + - + +
37B LEU* 3.7 16.4 - - + -
118B LYS* 3.2 49.2 - - + +
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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
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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