Contacts of the helix formed by residues 34 - 52 (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 LEU 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU 5.6 0.4 - - - -
19B TRP* 3.1 54.5 + - + +
21B HIS 5.9 0.9 + - - -
32B MET 3.1 1.8 + - - -
33B SER* 1.3 81.6 - - - +
35B SER* 1.3 64.6 + - - +
36B VAL 3.2 2.7 - - - -
37B LEU* 3.1 11.7 + - + +
38B GLU* 3.0 23.1 + - - +
117B PRO* 3.8 29.8 - - + +
118B LYS* 3.8 14.6 - - + +
121B ALA* 3.4 21.1 - - + -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B HIS 5.3 1.2 + - - -
22B ASP* 4.5 15.1 + - - -
32B MET* 2.9 35.9 + - - +
33B SER 3.0 2.9 + - - -
34B LEU* 1.3 77.5 - - - +
36B VAL* 1.3 61.3 + - - +
38B GLU* 3.5 7.2 + - - +
39B GLY* 2.9 25.8 + - - -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 3.6 38.8 - - + +
18B LEU* 4.2 26.5 - - + +
21B HIS* 3.0 43.6 + - - +
22B ASP* 4.4 1.8 - - - +
23B PRO* 4.1 11.0 - - + -
34B LEU 3.2 0.8 - - - -
35B SER* 1.3 76.4 - - - +
37B LEU* 1.3 68.3 + - - +
39B GLY* 3.0 3.5 + - - -
40B MET* 3.0 24.6 + - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B HIS* 5.8 0.4 - - + +
14B MET* 3.6 32.8 - - + +
15B VAL* 3.6 14.1 - - + +
18B LEU* 4.3 12.8 - - + +
19B TRP* 3.7 28.7 - - + -
34B LEU* 3.1 17.2 + - + +
36B VAL* 1.3 79.0 - - - +
38B GLU* 1.3 64.7 + - - +
40B MET* 3.2 10.7 + - - +
41B GLY 3.0 18.4 + - - -
118B LYS 3.6 23.8 - - - +
121B ALA* 3.6 9.9 - - + -
122B PHE* 3.5 26.1 - - + +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU 3.0 15.8 + - - +
35B SER* 3.7 8.3 - - - +
37B LEU* 1.3 76.8 - - - +
39B GLY* 1.3 58.4 + - - +
41B GLY 3.3 0.3 + - - -
42B PHE* 2.9 25.1 + - - +
121B ALA* 3.3 26.4 + - + +
124B CYS* 4.0 7.8 - - + +
125B GLY* 2.9 24.7 + - - +
128B ARG* 2.7 48.8 + - - +
140B VAL 5.4 3.8 - - - +
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER 2.9 15.9 + - - -
36B VAL* 3.0 5.3 + - - -
38B GLU* 1.3 82.0 + - - +
40B MET* 1.3 60.9 + - - +
42B PHE* 3.2 6.4 - - - +
43B ARG* 2.7 45.6 + - - -
128B ARG* 5.1 1.8 - - - -
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Residues in contact with MET 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.0 39.4 - - + +
26A LEU* 3.1 23.3 - - + +
29A GLN* 3.1 28.9 - - + +
14B MET* 3.4 18.6 - - + -
18B LEU* 4.1 19.3 - - + -
36B VAL* 3.0 15.9 + - - +
37B LEU* 3.2 13.0 + - - +
39B GLY* 1.3 73.0 - - - +
41B GLY* 1.3 67.0 + - - +
43B ARG* 3.4 8.7 + - - +
44B VAL* 3.0 27.9 + - - +
122B PHE* 3.6 12.8 - - + -
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU 3.0 11.1 + - - -
38B GLU 3.7 1.6 - - - -
40B MET* 1.3 75.4 - - - +
42B PHE* 1.3 52.4 + - - +
44B VAL 3.2 0.5 + - - -
45B GLY 2.6 32.7 + - - -
122B PHE* 3.2 38.1 - - - -
125B GLY 3.2 8.6 - - - +
126B LEU* 3.1 10.6 - - - +
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU 2.9 13.4 + - - +
39B GLY* 3.2 12.8 - - - +
41B GLY* 1.3 75.4 - - - +
43B ARG* 1.3 64.0 + - + +
45B GLY 3.2 0.2 + - - -
46B GLN* 2.7 57.6 + - - +
125B GLY* 2.9 14.9 + - - +
128B ARG* 3.4 45.3 - - + +
129B GLY* 3.2 38.2 - - - -
132B TYR* 3.8 35.7 - + + -
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Residues in contact with ARG 43 (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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25A ALA* 5.1 11.0 - - + +
28A THR* 5.3 10.0 - - - +
29A GLN* 5.7 5.4 + - - -
32A LYS* 4.2 22.6 - - - +
39B GLY* 2.7 46.7 + - - +
40B MET* 3.9 10.0 - - - +
42B PHE* 1.3 89.1 - - + +
44B VAL* 1.3 64.2 + - - +
46B GLN* 3.2 20.9 + - - +
47B ALA* 3.2 12.8 + - - +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.3 6.1 - - + -
21A LEU* 3.8 27.8 - - + +
22A THR* 3.7 28.9 - - - +
25A ALA* 3.9 7.6 - - + -
40B MET 3.0 19.6 + - - +
41B GLY 3.6 5.8 - - - +
43B ARG* 1.3 75.4 - - - +
45B GLY* 1.3 62.3 + - - +
47B ALA* 3.2 8.5 + - - +
48B LEU* 3.1 31.6 + - + +
122B PHE* 3.7 14.6 - - + -
126B LEU* 3.6 17.7 - - + -
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY 2.6 18.9 + - - -
42B PHE 3.6 0.9 - - - -
44B VAL* 1.3 73.7 - - - +
46B GLN* 1.3 61.7 + - - +
48B LEU* 3.3 8.2 + - - +
49B GLY 3.0 19.2 + - - -
73B LEU* 5.8 0.4 - - - -
126B LEU* 3.3 29.8 - - - -
129B GLY 3.5 7.0 - - - -
130B ALA* 3.4 10.3 - - - -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 2.7 40.3 + - - +
43B ARG* 3.3 13.4 - - - +
44B VAL 3.2 0.2 - - - -
45B GLY* 1.3 75.3 - - - +
47B ALA* 1.3 59.2 + - - +
49B GLY 3.6 1.0 + - - -
50B GLU* 3.3 16.3 + - - +
129B GLY* 3.2 17.6 - - - +
132B TYR* 3.8 31.0 - - + -
133B THR* 2.5 35.4 + - - +
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Residues in contact with ALA 47 (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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21A LEU* 3.8 28.3 - - + -
43B ARG 3.2 7.7 + - - +
44B VAL 3.2 9.0 + - - +
46B GLN* 1.3 77.1 - - - +
48B LEU* 1.3 65.0 + - - +
49B GLY 3.1 1.8 - - - -
50B GLU* 3.0 23.5 + - - +
51B ARG* 3.1 30.7 + - - +
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Residues in contact with LEU 48 (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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17A GLU* 5.5 4.3 - - + -
18A LEU* 4.5 14.1 - - + +
21A LEU* 4.2 17.3 - - + -
44B VAL* 3.1 30.0 + - + +
45B GLY* 3.7 7.2 - - - +
47B ALA* 1.3 76.3 - - - +
49B GLY* 1.3 61.7 + - - +
51B ARG* 4.5 6.5 - - + +
52B LEU* 3.1 47.8 + - + +
73B LEU* 3.8 21.1 - - + -
76B ALA* 5.8 2.9 - - + -
77B VAL* 3.7 30.3 - - + -
126B LEU* 4.5 9.0 - - + -
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Residues in contact with GLY 49 (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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45B GLY 3.0 15.5 + - - -
46B GLN 4.0 3.1 - - - -
47B ALA 3.1 0.4 - - - -
48B LEU* 1.3 79.5 - - - +
50B GLU* 1.3 57.7 + - - +
52B LEU 4.4 7.8 + - - +
68B PHE* 4.9 12.7 - - - -
130B ALA* 4.5 14.5 - - - +
133B THR* 3.7 19.8 - - - +
134B LEU* 4.3 12.9 - - - +
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Residues in contact with GLU 50 (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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46B GLN* 3.3 23.1 + - - +
47B ALA* 3.0 15.4 + - - +
49B GLY* 1.3 79.7 - - - +
51B ARG* 1.3 65.0 + - + +
52B LEU 3.5 4.2 + - - +
133B THR* 3.6 17.5 - - + +
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 2.6 41.5 + - - +
21A LEU* 3.7 22.8 - - - +
114A ASP* 2.8 39.5 + - - -
115A PHE* 4.3 13.8 - - - +
47B ALA* 3.1 25.7 + - - +
48B LEU* 3.4 7.4 + - + +
50B GLU* 1.3 82.3 + - + +
52B LEU* 1.3 67.3 + - + +
53B PRO* 4.4 1.6 - - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.1 27.1 + - + +
49B GLY 4.4 4.5 + - - +
50B GLU 3.5 5.9 - - - +
51B ARG* 1.3 85.7 - - + +
53B PRO* 1.3 81.0 - - + +
68B PHE* 3.6 20.2 - - + -
72B ASP* 4.2 3.8 - - + -
73B LEU* 3.7 48.7 - - + +
76B ALA* 4.1 22.2 - - + -
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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