Contacts of the helix formed by residues 26 - 42 (chain B) in PDB entry 2J3W
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 VAL 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL 3.6 1.2 + - - -
25B SER* 1.3 73.0 + - - +
27B SER* 1.3 62.0 + - - +
28B ALA 3.2 0.5 + - - -
29B PHE* 3.4 6.6 + - - +
30B ALA* 3.3 16.8 + - - +
126B ALA 3.3 10.8 - - - +
127B TYR* 2.9 49.5 - - + +
12E LYS* 3.1 38.7 + - + +
13E LYS 3.9 15.0 - - - +
14E MET* 4.1 17.9 - - + -
62E ARG* 5.8 2.5 - - - +
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.0 10.2 + - - -
26B VAL* 1.3 77.8 - - - +
28B ALA* 1.3 64.4 + - - +
30B ALA* 3.8 8.1 - - - -
31B LEU* 3.0 36.4 + - - +
127B TYR 4.2 6.3 + - - -
128B ILE* 5.9 0.3 - - - -
58E ASP* 3.2 27.1 + - - -
62E ARG* 3.0 26.7 + - - +
86E TYR* 4.5 4.5 - - - -
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.1 22.4 - - + -
25B SER* 2.8 16.8 + - - +
27B SER* 1.3 80.6 - - - +
29B PHE* 1.3 63.2 + - - +
31B LEU* 4.0 1.7 - - - +
32B LEU* 3.1 14.9 + - - +
19E PHE* 3.0 25.9 - - + -
86E TYR* 3.6 22.6 - - + +
1068E PLM 4.2 10.5 - - + +
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 5.0 0.4 - - + +
25B SER 3.9 1.2 + - - -
26B VAL 3.4 7.4 + - - +
28B ALA* 1.3 78.1 - - - +
30B ALA* 1.3 56.2 + - - +
32B LEU* 3.2 1.8 + - + +
33B PHE* 2.7 70.4 + + + +
124B ILE* 5.3 1.1 - - + -
127B TYR* 3.4 49.8 - + + -
139B CYS* 5.3 4.5 - - - -
142B PHE* 4.3 11.7 - + - -
14E MET* 4.5 11.2 - - + -
18E LEU* 3.8 27.8 - - + -
19E PHE* 3.4 20.5 - + + -
22E THR* 3.5 35.4 - - + -
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL 3.3 3.4 + - - +
27B SER* 3.6 9.6 - - - +
29B PHE* 1.3 83.2 - - - +
31B LEU* 1.3 59.5 + - + +
33B PHE* 3.8 3.2 - - - +
34B SER* 2.9 32.5 + - - -
124B ILE* 5.2 7.5 - - + +
127B TYR* 3.7 35.7 - - + +
128B ILE* 4.4 11.7 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.0 35.7 + - - +
28B ALA* 4.0 3.4 - - - +
30B ALA* 1.3 74.6 - - + +
32B LEU* 1.3 63.9 + - - +
34B SER* 3.5 6.5 + - - -
35B GLU* 3.2 16.8 + - - +
51E ILE* 3.8 26.7 - - + +
54E ARG* 3.9 37.7 - - + +
55E LEU* 4.0 35.4 - - + +
58E ASP* 4.7 7.4 - - + +
86E TYR* 4.5 4.5 - - + -
1068E PLM 5.0 1.1 - - + -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.1 18.1 + - - +
29B PHE* 3.6 3.8 - - + +
31B LEU* 1.3 75.0 - - - +
33B PHE* 1.3 62.7 + - - +
35B GLU* 3.1 6.0 + - + +
36B MET* 3.0 38.2 + - + +
19E PHE* 3.7 29.8 - - + +
22E THR* 4.0 14.8 - - + -
23E TYR* 4.2 22.4 - - + +
26E LEU* 4.0 25.4 - - + -
51E ILE* 3.9 20.6 - - + +
130E LEU* 4.5 10.3 - - + -
1068E PLM 5.2 0.8 - - + +
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 2.7 50.8 + + + +
30B ALA* 3.8 3.8 - - - +
32B LEU* 1.3 72.7 - - - +
34B SER* 1.3 59.7 + - - +
36B MET* 3.2 19.0 + - + +
37B VAL* 2.9 53.3 + - + +
54B LEU* 4.6 7.4 - - + -
124B ILE* 4.4 17.7 - - + -
138B ASN* 3.6 11.2 - - + -
139B CYS* 3.5 39.7 - - + -
142B PHE* 3.6 33.2 - + + -
22E THR* 5.1 0.7 - - + -
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Residues in contact with SER 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 2.9 19.1 + - - -
31B LEU* 3.7 8.1 - - - -
33B PHE* 1.3 80.5 - - - +
35B GLU* 1.3 63.1 + - - +
37B VAL* 3.4 7.5 + - - +
38B GLN* 3.1 27.0 + - - +
54E ARG* 3.2 26.0 + - - -
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 3.2 6.2 + - - +
32B LEU* 3.1 10.3 + - + +
34B SER* 1.3 76.2 - - - +
36B MET* 1.3 60.8 + - - +
38B GLN* 3.2 28.7 + - - +
39B TYR* 2.9 30.7 + - - +
47E MET* 3.6 29.6 - - + +
50E ASN* 3.1 42.1 + - + +
51E ILE* 3.3 33.0 - - + +
54E ARG* 4.7 8.9 + - - +
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Residues in contact with MET 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.0 31.9 + - + +
33B PHE* 3.2 17.2 + - + +
35B GLU* 1.3 74.4 - - - +
37B VAL* 1.3 60.0 + - + +
39B TYR* 3.4 1.9 + - - +
40B CYS* 3.0 36.2 + - - -
54B LEU* 5.0 5.2 - - + -
57B MET* 3.3 37.7 - - + -
142B PHE* 5.0 6.7 - - + -
22E THR* 3.4 43.3 - - + +
25E ALA* 4.9 2.0 - - + -
26E LEU* 3.8 26.9 - - + +
47E MET* 4.0 7.0 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 2.9 48.4 + - + +
34B SER* 3.6 11.0 - - - +
36B MET* 1.3 74.0 - - - +
38B GLN* 1.3 69.2 + - + +
40B CYS* 3.3 3.8 + - - +
41B GLN* 2.9 33.9 + - - +
50B LEU* 4.0 5.3 - - + +
54B LEU* 4.3 13.5 - - + -
138B ASN* 3.6 33.4 - - + +
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Residues in contact with GLN 38 (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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34B SER* 3.1 15.9 + - - +
35B GLU* 3.2 32.9 + - - +
37B VAL* 1.3 80.4 - - + +
39B TYR* 1.3 63.2 + - - +
41B GLN* 3.3 13.6 + - - +
42B SER* 3.1 22.2 + - - -
50E ASN* 5.0 5.5 - - - +
54E ARG* 3.0 30.4 + - - +
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Residues in contact with TYR 39 (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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35B GLU* 2.9 17.6 + - - +
36B MET* 3.6 3.4 - - - +
37B VAL 3.2 0.2 - - - -
38B GLN* 1.3 76.4 - - - +
40B CYS* 1.3 73.8 + - - +
42B SER* 2.7 27.9 + - - -
43B ARG* 2.9 32.9 + - + +
53B ARG* 4.5 4.7 - - - -
57B MET* 6.2 0.7 - - + -
26E LEU* 4.8 6.5 - - + -
29E GLN* 5.7 3.4 - - + -
30E LEU* 3.3 24.9 - - + +
33E ASP* 2.7 40.4 + - - +
34E TYR* 3.4 18.3 - - - -
43E GLN* 3.3 27.1 - - + +
47E MET* 3.6 18.8 - - + -
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Residues in contact with CYS 40 (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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36B MET 3.0 21.4 + - - +
37B VAL 3.7 1.1 - - - +
39B TYR* 1.3 90.5 - - - +
41B GLN* 1.3 62.1 + - - +
43B ARG* 3.1 12.4 + - - +
44B VAL* 3.1 19.8 + - - +
50B LEU* 3.7 18.2 - - + -
53B ARG* 3.2 37.9 - - + +
54B LEU* 4.3 10.5 - - + -
57B MET* 4.1 20.9 - - - -
29E GLN* 6.1 0.2 - - - -
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Residues in contact with GLN 41 (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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37B VAL* 2.9 26.1 + - - +
38B GLN* 3.3 13.0 - - - +
39B TYR 3.1 0.2 - - - -
40B CYS* 1.3 78.8 - - - +
42B SER* 1.3 56.6 + - - +
43B ARG 3.1 4.2 + - - -
44B VAL* 3.6 17.7 + - - +
50B LEU* 3.6 31.1 - - + +
138B ASN* 4.9 3.2 - - - +
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Residues in contact with SER 42 (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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38B GLN 3.1 10.0 + - - -
39B TYR* 2.7 26.8 + - - -
41B GLN* 1.3 73.9 - - - +
43B ARG* 1.3 64.2 + - - +
44B VAL 5.0 0.9 - - - -
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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
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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