Contacts of the helix formed by residues 35 - 55 (chain C) 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 ARG 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C TYR* 5.6 0.5 - - - -
21C GLU* 4.7 15.0 - - - +
36C HIS* 1.3 72.2 + - + +
37C LEU* 3.3 4.6 - - - +
38C ASN* 3.4 28.7 + - - +
39C GLN* 3.4 22.4 + - - +
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Residues in contact with HIS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 1.3 79.1 - - + +
37C LEU* 1.3 66.0 + - - +
39C GLN* 3.4 29.4 + - - +
40C PHE* 3.2 23.5 + - + +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 3.3 2.7 - - - +
36C HIS* 1.3 75.5 - - - +
38C ASN* 1.3 59.7 + - - +
40C PHE* 2.8 22.8 + - + +
41C ILE* 2.7 58.2 + - + +
67C PHE* 4.1 19.5 - - + -
70C TRP* 5.5 7.2 - - + +
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Residues in contact with ASN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 3.5 44.3 - - + +
21C GLU* 5.0 5.4 + - - -
35C ARG* 3.6 25.9 + - - +
37C LEU* 1.3 77.7 - - - +
39C GLN* 1.3 58.0 + - - +
40C PHE 3.1 0.2 + - - -
41C ILE* 4.5 3.8 - - - +
42C ALA* 2.8 34.3 + - - +
70C TRP* 5.7 9.7 - - - -
86C LEU* 3.4 19.6 - - + +
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C TYR* 4.3 17.2 - - + +
19C GLU* 4.5 10.0 - - - +
35C ARG* 3.4 20.7 - - - +
36C HIS* 3.5 29.3 + - - +
38C ASN* 1.3 75.9 - - - +
40C PHE* 1.3 64.7 + - + +
42C ALA* 4.0 4.7 - - - +
43C HIS* 3.2 26.3 + - - +
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Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C HIS* 3.2 11.3 + - + +
37C LEU* 2.8 26.3 + - + +
39C GLN* 1.3 81.1 - - + +
41C ILE* 1.3 65.4 + - + +
43C HIS* 4.0 3.5 - - + +
44C ALA* 3.0 26.3 + - - +
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 2.7 43.4 + - + +
38C ASN* 4.0 4.0 - - - +
40C PHE* 1.3 70.7 - - - +
42C ALA* 1.3 63.0 + - - +
44C ALA* 3.9 5.5 - - - +
45C ALA* 3.2 21.5 + - - +
65C ASP* 5.0 4.7 - - - +
67C PHE* 3.2 47.6 - - + -
70C TRP* 4.4 18.4 - - + -
72C VAL* 3.9 11.9 - - + -
86C LEU* 3.5 26.2 - - + -
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C TYR* 4.2 16.8 - - + +
8C VAL* 4.4 8.1 - - + -
38C ASN 2.8 18.0 + - - +
39C GLN* 4.0 4.9 - - - +
41C ILE* 1.3 75.0 - - - +
43C HIS* 1.3 66.9 + - - +
45C ALA* 2.9 19.3 + - - +
46C LEU* 3.4 10.1 + - - +
84C ILE* 3.9 27.9 - - + +
86C LEU* 4.2 6.0 - - + +
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Residues in contact with HIS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ASP* 4.7 26.1 + - + +
39C GLN 3.2 17.0 + - - +
40C PHE* 4.0 4.9 - - + +
42C ALA* 1.3 78.2 - - - +
44C ALA* 1.3 63.5 + - - +
46C LEU* 3.1 37.8 + - + +
47C ASP* 4.0 9.5 + - - +
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE 3.0 18.6 + - - +
41C ILE* 3.9 6.5 - - - +
43C HIS* 1.3 81.0 + - - +
45C ALA* 1.3 61.3 + - - +
46C LEU 3.3 0.3 + - - -
47C ASP* 3.6 14.1 - - - +
48C LEU* 3.4 14.4 - - - +
65C ASP* 6.0 0.2 - - - -
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ILE 3.2 14.1 + - - +
42C ALA* 2.9 13.3 + - - +
44C ALA* 1.3 74.9 - - - +
46C LEU* 1.3 63.6 + - - +
47C ASP 3.3 0.2 - - - -
48C LEU* 3.0 25.6 + - - +
49C VAL* 3.0 17.4 + - + +
64C VAL* 4.9 2.5 - - + -
65C ASP* 4.7 10.5 - - + +
72C VAL* 3.5 31.9 - - + -
84C ILE* 5.2 1.8 - - + -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 4.2 22.0 - - + -
14C ASP* 4.4 16.8 - - + +
42C ALA 3.4 5.6 + - - +
43C HIS* 3.1 33.0 + - + +
45C ALA* 1.3 74.3 - - - +
47C ASP* 1.3 68.0 + - - +
49C VAL* 2.9 6.2 + - + +
50C ASP* 2.8 29.1 + - - +
82C ARG* 4.0 40.6 - - + +
84C ILE* 3.9 31.0 - - + -
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Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C HIS* 4.0 14.0 + - - +
44C ALA* 3.6 15.9 - - - +
45C ALA 3.3 0.6 - - - -
46C LEU* 1.3 74.6 - - - +
48C LEU* 1.3 62.7 + - + +
50C ASP* 3.6 8.5 + - - +
51C GLU* 3.0 34.8 + - - +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA 3.4 22.9 - - - +
45C ALA* 3.0 10.7 + - - +
47C ASP* 1.3 79.9 - - + +
49C VAL* 1.3 59.6 + - - +
51C GLU* 3.1 12.6 + - - +
52C ASN* 2.8 40.2 + - - +
64C VAL* 3.3 21.1 - - + +
65C ASP* 3.3 41.7 - - + +
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ALA* 3.0 15.3 + - + +
46C LEU* 2.9 12.3 + - + +
48C LEU* 1.3 76.1 - - - +
50C ASP* 1.3 55.4 + - - +
52C ASN* 4.6 1.3 - - - +
53C MET* 2.7 55.5 + - + +
61C LEU* 3.7 21.7 - - + +
64C VAL* 4.5 9.8 - - + +
74C ALA* 3.8 24.2 - - + -
76C VAL* 3.8 8.5 - - + -
82C ARG* 4.3 13.0 - - + -
84C ILE* 3.9 16.2 - - + -
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 2.8 24.8 + - - +
47C ASP* 3.7 9.0 - - - +
49C VAL* 1.3 71.5 - - - +
51C GLU* 1.3 60.0 + - + +
53C MET* 3.1 22.6 - - - +
54C TRP* 3.0 31.9 - - + +
82C ARG* 3.3 28.2 + - - -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ASP* 3.0 20.6 - - - +
48C LEU* 3.1 14.5 + - - +
50C ASP* 1.3 76.9 - - + +
52C ASN* 1.3 72.8 + - - +
53C MET 3.3 0.3 + - - -
54C TRP* 3.4 12.2 + - - +
55C LEU* 3.4 22.4 - - + +
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Residues in contact with ASN 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 2.8 24.8 + - - +
49C VAL* 4.1 2.2 - - - +
51C GLU* 1.3 81.3 + - - +
53C MET* 1.3 62.3 + - - +
55C LEU* 3.4 20.5 + - - +
56C SER* 3.6 16.6 + - - -
61C LEU* 4.3 15.7 - - + +
64C VAL* 3.8 29.1 - - + +
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Residues in contact with MET 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 2.7 35.1 + - + +
50C ASP* 3.1 47.8 - - - +
52C ASN* 1.3 74.5 - - - +
54C TRP* 1.3 76.2 + - + +
56C SER 2.7 27.0 - - - +
61C LEU* 4.4 4.7 - - + +
76C VAL* 4.1 21.1 - - + -
80C HIS* 4.2 23.1 - - - +
82C ARG* 4.0 15.0 - - + -
78F ARG* 2.8 24.0 + - - +
80F THR* 3.5 4.0 - - - +
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Residues in contact with TRP 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ASP* 3.0 25.9 - - + +
51C GLU* 3.4 6.5 + - - +
52C ASN 3.4 0.4 - - - -
53C MET* 1.3 94.1 - - + +
55C LEU* 1.3 59.2 + - - +
56C SER 3.3 2.5 + - - -
80C HIS* 3.5 29.6 - + - -
79F GLU 4.4 2.0 - - - -
80F THR* 3.5 59.0 + - + +
154F SER 4.2 6.1 - - - -
155F GLY* 3.8 10.5 - - - -
156F PHE* 4.0 6.1 - + - -
181F ARG* 3.4 53.5 - - + +
185F LEU* 3.9 27.2 - - + +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLU* 3.4 24.7 - - + +
52C ASN* 3.4 14.7 + - - +
53C MET 3.2 0.8 - - - -
54C TRP* 1.3 77.0 - - - +
56C SER* 1.3 61.6 + - - +
185F LEU* 4.0 23.3 - - + +
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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