Contacts of the helix formed by residues 38 - 60 (chain B) in PDB entry 2E98
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 ILE 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA* 3.4 10.0 - - - +
37B LYS* 1.3 80.0 - - - +
39B ARG* 1.3 66.2 + - - +
40B ALA* 3.9 22.0 - - + +
41B PHE* 3.0 25.9 + - + +
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN 5.8 0.2 - - - -
29B GLY* 5.1 9.5 - - - -
32B ALA* 4.6 5.1 - - - +
38B ILE* 1.3 74.2 - - - +
40B ALA* 1.3 57.1 + - - +
42B GLY* 3.1 4.0 + - - +
43B HIS* 2.9 47.7 + - + +
71B SER* 4.9 2.2 + - - -
505B B29 2.8 46.7 + - - +
506B B29 3.9 21.4 + - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.2 21.1 - - + +
39B ARG* 1.3 77.8 - - - +
41B PHE* 1.3 58.2 + - - +
43B HIS* 3.2 3.5 + - - +
44B LYS* 2.9 31.9 + - - +
506B B29 3.4 38.4 + - - +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 3.6 32.3 - + - -
32B ALA* 4.9 1.6 - - + -
35B GLN* 4.7 7.6 - - + -
37B LYS* 3.5 48.2 - - + -
38B ILE* 3.0 19.1 + - + +
40B ALA* 1.3 76.9 - - - +
42B GLY* 1.3 64.9 + - - +
44B LYS* 3.3 10.9 + - + +
45B ALA* 3.1 20.5 + - + +
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Residues in contact with GLY 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 3.7 35.1 - - - +
31B TRP* 3.9 9.2 - - - -
32B ALA* 3.7 9.0 - - - +
38B ILE 3.5 4.2 + - - -
39B ARG 3.1 7.2 + - - -
41B PHE* 1.3 77.7 - - - +
43B HIS* 1.3 57.8 + - - +
45B ALA* 3.3 2.1 + - - +
46B GLY* 2.8 26.5 + - - -
222B PRO* 4.3 0.5 - - - +
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 4.8 0.9 - - + -
39B ARG* 2.9 39.0 + - + +
40B ALA 3.2 7.2 + - - +
42B GLY* 1.3 78.0 - - - +
44B LYS* 1.3 63.4 + - - +
46B GLY 3.1 0.9 + - - -
47B ALA* 2.9 21.3 + - - +
505B B29 2.7 57.2 + + - -
506B B29 2.6 83.0 + + + +
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Residues in contact with LYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA* 2.9 17.6 + - + +
41B PHE* 3.6 13.9 - - + +
42B GLY 3.3 0.2 - - - -
43B HIS* 1.3 78.3 - - + +
45B ALA* 1.3 62.6 + - - +
47B ALA* 3.3 10.0 + - + +
48B LYS* 3.3 46.0 + - - +
51B ARG* 5.1 9.7 - - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 3.5 40.6 - - + -
41B PHE* 3.1 6.1 + - + +
42B GLY 3.9 1.1 - - - +
44B LYS* 1.3 80.2 - - - +
46B GLY* 1.3 62.9 + - - +
48B LYS* 3.3 14.2 + - - +
49B SER* 3.0 22.5 + - - -
222B PRO* 3.8 15.6 - - + +
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 3.3 26.0 + - - -
42B GLY 2.8 11.2 + - - -
43B HIS 3.5 3.8 - - - -
44B LYS 3.1 0.2 - - - -
45B ALA* 1.3 78.5 - - - +
47B ALA* 1.3 60.6 + - - +
49B SER* 3.1 2.2 + - - -
50B VAL* 3.0 20.3 + - - +
221B TRP* 3.2 16.7 + - - -
222B PRO* 4.6 0.7 - - - -
505B B29 4.2 7.4 - - - -
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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
----------------------------------------------------------
43B HIS 2.9 13.0 + - - +
44B LYS* 3.3 11.6 + - + +
45B ALA 3.3 0.4 - - - -
46B GLY* 1.3 75.9 - - - +
48B LYS* 1.3 62.6 + - + +
50B VAL* 3.2 7.6 + - - +
51B ARG* 2.9 32.7 + - - +
505B B29 3.7 25.9 - - + -
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Residues in contact with LYS 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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44B LYS* 3.3 35.2 + - - +
45B ALA* 3.5 13.2 - - - +
46B GLY 3.2 0.6 - - - -
47B ALA* 1.3 79.8 - - - +
49B SER* 1.3 56.8 + - - +
51B ARG* 3.3 27.7 + - - +
52B ARG* 3.0 30.8 + - - +
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA 3.0 13.2 + - - -
46B GLY 3.4 9.0 - - - -
48B LYS* 1.3 74.4 - - - +
50B VAL* 1.3 67.4 + - - +
52B ARG* 3.4 19.0 + - - +
53B ALA* 2.9 24.8 + - - +
221B TRP* 2.6 44.2 + - - -
222B PRO* 4.1 2.0 - - - -
224B PHE 3.3 16.5 + - - +
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 3.8 14.8 - - - -
46B GLY 3.0 18.6 + - - +
47B ALA* 3.2 8.0 + - - +
49B SER* 1.3 76.8 - - - +
51B ARG* 1.3 65.3 + - - +
53B ALA* 3.2 2.6 + - - +
54B VAL* 2.9 34.9 + - + +
67B LEU* 3.8 21.5 - - + -
139B LEU* 6.1 0.9 - - + -
141B ILE* 5.7 0.2 - - + -
221B TRP* 3.7 17.9 - - - +
505B B29 3.7 43.7 - - + -
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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
----------------------------------------------------------
44B LYS* 5.1 9.5 - - - +
47B ALA* 2.9 18.4 + - - +
48B LYS* 3.5 35.7 - - - +
50B VAL* 1.3 79.4 - - - +
52B ARG* 1.3 62.8 + - - +
54B VAL* 3.4 5.9 + - - +
55B SER* 3.0 31.5 + - - +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LYS* 3.0 16.7 + - - +
49B SER* 3.4 17.2 + - - +
51B ARG* 1.3 77.6 - - - +
53B ALA* 1.3 59.4 + - - +
55B SER* 3.4 5.9 + - - -
56B PHE* 2.9 30.4 + - + +
222B PRO 2.9 25.7 + - - -
223B ASP 4.0 2.2 - - - -
224B PHE 2.9 30.7 + - - -
225B ASP* 3.7 13.4 - - - +
226B GLU* 3.5 43.9 + - + +
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 4.6 4.7 - - + -
49B SER 2.9 18.6 + - - +
50B VAL* 3.7 3.6 - - - +
52B ARG* 1.3 77.2 - - - +
54B VAL* 1.3 58.6 + - + +
56B PHE* 3.4 0.8 + - - -
57B ALA* 3.0 30.7 + - - +
65B LEU* 3.9 6.0 - - + +
67B LEU* 5.4 2.7 - - + -
221B TRP* 3.9 22.9 - - + -
224B PHE* 5.1 3.6 - - + +
229B PHE* 3.6 25.4 - - + -
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Residues in contact with VAL 54 (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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50B VAL* 2.9 34.7 + - + +
51B ARG* 3.7 6.1 - - - +
53B ALA* 1.3 73.2 - - - +
55B SER* 1.3 65.9 + - - +
57B ALA* 3.4 2.4 + - - +
58B ALA* 3.0 24.4 + - + +
65B LEU* 3.8 12.3 - - + -
67B LEU* 4.2 2.2 - - + -
100B LEU* 5.2 9.4 - - + -
105B VAL* 5.3 5.8 - - + -
137B LEU* 4.0 17.4 - - + +
139B LEU* 4.0 37.0 - - + -
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Residues in contact with SER 55 (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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51B ARG* 3.0 22.2 + - - +
52B ARG* 3.8 5.6 - - - -
54B VAL* 1.3 78.5 - - - +
56B PHE* 1.3 64.9 + - - +
58B ALA* 3.3 5.5 + - - +
59B ASN* 2.9 38.5 + - - +
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Residues in contact with PHE 56 (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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52B ARG* 2.9 18.7 + - + +
53B ALA* 3.7 4.9 - - - +
54B VAL 3.3 0.2 - - - -
55B SER* 1.3 78.5 - - - +
57B ALA* 1.3 64.4 + - - +
59B ASN* 3.2 3.4 + - - -
60B ASN* 2.8 58.8 + - + +
62B ILE* 5.0 0.2 - - + -
226B GLU* 3.6 50.5 - - + -
229B PHE* 3.4 32.5 - + + -
230B GLU* 3.9 17.3 - - + -
233B LEU* 3.6 28.0 - - + -
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Residues in contact with ALA 57 (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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53B ALA 3.0 16.8 + - - +
54B VAL 3.8 3.6 - - - +
55B SER 3.3 0.2 - - - -
56B PHE* 1.3 78.3 - - - +
58B ALA* 1.3 63.3 + - - +
60B ASN 3.3 5.2 + - - -
62B ILE* 3.1 61.3 + - + +
65B LEU* 3.9 21.5 - - + -
137B LEU* 4.5 4.3 - - + -
229B PHE* 4.2 5.6 - - + -
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.0 19.0 + - + +
55B SER* 3.8 6.1 - - - +
57B ALA* 1.3 78.8 - - - +
59B ASN* 1.3 65.0 + - - +
60B ASN 3.4 0.2 + - - -
61B GLY* 3.4 10.0 + - - -
62B ILE 4.8 2.2 - - - +
103B HIS 6.1 0.7 - - - +
105B VAL* 5.8 4.7 - - + -
137B LEU* 4.3 25.5 - - + +
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Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 2.9 31.6 + - - +
56B PHE* 3.7 6.0 + - - +
58B ALA* 1.3 80.8 - - - +
60B ASN* 1.3 65.7 + - - +
61B GLY 3.4 1.0 + - - -
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Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 2.8 67.4 + - + +
57B ALA* 3.3 2.9 + - - +
58B ALA 3.2 0.4 - - - -
59B ASN* 1.3 87.7 - - - +
61B GLY* 1.3 58.9 + - - +
62B ILE* 3.3 12.5 + - + +
233B LEU* 5.1 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