Contacts of the helix formed by residues 36 - 58 (chain B) in PDB entry 2VDE
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 ASN 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ARG* 3.9 4.2 - - - +
32B ALA 2.7 23.9 + - - +
33B ARG 4.3 1.3 + - - +
34B LEU 3.9 0.4 - - - -
35B SER* 1.3 67.9 - - - +
37B PRO* 1.3 66.6 - - - +
38B GLU* 3.3 28.0 + - - +
39B LEU* 3.0 36.7 + - + +
40B ARG* 3.1 21.0 + - - +
127B LEU* 3.5 33.4 - - + +
207B ILE* 3.0 30.4 + - - +
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Residues in contact with PRO 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLU* 3.3 41.1 - - - +
339A GLU* 3.6 22.4 - - + -
340A SER* 3.4 21.8 + - - +
343A ARG* 3.6 26.7 - - + +
35B SER 3.0 6.5 - - - +
36B ASN* 1.3 86.0 - - - +
38B GLU* 1.3 70.6 + - - +
40B ARG 4.1 0.2 - - - -
41B LYS* 3.2 24.6 + - - +
206B GLN 5.2 0.7 - - - +
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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
----------------------------------------------------------
340A SER* 2.5 31.5 + - - +
36B ASN* 3.3 27.1 + - - +
37B PRO* 1.3 83.9 - - - +
39B LEU* 1.3 61.9 + - - +
41B LYS* 3.6 6.0 - - - +
42B SER* 3.2 21.3 + - - -
123B ASP* 6.3 0.4 - - - -
206B GLN 4.3 8.4 - - - +
207B ILE* 5.2 1.0 - - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 4.4 23.6 - - + +
36B ASN* 3.0 22.3 + - + +
38B GLU* 1.3 74.0 - - - +
40B ARG* 1.3 62.3 + - + +
42B SER* 3.1 8.9 + - - -
43B ALA* 2.9 25.2 + - - +
120B TYR* 3.9 17.5 - - + +
123B ASP* 3.6 31.4 - - + +
124B GLN* 3.7 29.2 - - + +
127B LEU* 3.8 26.2 - - + -
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL* 5.1 3.3 - - + +
336A GLU* 2.9 43.1 + - - +
33B ARG 4.7 5.6 - - - +
34B LEU 2.9 32.3 + - - -
35B SER* 4.0 11.4 - - - +
36B ASN 3.1 17.2 + - - +
39B LEU* 1.3 74.6 - - + +
41B LYS* 1.3 59.8 + - - +
43B ALA* 3.1 11.3 - - + +
44B ALA* 3.0 25.3 + - - +
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Residues in contact with LYS 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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333A GLY* 3.7 13.0 - - - +
336A GLU* 3.8 15.1 - - + +
337A GLN* 3.7 42.2 - - + +
37B PRO 3.2 20.6 + - - +
38B GLU* 3.6 7.2 - - - +
40B ARG* 1.3 71.4 - - - +
42B SER* 1.3 58.8 + - - +
43B ALA 2.9 4.3 - - - -
44B ALA* 2.9 24.7 + - - +
45B ASP* 2.8 49.6 + - - +
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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 GLU 3.2 10.2 + - - -
39B LEU* 3.1 12.2 + - - -
41B LYS* 1.3 81.5 - - - +
43B ALA* 1.3 58.6 + - - +
45B ASP* 3.9 10.9 + - - +
46B ARG* 3.6 14.7 + - - +
116B GLN* 4.5 3.0 + - - +
120B TYR* 3.2 29.0 + - - +
123B ASP* 2.9 34.8 + - - +
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Residues in contact with ALA 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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39B LEU 2.9 8.2 + - - +
40B ARG* 3.1 16.6 - - + +
41B LYS 2.9 0.2 - - - -
42B SER* 1.3 76.4 - - - +
44B ALA* 1.3 62.0 + - - +
46B ARG* 2.9 8.6 + - - +
47B ASP* 2.8 40.9 + - - +
120B TYR* 3.6 26.7 - - + +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A TYR* 3.4 27.1 - - + +
330A ASN* 5.4 1.1 - - - -
332A VAL* 4.2 10.3 - - + -
333A GLY* 3.8 18.4 - - - +
40B ARG 3.0 11.4 + - - +
41B LYS 2.9 10.4 + - - +
43B ALA* 1.3 71.6 - - - +
45B ASP* 1.3 57.1 + - - +
47B ASP* 3.8 9.8 + - - +
48B ALA* 2.8 37.0 + - - +
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASN* 6.0 1.6 - - - -
333A GLY* 5.4 1.6 - - - -
41B LYS* 2.8 54.6 + - - +
42B SER* 3.9 8.8 - - - +
44B ALA* 1.3 77.6 - - - +
46B ARG* 1.3 56.9 + - - +
48B ALA* 4.2 3.8 - - - +
49B ALA* 3.4 14.8 + - - +
116B GLN* 3.3 30.9 - - - +
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B SER 3.6 11.5 + - - +
43B ALA* 2.9 12.9 + - - +
45B ASP* 1.3 78.3 - - - +
47B ASP* 1.3 86.8 + - - +
48B ALA 3.2 1.3 - - - -
49B ALA* 3.7 0.3 - - - +
50B PHE* 2.9 43.2 + - + +
116B GLN* 3.6 27.6 - - + +
117B ASP* 3.3 34.2 + - - +
120B TYR* 3.7 36.5 + - + -
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Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A TYR* 3.2 39.7 - - + -
43B ALA* 2.8 21.5 + - - +
44B ALA* 3.8 7.3 + - - +
46B ARG* 1.3 109.1 + - - +
48B ALA* 1.3 62.1 + - - +
50B PHE* 4.0 5.4 - - - +
51B GLU 3.1 15.9 + - - -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLN* 4.0 19.2 - - + +
329A TYR* 3.6 22.3 - - + -
330A ASN* 4.8 7.2 - - + +
44B ALA 2.8 17.3 + - - +
45B ASP* 4.4 5.4 - - - +
47B ASP* 1.3 76.7 - - - +
49B ALA* 1.3 62.9 + - - +
51B GLU* 3.1 6.4 + - - +
52B LYS* 3.0 21.0 + - - +
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Residues in contact with ALA 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 ASP 3.4 18.2 + - - +
46B ARG 3.3 2.6 + - - +
48B ALA* 1.3 78.7 - - - +
50B PHE* 1.3 61.1 + - - +
52B LYS* 3.2 13.6 + - - -
53B ILE* 4.0 1.0 + - - +
109B GLN* 3.2 23.5 + - - +
112B ALA 5.1 1.1 - - - +
113B ALA* 3.9 12.1 - - - +
116B GLN* 3.6 25.8 - - + +
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Residues in contact with PHE 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 ARG* 2.9 29.3 + - + +
47B ASP* 4.0 6.3 - - - +
49B ALA* 1.3 75.6 - - + +
51B GLU* 1.3 62.3 + - - +
53B ILE* 3.0 27.8 + - + +
54B ASN* 5.7 0.3 - - - -
113B ALA* 3.3 40.6 - - + -
114B GLY* 5.8 1.1 - - - -
117B ASP* 4.0 26.2 - - + -
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Residues in contact with GLU 51 (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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321A ASN 4.9 0.2 - - - -
322A SER* 2.8 50.3 + - - +
325A LYS* 2.8 55.1 + - + +
326A GLN* 4.1 5.2 - - + +
329A TYR* 4.0 9.6 - - + -
47B ASP 3.1 16.1 + - - +
48B ALA* 3.1 7.2 + - - +
50B PHE* 1.3 79.8 - - - +
52B LYS* 1.3 54.5 + - - +
53B ILE 3.1 0.4 - - - -
54B ASN* 3.0 37.3 + - - +
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Residues in contact with LYS 52 (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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326A GLN* 3.1 26.4 + - - +
48B ALA 3.0 10.8 + - - +
49B ALA* 3.3 15.7 - - - +
50B PHE 3.1 1.2 - - - -
51B GLU* 1.3 73.2 - - - +
53B ILE* 1.3 58.3 + - - +
54B ASN 3.2 0.4 - - - -
55B GLU* 3.0 31.1 + - + +
56B ALA* 2.9 29.7 + - + +
109B GLN* 3.0 33.2 - - - +
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Residues in contact with ILE 53 (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 PHE* 3.0 27.3 + - + +
51B GLU 3.1 0.2 - - - -
52B LYS* 1.3 76.9 - - - +
54B ASN* 1.3 57.5 + - - +
56B ALA* 3.3 1.1 + - - -
57B ARG* 2.9 46.6 + - - +
106B LEU* 3.6 15.2 - - + +
109B GLN* 3.3 34.1 - - + +
110B GLU* 3.4 35.0 - - + +
113B ALA* 4.4 6.5 - - + -
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Residues in contact with ASN 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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317A GLY 4.2 5.1 - - - +
318A GLY 5.1 2.1 - - - +
322A SER* 3.4 19.7 - - - +
325A LYS* 5.1 0.6 - - - +
50B PHE 5.7 0.2 - - - -
51B GLU* 3.0 32.5 + - - +
53B ILE* 1.3 80.1 - - - +
55B GLU* 1.3 57.4 + - - +
57B ARG* 3.0 33.0 + - - +
58B SER* 3.1 26.0 + - - -
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Residues in contact with GLU 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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319A MET* 4.2 28.8 - - + +
322A SER* 3.5 8.1 + - - +
323A GLN* 4.2 20.4 + - + +
326A GLN* 2.7 38.2 + - - +
52B LYS* 3.0 32.3 + - - +
54B ASN* 1.3 77.0 - - - +
56B ALA* 1.3 62.8 + - - +
58B SER* 3.2 19.2 + - - -
59B PRO* 3.3 10.0 - - - +
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Residues in contact with ALA 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 LYS* 2.9 19.5 + - + +
53B ILE 3.7 3.8 - - - +
55B GLU* 1.3 76.0 - - - +
57B ARG* 1.3 58.3 + - - +
59B PRO* 3.5 13.8 - - - +
60B LEU* 5.4 1.0 - - - +
102B LYS 4.4 4.2 - - - +
105B ALA* 4.0 15.0 - - + +
106B LEU* 4.0 18.9 + - + +
109B GLN* 3.6 27.6 - - + +
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Residues in contact with ARG 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 ILE* 2.9 30.8 + - - +
54B ASN* 3.0 32.8 + - - +
55B GLU 3.1 0.2 - - - -
56B ALA* 1.3 75.2 - - - +
58B SER* 1.3 65.0 + - - +
59B PRO* 3.2 4.5 - - - -
60B LEU* 2.9 26.4 + - + +
61B LEU* 3.9 24.7 + - + +
106B LEU* 3.7 33.4 - - + +
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLN 3.5 4.9 + - - -
317A GLY* 3.2 37.5 - - - -
319A MET* 3.3 33.0 - - - +
54B ASN 3.1 10.7 + - - -
55B GLU 3.4 10.2 + - - -
57B ARG* 1.3 75.4 - - - +
59B PRO* 1.4 65.1 - - - +
60B LEU 3.0 5.5 + - - -
61B LEU* 3.2 10.7 + - - +
63B GLN* 2.8 19.1 + - - -
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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