Contacts of the helix formed by residues 36 - 54 (chain B) in PDB entry 2V1C
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 PRO 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B GLU 4.1 3.6 - - - +
35B GLN* 1.3 98.4 - - + +
37B ARG* 1.3 70.6 + - - +
38B GLU* 2.8 19.1 + - - +
39B ASP* 3.1 28.9 + - - +
40B ILE* 3.8 3.2 + - - +
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Residues in contact with ARG 37 (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 GLN 3.8 2.0 + - - -
36B PRO* 1.3 72.5 - - - +
38B GLU* 1.3 77.1 + - - +
39B ASP 3.1 0.2 - - - -
40B ILE* 3.4 12.4 + - + +
41B GLU* 2.9 62.4 + - - +
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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
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36B PRO* 2.8 24.0 + - + +
37B ARG* 1.3 89.0 + - + +
39B ASP* 1.3 62.8 + - - +
41B GLU* 3.7 8.7 - - - +
42B ARG* 3.0 37.6 + - - +
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Residues in contact with ASP 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 4.1 18.3 - - + +
36B PRO* 3.1 20.2 + - - +
38B GLU* 1.3 78.6 - - - +
40B ILE* 1.3 61.9 + - + +
41B GLU 3.1 1.3 - - - -
42B ARG* 2.8 32.9 + - - +
43B LEU* 2.6 36.3 + - - +
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Residues in contact with ILE 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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32B LEU* 3.6 48.0 - - + +
35B GLN* 3.8 17.5 - - + +
36B PRO 3.9 13.0 - - - +
37B ARG* 3.4 13.6 + - + +
39B ASP* 1.3 76.2 - - + +
41B GLU* 1.3 58.3 + - + +
43B LEU* 3.2 9.2 + - + +
44B ALA* 2.8 31.2 + - + +
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Residues in contact with GLU 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 ARG* 2.9 59.3 + - - +
38B GLU* 3.7 7.6 - - - +
39B ASP 3.1 0.4 - - - -
40B ILE* 1.3 77.8 - - + +
42B ARG* 1.3 54.3 + - - +
44B ALA* 3.0 7.6 + - - +
45B SER* 2.6 38.0 + - - -
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Residues in contact with ARG 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* 3.0 31.5 + - - +
39B ASP* 2.8 36.0 + - - +
41B GLU* 1.3 73.7 - - - +
43B LEU* 1.3 57.3 + - - +
45B SER* 3.1 10.9 + - - +
46B ALA* 3.0 32.0 + - + +
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Residues in contact with LEU 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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32B LEU* 4.5 23.8 - - + -
39B ASP 2.6 16.7 + - - +
40B ILE* 3.4 12.6 - - + +
42B ARG* 1.3 71.5 - - - +
44B ALA* 1.3 66.3 + - - +
46B ALA* 3.2 7.1 + - + +
47B LEU* 3.0 39.6 + - + +
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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
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40B ILE* 2.8 15.0 + - + +
41B GLU* 3.4 10.5 - - - +
43B LEU* 1.3 75.6 - - - +
45B SER* 1.3 64.3 - - - +
47B LEU* 3.1 15.8 + - - +
48B LEU* 3.0 32.9 + - + +
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Residues in contact with SER 45 (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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41B GLU 2.6 18.0 + - - -
42B ARG* 3.1 18.6 + - - +
44B ALA* 1.3 72.1 - - - +
46B ALA* 1.3 63.3 + - - +
48B LEU* 3.0 9.0 + - - +
49B GLU* 2.6 56.2 + - - +
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Residues in contact with ALA 46 (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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42B ARG* 3.0 18.5 + - + +
43B LEU* 3.2 9.4 + - + +
45B SER* 1.3 79.6 + - - +
47B LEU* 1.3 63.4 + - - +
49B GLU* 3.9 14.0 - - - +
50B ALA* 3.0 25.3 + - - +
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Residues in contact with LEU 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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43B LEU* 3.0 36.0 + - + +
44B ALA* 3.2 14.4 - - - +
46B ALA* 1.3 78.9 - - - +
48B LEU* 1.3 55.5 + - + +
50B ALA* 3.2 4.9 - - - +
51B LYS* 2.7 34.3 + - - +
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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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44B ALA* 3.0 22.6 + - + +
45B SER* 3.6 8.7 - - - +
47B LEU* 1.3 79.0 - - + +
49B GLU* 1.3 67.6 + - - +
50B ALA 2.9 1.3 - - - -
51B LYS* 2.8 11.4 + - + +
52B ARG* 2.8 26.4 + - - +
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Residues in contact with GLU 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 SER* 2.6 50.5 + - - +
46B ALA* 3.9 9.4 - - - +
48B LEU* 1.3 70.1 - - - +
50B ALA* 1.3 54.2 + - - +
52B ARG* 3.7 16.3 - - - +
53B ASP* 2.6 54.1 + - - +
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Residues in contact with ALA 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 ALA 3.0 17.1 + - - +
47B LEU* 3.2 6.5 - - - +
48B LEU 2.9 0.2 - - - -
49B GLU* 1.3 83.1 - - - +
51B LYS* 1.3 58.6 + - - +
53B ASP* 4.8 0.4 - - - -
54B LEU* 2.7 61.3 + - + +
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Residues in contact with LYS 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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47B LEU 2.7 17.3 + - - +
48B LEU* 2.8 17.1 + - + +
50B ALA* 1.3 72.2 - - - +
52B ARG* 1.3 59.8 + - - +
54B LEU* 4.0 9.1 - - - +
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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
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48B LEU 2.8 14.8 + - - +
49B GLU* 4.5 15.3 + - - +
51B LYS* 1.3 79.8 - - - +
53B ASP* 1.3 89.6 + - - +
54B LEU 3.4 4.3 + - - +
55B HIS* 5.4 2.6 - - - +
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Residues in contact with ASP 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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49B GLU* 2.6 32.7 + - - +
52B ARG* 1.3 105.3 + - - +
54B LEU* 1.3 63.7 + - + +
55B HIS* 3.5 8.8 - - - -
65B ASP* 3.3 36.6 - - + +
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Residues in contact with LEU 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 ALA* 2.7 44.8 + - + +
51B LYS* 4.0 11.9 - - - +
52B ARG 4.1 2.3 - - - +
53B ASP* 1.3 80.2 - - + +
55B HIS* 1.3 60.9 + - - +
63B ILE* 3.7 35.0 - - + -
64B THR* 3.6 8.7 - - - +
65B ASP* 5.0 4.3 - - + -
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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
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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