Contacts of the helix formed by residues 36 - 54 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU 4.1 4.3 - - - +
35A GLN* 1.3 97.5 - - + +
37A ARG* 1.3 65.2 + - - +
38A GLU* 3.4 16.8 - - - +
39A ASP* 3.8 20.7 + - - +
40A ILE* 2.9 26.6 + - - +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PRO* 1.3 78.2 - - - +
38A GLU* 1.3 79.5 + - - +
40A ILE* 3.4 9.5 + - - +
41A GLU* 2.9 67.5 + - - +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.4 16.5 - - - +
37A ARG* 1.3 92.9 + - + +
39A ASP* 1.3 65.0 + - - +
41A GLU* 3.7 9.5 + - - +
42A ARG* 3.0 36.8 + - - +
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Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLN* 4.3 14.9 - - + +
36A PRO* 3.8 23.4 + - + +
37A ARG 3.1 0.8 - - - -
38A GLU* 1.3 80.1 - - - +
40A ILE* 1.3 72.0 + - + +
41A GLU 3.1 1.1 - - - -
42A ARG* 2.8 33.7 + - - +
43A LEU* 2.7 24.7 + - - +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.7 32.3 - - + +
35A GLN* 3.5 31.4 - - + +
36A PRO 2.9 17.9 - - - +
37A ARG* 3.4 8.5 + - - +
39A ASP* 1.3 75.7 - - + +
41A GLU* 1.3 59.0 + - + +
43A LEU* 3.1 13.4 + - + +
44A ALA* 2.9 31.2 + - + +
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 2.9 60.1 + - - +
38A GLU* 3.7 7.5 - - - +
39A ASP 3.1 0.4 - - - -
40A ILE* 1.3 77.1 - - + +
42A ARG* 1.3 56.5 + - - +
44A ALA* 3.1 6.5 + - - +
45A SER* 2.6 38.3 + - - -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.0 26.1 + - - +
39A ASP* 2.8 36.5 + - - +
41A GLU* 1.3 80.9 - - - +
43A LEU* 1.3 55.4 + - - +
45A SER* 3.4 9.7 + - - +
46A ALA* 2.9 33.0 + - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.1 27.6 - - + -
39A ASP 2.7 16.2 + - - +
40A ILE* 3.5 16.4 - - + +
42A ARG* 1.3 71.8 - - - +
44A ALA* 1.3 52.4 + - + +
46A ALA* 3.5 4.4 - - - +
47A LEU* 2.8 64.4 + - + +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 2.9 21.5 + - + +
41A GLU* 3.6 6.1 - - - +
43A LEU* 1.3 70.9 - - + +
45A SER* 1.4 63.9 + - - +
47A LEU* 3.1 15.2 + - + +
48A LEU* 2.9 32.8 + - + +
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLU* 2.6 19.7 + - - -
42A ARG* 3.4 16.3 + - - +
44A ALA* 1.4 71.4 - - - +
46A ALA* 1.3 60.1 + - - +
48A LEU* 3.7 8.5 - - - +
49A GLU* 2.3 60.8 + - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 2.9 19.9 + - + +
43A LEU* 3.5 7.2 - - + +
45A SER* 1.3 81.6 + - - +
47A LEU* 1.3 65.4 + - + +
49A GLU* 3.4 15.0 - - - +
50A ALA* 3.1 25.6 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 2.8 49.1 + - + +
44A ALA* 3.1 14.8 + - + +
46A ALA* 1.3 75.7 - - + +
48A LEU* 1.3 65.9 + - + +
49A GLU 2.9 3.3 + - - -
50A ALA* 3.2 3.3 + - - +
51A LYS* 3.1 25.1 + - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 2.9 25.3 + - + +
45A SER* 3.7 9.4 - - - +
47A LEU* 1.3 73.3 - - + +
49A GLU* 0.8 85.9 - - + +
51A LYS* 3.6 7.2 + - + +
52A ARG* 3.3 11.1 + - - +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A SER* 2.3 47.1 + - - +
46A ALA* 3.4 11.9 - - - +
48A LEU* 0.8 106.2 - - + +
50A ALA* 1.4 55.6 - - - +
52A ARG* 2.1 61.1 + - - +
53A ASP* 3.2 8.7 + - - +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA 3.1 14.2 + - - +
47A LEU* 3.8 3.8 - - - +
49A GLU* 1.4 78.1 - - - +
51A LYS* 1.3 68.5 + - - +
52A ARG 2.6 1.7 + - - -
53A ASP* 4.4 5.8 - - - +
54A LEU* 2.8 49.2 + - + +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU 3.1 14.5 + - - +
48A LEU* 3.8 7.6 - - + +
50A ALA* 1.3 80.2 - - - +
52A ARG* 1.3 60.4 + - - +
54A LEU* 4.0 10.2 - - - +
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU 3.6 6.3 - - - +
49A GLU* 2.1 48.0 + - - +
50A ALA 2.6 0.2 + - - -
51A LYS* 1.3 71.0 - - - +
53A ASP* 1.3 89.0 + - - +
54A LEU 3.4 3.5 + - - +
55A HIS* 4.9 6.1 - - - +
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Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 3.2 10.1 + - - +
50A ALA* 3.1 5.7 + - - +
52A ARG* 1.3 111.6 + - - +
54A LEU* 1.3 60.4 + - + +
55A HIS* 3.6 5.2 - - - -
64A THR 3.1 0.3 - - - +
65A ASP* 2.5 55.0 - - + +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 2.8 33.9 + - + +
51A LYS* 4.0 12.6 - - - +
52A ARG 4.1 1.7 - - - +
53A ASP* 1.3 86.7 - - + +
55A HIS* 1.1 62.1 + - - +
63A ILE* 3.3 34.3 - - + -
64A THR* 2.9 15.7 - - - +
65A ASP* 4.6 6.1 - - + +
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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
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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