Contacts of the helix formed by residues 40 - 55 (chain A) in PDB entry 5CVA
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 THR 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ALA 3.6 5.3 + - - +
39A PRO* 1.3 77.0 - - - +
41A ASP* 1.3 66.2 + - - +
42A GLN* 3.6 8.1 + - - +
43A HIS* 3.2 24.6 + - - +
44A ILE* 3.1 21.1 + - - +
43C ARG* 3.6 3.1 - - - +
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A THR* 1.3 72.8 - - - +
42A GLN* 1.3 62.9 + - - +
44A ILE* 3.1 4.5 + - - +
45A LYS* 3.0 28.6 + - - +
43C ARG* 2.8 34.6 + - - +
47C LEU* 3.6 31.2 - - + +
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Residues in contact with GLN 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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40A THR* 3.2 7.4 + - - +
41A ASP* 1.3 79.5 - - - +
43A HIS* 1.3 62.0 + - - +
45A LYS* 3.3 24.2 + - - +
46A GLN* 3.0 48.8 + - - +
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Residues in contact with HIS 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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39A PRO* 4.1 20.2 - - + -
40A THR* 3.2 26.7 + - - +
42A GLN* 1.3 76.6 - - - +
44A ILE* 1.3 64.0 + - - +
46A GLN* 3.1 18.6 + - + +
47A VAL* 2.9 33.8 + - + +
41B ASP* 2.6 38.8 + - - -
44B ILE* 4.1 3.1 - - + -
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Residues in contact with ILE 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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39A PRO* 3.9 13.7 - - + -
40A THR 3.1 12.3 + - - +
41A ASP 3.1 6.7 + - - +
43A HIS* 1.3 75.1 - - - +
45A LYS* 1.3 65.2 + - - +
47A VAL* 3.2 4.3 + - - +
48A CYS* 3.0 22.2 + - - -
44B ILE* 4.0 27.3 - - + +
39C ALA* 3.6 28.7 - - + -
43C ARG* 3.7 17.7 - - + +
44C ILE* 4.2 11.2 - - + -
47C LEU* 3.7 30.3 - - + -
48C CYS* 3.9 16.8 - - - -
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Residues in contact with LYS 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 ASP* 3.0 15.9 + - - +
42A GLN* 3.6 31.1 + - - +
44A ILE* 1.3 76.6 - - - +
46A GLN* 1.3 56.9 + - - +
48A CYS* 3.2 3.3 + - - +
49A MSE 3.0 26.7 + - - +
47C LEU* 3.8 49.1 - - + +
48C CYS* 4.3 4.3 - - - -
51C MET* 3.6 22.6 - - + +
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Residues in contact with GLN 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 GLN* 3.0 40.1 + - - +
43A HIS* 3.1 24.5 + - + +
45A LYS* 1.3 76.9 - - - +
47A VAL* 1.3 62.5 + - + +
49A MSE 3.5 5.4 + - - +
50A ARG* 3.1 21.5 + - - +
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Residues in contact with VAL 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 HIS* 2.9 45.1 + - + +
44A ILE 3.2 6.9 + - - +
46A GLN* 1.3 75.5 - - + +
48A CYS* 1.3 63.2 + - - +
50A ARG* 3.1 20.5 + - - +
51A VAL* 2.9 23.1 + - + +
41B ASP* 3.7 16.8 - - + +
44B ILE* 3.6 25.8 - - + -
45B VAL* 3.9 26.2 - - + +
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Residues in contact with CYS 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 ILE 3.0 11.8 + - - -
45A LYS 3.6 5.8 - - - +
47A VAL* 1.3 75.2 - - - +
49A MSE 1.3 58.1 + - - +
51A VAL* 3.3 7.9 + - - +
52A ILE* 3.0 33.4 + - + +
44B ILE* 4.1 15.0 - - - -
48B ALA* 4.2 18.6 - - + +
44C ILE* 4.3 4.3 - - - -
48C CYS* 2.0 54.1 - - + -
51C MET* 4.0 8.1 - - - -
52C ILE* 5.4 1.8 - - + -
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Residues in contact with MSE 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 LYS 3.0 15.6 + - - +
46A GLN* 4.0 6.1 - - - +
47A VAL 3.2 0.2 - - - -
48A CYS* 1.3 73.4 - - - +
50A ARG* 1.3 66.8 + - - +
52A ILE* 3.2 20.7 + - + +
53A GLN* 2.9 62.9 + - + +
56A PHE* 6.2 0.9 - - + -
51C MET* 3.7 16.8 - - + +
55C GLN* 4.2 29.6 - - - +
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Residues in contact with ARG 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 GLN 3.1 14.9 + - - +
47A VAL* 3.1 17.1 + - - +
49A MSE 1.3 76.3 - - - +
51A VAL* 1.3 58.7 + - - +
53A GLN* 3.1 14.3 + - - +
54A GLU* 2.8 68.1 + - + +
101A GOL 4.2 13.1 - - - -
41B ASP* 4.1 23.4 + - - +
45B VAL* 4.0 22.4 - - - +
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Residues in contact with VAL 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 VAL* 2.9 19.8 + - + +
48A CYS 3.6 6.7 - - - +
49A MSE 3.3 0.2 - - - -
50A ARG* 1.3 79.1 - - + +
52A ILE* 1.3 64.3 + - + +
54A GLU 3.2 0.9 + - - -
55A HIS* 3.0 24.9 + - + +
101A GOL 3.8 18.6 - - - +
45B VAL* 3.9 34.8 - - + -
48B ALA* 4.0 20.0 - - + -
49B LEU* 3.8 31.2 - - + +
52B LEU* 4.5 8.3 - - + -
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Residues in contact with ILE 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 CYS 3.0 18.9 + - - +
49A MSE 3.4 14.4 - - + +
51A VAL* 1.3 74.3 - - + +
53A GLN* 1.3 58.9 + - - +
55A HIS 3.1 4.0 + - - -
56A PHE* 2.9 36.4 + - + -
59A MSE 3.7 20.6 - - + +
48B ALA* 6.5 0.2 - - + -
52B LEU* 4.4 12.1 - - + -
51C MET* 3.7 31.9 - - + -
52C ILE* 3.8 29.4 - - + -
55C GLN* 3.8 32.3 - - + +
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Residues in contact with GLN 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 MSE 2.9 52.9 + - + +
50A ARG* 3.6 13.0 - - - +
52A ILE* 1.3 77.2 - - + +
54A GLU* 1.3 62.9 + - + +
55A HIS 3.3 0.5 + - - -
56A PHE* 3.4 24.1 + - + +
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Residues in contact with GLU 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 ARG* 2.8 62.0 + - + +
51A VAL 3.2 1.1 + - - +
53A GLN* 1.3 78.7 - - + +
55A HIS* 1.3 65.6 + - + +
56A PHE 3.5 0.2 - - - -
57A ALA* 5.2 3.0 + - - +
58A GLU* 5.5 0.7 - - - +
101A GOL 3.1 28.4 + - - +
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Residues in contact with HIS 55 (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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51A VAL 3.0 19.9 + - - +
52A ILE 3.1 3.3 + - - -
54A GLU* 1.3 81.9 + - - +
56A PHE* 1.3 64.3 + - - +
57A ALA* 3.1 3.4 - - - +
58A GLU* 2.5 44.1 + - + +
59A MSE 2.9 25.1 + - + +
101A GOL 2.6 46.4 + - - -
49B LEU* 3.5 27.6 - - + +
52B LEU* 4.2 14.8 - - + -
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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