Contacts of the helix formed by residues 36 - 50 (chain A) in PDB entry 6P59
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 ASP 4.5 1.3 - - - +
35A ARG* 1.3 92.6 - - + +
37A HIS* 1.3 66.9 + - - +
38A GLU* 3.3 6.7 - - + +
39A GLU* 3.1 20.8 + - + +
40A ARG* 3.1 17.3 + - - +
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Residues in contact with HIS 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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35A ARG 3.7 0.4 + - - -
36A PRO* 1.3 74.3 - - - +
38A GLU* 1.3 64.3 + - + +
40A ARG* 3.0 23.7 + - - +
41A GLN* 3.1 35.0 + - - +
117A GLN* 2.6 29.4 + - + -
118A ARG* 4.1 15.0 - - - -
119A LEU* 4.2 20.6 - - + +
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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
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36A PRO* 3.3 5.5 - - + +
37A HIS* 1.3 78.6 - - + +
39A GLU* 1.3 60.3 + - - +
41A GLN* 3.5 32.6 + - - +
42A ALA* 3.7 11.3 + - - +
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Residues in contact with GLU 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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32A PHE* 6.1 0.4 - - + -
35A ARG* 3.4 46.7 + - + +
36A PRO* 3.1 22.2 + - + +
38A GLU* 1.3 77.5 - - - +
40A ARG* 1.3 59.7 + - - +
42A ALA* 3.2 7.7 + - + +
43A ARG* 2.9 45.6 + - + +
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Residues in contact with ARG 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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29A TYR* 2.8 29.1 + - + -
30A THR* 4.7 0.6 - - - +
31A GLY 2.5 28.7 + - - +
32A PHE* 3.0 40.0 + - + +
33A ARG* 3.2 20.0 - - - +
35A ARG* 3.5 14.6 - - + +
36A PRO 3.1 10.5 + - - +
37A HIS* 3.0 19.8 + - - +
39A GLU* 1.3 77.1 - - - +
41A GLN* 1.3 58.4 + - - +
43A ARG* 3.0 8.6 + - - +
44A PHE* 2.9 29.3 + - - +
119A LEU* 3.6 30.1 + - + +
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Residues in contact with GLN 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 HIS* 3.1 25.8 + - - +
38A GLU* 3.5 45.8 + - - +
40A ARG* 1.3 73.7 - - - +
42A ALA* 1.3 57.0 + - - +
44A PHE* 3.9 2.1 - - - +
45A GLN* 2.9 30.1 + - - +
116A LEU* 3.6 19.5 - - + +
117A GLN* 3.5 27.4 - - - +
119A LEU* 4.1 16.2 - - + +
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Residues in contact with ALA 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 3.7 10.3 + - - +
39A GLU* 3.2 10.9 + - + +
40A ARG 3.1 0.6 - - - -
41A GLN* 1.3 80.9 - - - +
43A ARG* 1.3 64.3 + - - +
45A GLN* 3.6 5.3 - - - +
46A ASN* 3.1 33.2 + - - +
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Residues in contact with ARG 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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29A TYR* 4.4 2.4 + - - -
32A PHE* 3.5 51.1 - - + -
35A ARG* 4.8 7.9 - - - +
39A GLU* 2.9 36.5 + - + +
40A ARG 3.0 6.9 + - - +
42A ALA* 1.3 77.7 - - + +
44A PHE* 1.3 57.5 + - - +
46A ASN* 3.4 10.7 + - - +
47A ALA* 3.0 26.7 + - - +
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Residues in contact with PHE 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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29A TYR* 3.5 44.5 + + + -
40A ARG 2.9 15.0 + - - +
41A GLN 4.1 3.1 - - - +
43A ARG* 1.3 73.6 - - - +
45A GLN* 1.3 71.3 + - - +
47A ALA* 3.4 2.8 + - - +
48A CYS* 3.2 49.2 + - - -
55A ILE* 4.5 7.0 - - + -
57A PHE* 3.7 32.1 - + - -
88A LEU* 5.5 0.2 - - + -
95A VAL* 3.6 28.3 - - + -
114A ILE* 4.3 8.5 - - + -
116A LEU* 4.0 20.4 - - + -
119A LEU* 4.0 17.9 - - + -
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Residues in contact with GLN 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 GLN 2.9 21.0 + - - +
42A ALA* 3.6 9.6 - - - +
43A ARG 3.3 0.2 - - - -
44A PHE* 1.3 81.6 - - - +
46A ASN* 1.3 65.5 + - - +
48A CYS* 3.5 5.1 + - - +
49A ARG* 3.0 59.6 + - + +
88A LEU* 5.1 6.5 - - - +
116A LEU* 3.1 35.9 - - - +
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Residues in contact with ASN 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 ALA* 3.1 19.3 + - - +
43A ARG* 3.8 11.4 - - - +
44A PHE 3.3 0.2 - - - -
45A GLN* 1.3 80.1 - - - +
47A ALA* 1.3 58.5 + - - +
49A ARG* 4.3 5.8 - - - +
50A ASP* 2.6 42.9 + - + +
53A SER* 4.9 0.4 - - - -
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Residues in contact with ALA 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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29A TYR* 5.0 6.3 - - + +
43A ARG 3.0 17.3 + - - +
44A PHE* 3.6 9.0 - - + +
45A GLN 3.3 0.6 - - - -
46A ASN* 1.3 76.5 - - - +
48A CYS* 1.3 61.4 + - - +
49A ARG 3.4 0.3 + - - -
50A ASP 3.9 4.2 + - - +
53A SER* 3.4 34.8 - - - +
54A GLU 3.9 11.2 - - - +
55A ILE* 3.5 21.5 - - + +
6B TRP* 4.0 4.3 - - - -
77B THR* 6.5 0.4 - - + -
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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 PHE* 3.2 50.6 + - - -
45A GLN* 3.9 6.7 - - - +
46A ASN 3.3 0.2 - - - -
47A ALA* 1.3 76.5 - - - +
49A ARG* 1.3 60.2 + - - +
55A ILE* 4.3 11.2 - - - -
86A VAL* 4.9 6.0 - - + +
88A LEU* 3.6 36.4 - - + +
95A VAL* 4.9 3.8 - - - -
4B LYS* 3.8 6.6 - - - +
6B TRP* 3.7 24.2 - - - -
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Residues in contact with ARG 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 GLN* 3.0 46.7 - - + +
46A ASN* 3.0 6.8 + - - +
48A CYS* 1.3 79.2 - - + +
50A ASP* 1.3 67.0 + - - +
51A GLY* 3.7 0.9 + - - -
88A LEU* 4.3 29.0 - - - +
89A GLU* 5.6 7.5 + - - +
4B LYS* 4.5 6.2 - - - +
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Residues in contact with ASP 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 ASN* 2.6 22.7 + - + +
47A ALA 3.9 2.1 + - - +
49A ARG* 1.3 73.6 - - - +
51A GLY* 1.3 68.2 + - - +
52A ARG* 2.7 28.7 + - - +
53A SER* 3.1 26.8 + - - +
4B LYS* 2.4 33.8 + - - -
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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