Contacts of the helix formed by residues 29 - 43 (chain C) in PDB entry 4NAW
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 ARG 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ASP* 5.2 2.2 + - - +
13B PHE* 2.9 35.0 + - - +
14B GLY* 4.3 2.0 - - - +
15B ARG* 3.8 33.8 - - + +
38B LEU* 4.3 15.8 - - + +
25C ASP* 3.0 48.4 + - - +
28C GLN* 1.3 78.2 - - - +
30C GLN* 1.3 70.4 + - - +
31C ALA 3.1 1.8 - - - -
32C PHE* 2.9 13.7 + - - +
33C GLU* 3.0 29.0 + - - +
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Residues in contact with GLN 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASP 2.9 14.3 + - - +
26C ARG* 3.5 30.8 - - - +
29C ARG* 1.3 75.8 - - - +
31C ALA* 1.3 61.2 + - - +
32C PHE 3.3 0.7 + - - -
33C GLU* 3.6 31.5 + - - +
34C GLU* 4.8 2.1 + - - +
95F ALA* 3.8 23.8 - - + +
96F LEU 4.5 2.0 - - - +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG 3.3 8.4 + - - +
27C LEU* 3.7 23.6 - - + +
29C ARG 3.1 1.4 - - - -
30C GLN* 1.3 79.1 - - - +
32C PHE* 1.3 68.5 + - + +
34C GLU 5.5 0.4 + - - -
35C ILE* 4.4 4.2 + - - +
95F ALA* 4.7 1.8 - - + -
96F LEU* 3.2 32.1 - - + +
97F PRO* 3.3 23.8 - - - +
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Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 3.7 23.3 - - + -
36B TYR* 6.6 0.2 - + - -
38B LEU* 4.6 1.6 - - + -
96B LEU* 3.9 37.7 - - + -
97B PRO* 3.9 23.8 - - + -
27C LEU 4.1 6.5 - - - -
28C GLN 3.5 16.8 - - - +
29C ARG 2.9 6.0 + - - +
31C ALA* 1.3 91.0 - - + +
33C GLU* 1.3 64.3 + - - +
34C GLU 3.3 2.5 - - - -
35C ILE* 3.3 18.1 - - + +
36C ILE* 2.9 35.1 + - + +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.8 24.1 - - + +
29C ARG* 3.0 28.0 + - - +
30C GLN* 3.6 32.7 - - - +
31C ALA 3.8 0.2 - - - -
32C PHE* 1.3 77.2 - - - +
34C GLU* 1.3 71.0 + - + +
36C ILE* 4.0 1.7 - - - +
37C LEU* 3.0 29.7 + - - +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLN 4.8 2.1 + - - +
31C ALA 5.5 0.4 + - - -
32C PHE 3.3 0.4 - - - -
33C GLU* 1.3 90.8 - - + +
35C ILE* 1.3 61.8 + - - +
37C LEU* 3.7 8.7 - - + +
38C GLN* 2.9 30.5 + - - +
19F CYS* 5.5 2.8 - - - -
36F TYR* 4.0 9.9 + - - +
97F PRO* 6.5 1.3 - - + -
99F ASN* 4.5 14.4 + - - +
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ALA 4.4 5.1 + - - +
32C PHE* 3.3 32.5 - - + +
34C GLU* 1.3 74.7 - - - +
36C ILE* 1.3 67.1 + - + +
38C GLN* 3.7 1.7 - - + +
39C TYR* 2.8 31.5 + - + +
36F TYR* 3.5 53.5 + - + +
97F PRO* 5.2 8.7 - - + +
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO* 3.9 17.3 - - + -
18B THR 4.7 1.6 - - - +
36B TYR* 3.7 42.0 - - + +
37B LEU* 4.0 18.6 - - + +
38B LEU* 4.0 18.4 - - + +
97B PRO* 6.0 0.4 - - + -
32C PHE* 2.9 40.6 + - + +
33C GLU* 4.0 3.8 - - - +
35C ILE* 1.3 81.4 - - + +
37C LEU* 1.3 63.0 + - - +
39C TYR* 3.3 5.4 + - - +
40C ASN* 3.0 32.7 + - - +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU 3.0 20.0 + - - +
34C GLU* 3.7 8.7 - - + +
36C ILE* 1.3 77.4 - - - +
38C GLN* 1.3 58.6 + - - +
40C ASN* 3.3 8.5 + - + +
41C LYS* 2.9 29.4 + - + +
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Residues in contact with GLN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU 2.9 17.8 + - - +
35C ILE* 3.7 7.4 - - - +
37C LEU* 1.3 73.9 - - - +
39C TYR* 1.3 65.7 + - - +
41C LYS* 3.0 42.5 + - - +
42C LEU* 3.3 27.3 + - + +
33F GLU* 2.7 25.6 - - - +
34F PRO* 3.4 25.1 - - + +
36F TYR* 4.3 21.3 - - + +
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Residues in contact with TYR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLU* 4.0 8.1 - - - +
34B PRO* 2.7 44.8 + - - +
36B TYR* 3.6 41.7 - + + -
35C ILE* 2.8 20.4 + - + +
36C ILE* 3.5 7.2 - - - +
38C GLN* 1.3 77.1 - - - +
40C ASN* 1.3 64.7 + - - +
42C LEU* 3.2 7.3 + - - +
43C LEU* 3.0 47.5 + - + +
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Residues in contact with ASN 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.4 34.8 + - - -
36B TYR 3.0 25.0 + - - -
37B LEU* 5.9 0.8 - - - +
36C ILE* 3.0 32.7 + - - +
37C LEU* 3.7 10.3 - - + +
39C TYR* 1.3 81.5 - - - +
41C LYS* 1.3 66.3 + - - +
43C LEU* 3.3 22.7 + - - +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 2.9 16.8 + - + +
38C GLN* 3.0 35.7 + - - +
39C TYR 3.2 0.2 - - - -
40C ASN* 1.3 78.6 - - - +
42C LEU* 1.3 68.5 + - + +
43C LEU 3.7 2.8 + - - +
33F GLU* 2.6 36.0 + - - +
34F PRO* 4.9 0.2 - - - +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 3.3 29.8 + - + +
39C TYR* 3.2 6.1 + - - +
41C LYS* 1.3 84.7 - - + +
43C LEU* 1.3 68.6 + - - +
33F GLU* 3.9 35.9 - - + +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLU* 3.9 43.3 - - + +
34B PRO 4.5 1.1 - - - +
35B TYR* 3.8 33.4 - - + -
55B HIS* 4.0 12.8 - - + +
39C TYR* 3.0 41.3 + - + +
40C ASN* 3.3 19.9 + - - +
41C LYS 4.3 2.9 - - - +
42C LEU* 1.3 84.0 - - - +
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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