Contacts of the helix formed by residues 46 - 58 (chain A) in PDB entry 1NCS
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.6 21.3 - - - -
43A PHE* 6.0 0.9 - - + -
44A LYS* 2.5 14.4 + - + +
45A ARG* 1.3 79.9 - - - +
47A TYR* 1.3 79.8 + - + +
48A ASN* 3.2 53.1 + - + +
49A ILE* 4.2 11.2 - - + +
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Residues in contact with TYR 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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45A ARG* 5.8 0.9 - - + -
46A ARG* 1.3 91.3 - - + +
48A ASN* 1.3 70.4 + - - +
49A ILE* 3.6 1.3 - - - -
50A ARG* 2.9 56.7 + - - +
51A SER* 4.4 1.9 + - - -
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Residues in contact with ASN 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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43A PHE* 5.6 1.3 - - + -
46A ARG* 3.2 48.1 + - + +
47A TYR* 1.3 87.8 + - - +
49A ILE* 1.3 69.6 + - + +
50A ARG 3.1 1.6 - - - -
51A SER* 3.1 16.6 + - - -
52A HIS* 3.2 9.8 + - - +
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Residues in contact with ILE 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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24A VAL* 4.2 15.3 - - + -
32A PHE* 3.5 36.6 - - + -
34A CYS* 5.4 4.0 - - + -
43A PHE* 2.8 67.5 - - + -
44A LYS 4.8 1.3 - - - +
46A ARG* 4.2 13.5 - - + +
47A TYR* 5.2 0.2 - - - -
48A ASN* 1.3 76.8 - - + +
50A ARG* 1.3 88.4 + - + +
52A HIS* 2.8 25.8 + - + +
53A ILE* 3.0 13.8 + - + +
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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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20A ILE* 3.7 19.3 - - + +
21A ASP* 6.1 0.9 - - - +
24A VAL* 5.6 1.8 - - + -
47A TYR* 2.9 51.8 + - - +
49A ILE* 1.3 90.7 - - + +
51A SER* 1.3 76.8 + - - +
53A ILE* 3.0 29.9 + - + +
54A GLN* 3.6 5.5 + - - +
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Residues in contact with SER 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 TYR 4.8 2.5 - - - -
48A ASN* 3.1 12.0 + - - -
50A ARG* 1.3 90.0 - - - +
52A HIS* 1.3 57.7 + - - +
54A GLN* 2.9 41.0 + - - +
55A THR* 3.7 4.7 + - - -
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Residues in contact with HIS 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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34A CYS* 3.6 6.9 - - - -
39A CYS* 4.0 4.3 - - - -
41A LYS* 3.4 30.8 + - - -
43A PHE* 4.0 17.3 - + + -
48A ASN 3.2 6.4 + - - +
49A ILE* 2.8 23.0 + - + +
51A SER* 1.3 79.0 - - - +
53A ILE* 1.3 64.8 + - - +
54A GLN 3.0 1.1 + - - -
55A THR* 3.3 9.6 + - - +
56A HIS* 3.1 24.2 + + - -
61A ZN 2.0 38.1 - - - -
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Residues in contact with ILE 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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19A SER 4.8 1.8 - - - +
20A ILE* 3.3 30.3 - - + +
23A TYR* 3.8 21.8 - - + +
24A VAL* 3.0 37.2 - - + -
34A CYS* 4.9 2.5 - - - -
36A PHE* 4.9 2.7 - - + -
49A ILE* 3.0 17.7 - - + +
50A ARG* 3.0 13.9 + - - +
52A HIS* 1.3 79.4 - - + +
54A GLN* 1.3 55.8 + - - +
56A HIS* 2.8 23.1 - - + +
57A LEU* 2.6 45.7 - - + +
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Residues in contact with GLN 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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20A ILE* 3.4 45.0 - - - +
50A ARG* 3.6 4.6 + - - +
51A SER* 2.9 29.4 + - - +
53A ILE* 1.3 76.6 - - - +
55A THR* 1.3 53.4 + - - +
56A HIS 2.9 4.1 + - - -
57A LEU* 3.1 3.7 + - - -
58A GLU* 2.7 51.1 + - + +
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Residues in contact with THR 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 SER 3.7 3.5 + - - -
52A HIS* 3.3 11.6 + - - -
54A GLN* 1.3 79.4 - - - +
56A HIS* 1.3 64.2 + - - +
58A GLU* 3.4 23.4 + - + +
59A ASP 4.0 4.5 + - - -
60A ARG* 4.0 16.1 - - + +
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Residues in contact with HIS 56 (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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34A CYS* 4.0 2.9 - - - -
36A PHE* 2.8 60.0 - + + +
38A GLY 5.5 0.2 - - - -
39A CYS* 3.4 8.9 - - + -
52A HIS* 3.1 26.0 + + - -
53A ILE* 2.8 23.8 - - + +
54A GLN 2.9 0.4 - - - -
55A THR* 1.3 80.9 - - - +
57A LEU* 1.3 64.5 + - + +
60A ARG* 3.2 22.1 - - - +
61A ZN 2.0 38.2 - - - -
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Residues in contact with LEU 57 (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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19A SER* 3.5 25.8 - - - +
20A ILE* 4.6 8.3 - - + -
23A TYR* 5.5 7.2 - - + -
36A PHE* 4.1 18.2 - - + -
53A ILE* 2.6 43.7 - - + +
54A GLN* 3.1 3.7 + - - +
56A HIS* 1.3 84.1 - - + +
58A GLU* 1.3 60.7 + - - +
59A ASP 3.7 0.4 - - - -
60A ARG* 4.9 1.6 - - - -
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Residues in contact with GLU 58 (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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54A GLN* 2.7 39.0 + - + +
55A THR* 3.5 15.2 + - + -
56A HIS 3.3 1.8 - - - -
57A LEU* 1.3 77.0 - - - +
59A ASP* 1.3 74.2 + - + +
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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