Contacts of the helix formed by residues 50 - 69 (chain C) in PDB entry 1NQ3
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 GLY 50 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL 4.6 2.2 + - - -
48C PRO 3.7 1.2 - - - -
49C GLY* 1.3 78.8 - - - +
51C VAL* 1.3 65.9 + - - -
52C VAL 3.2 2.9 - - - -
53C GLU* 3.1 4.3 + - - +
54C GLU* 3.0 32.2 + - - +
120C ARG* 5.1 2.9 - - - -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLY* 1.3 70.1 - - - -
52C VAL* 1.3 69.8 + - + +
54C GLU* 3.4 3.8 + - - +
55C ALA* 2.9 27.7 + - - +
83C LEU* 5.1 0.2 - - + -
88C ASP* 3.8 35.0 - - + +
91C ALA* 5.0 5.2 - - + -
92C VAL* 3.6 25.4 - - + -
120C ARG* 3.8 41.7 - - + +
121C VAL* 4.0 5.1 - - + +
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY 5.6 1.8 - - - +
50C GLY 3.2 1.4 - - - -
51C VAL* 1.3 81.2 - - + +
53C GLU* 1.3 75.3 + - + +
55C ALA* 3.3 6.7 + - - +
56C LYS* 3.2 28.3 + - + +
91C ALA* 3.8 32.3 - - + +
92C VAL* 5.8 1.1 - - - -
95C VAL* 3.9 19.5 - - + +
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 4.0 13.0 - - + +
48C PRO 3.5 25.7 - - - +
49C GLY* 3.7 16.8 + - - +
50C GLY 3.1 7.4 + - - +
52C VAL* 1.3 83.6 - - + +
54C GLU* 1.3 62.9 + - - +
56C LYS* 2.6 43.4 + - - +
57C GLN* 3.1 22.9 + - - +
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Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLY* 3.2 29.6 + - - +
46C LEU* 4.4 16.9 - - + +
47C VAL* 4.0 19.1 - - - +
50C GLY* 3.0 18.5 + - - +
51C VAL 3.6 7.0 - - - +
53C GLU* 1.3 78.1 - - - +
55C ALA* 1.3 56.7 + - - +
57C GLN* 4.6 1.1 - - - -
58C ALA* 2.8 27.9 + - - +
118C GLY 5.2 0.2 - - - +
119C GLY* 3.6 7.4 - - - -
120C ARG* 2.7 51.0 + - - +
121C VAL* 3.7 15.0 + - + +
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL 2.9 17.2 + - - +
52C VAL* 3.6 9.0 - - - +
53C GLU 3.2 0.2 - - - -
54C GLU* 1.3 74.2 - - - +
56C LYS* 1.3 66.4 + - - +
58C ALA* 3.2 4.6 + - - +
59C LEU* 2.9 31.5 + - + +
92C VAL* 4.3 24.0 - - + -
95C VAL* 4.4 15.0 - - + -
121C VAL* 3.7 15.2 - - + +
123C ILE* 5.3 2.2 - - + -
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Residues in contact with LYS 56 (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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52C VAL* 3.2 17.0 + - + +
53C GLU* 2.6 52.1 + - - +
55C ALA* 1.3 78.1 - - - +
57C GLN* 1.3 57.4 + - - +
59C LEU* 3.2 0.7 + - - +
60C THR* 2.9 35.9 + - + +
95C VAL* 3.7 26.7 - - + -
99C TYR* 3.6 12.1 + - - +
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Residues in contact with GLN 57 (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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38C GLY* 3.7 15.9 - - - +
39C MET 3.3 22.4 + - - +
40C ASP* 4.7 1.1 - - - +
41C PRO* 3.7 14.7 - - - +
47C VAL* 3.9 18.9 - - + +
53C GLU 3.1 13.6 + - - +
54C GLU* 3.7 3.8 - - - +
56C LYS* 1.3 76.7 - - - +
58C ALA* 1.3 56.4 + - - +
60C THR* 2.8 18.6 + - - +
61C ASN* 2.7 67.8 + - - +
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Residues in contact with ALA 58 (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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36C GLN* 3.7 24.1 - - + +
37C LEU* 3.6 16.8 - - - +
38C GLY* 3.9 0.8 - - - +
54C GLU 2.8 22.1 + - - +
55C ALA* 3.5 8.3 - - - +
57C GLN* 1.3 73.3 - - - +
59C LEU* 1.3 59.4 + - - +
61C ASN* 3.2 5.9 - - - +
62C ILE* 3.0 32.4 + - - +
121C VAL* 5.1 3.8 - - + +
123C ILE* 4.4 14.4 - - + -
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 2.9 21.8 + - + +
56C LYS 3.7 3.4 - - - +
58C ALA* 1.3 74.6 - - - +
60C THR* 1.3 60.3 + - - +
62C ILE* 3.2 13.7 + - + +
63C GLY 2.8 23.2 + - - -
73C PHE* 3.2 24.4 - - + -
92C VAL* 5.6 0.9 - - + +
95C VAL* 3.9 13.7 - - + -
96C TYR* 4.0 27.4 - - + +
99C TYR* 3.7 41.1 - - + -
100C PHE* 5.1 4.3 - - + -
123C ILE* 3.6 28.9 - - + -
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Residues in contact with THR 60 (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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56C LYS* 2.9 25.3 + - + +
57C GLN* 2.8 36.4 + - - +
59C LEU* 1.3 76.4 - - - +
61C ASN* 1.3 62.5 + - - +
63C GLY* 3.1 2.7 + - - +
64C GLU* 3.0 30.8 + - - +
73C PHE* 5.7 0.4 - - - -
99C TYR* 3.6 20.2 - - + +
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Residues in contact with ASN 61 (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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13C LYS 4.3 3.6 + - - -
14C ALA* 4.0 3.5 - - - +
15C PRO* 3.3 26.4 - - + +
36C GLN* 3.8 15.7 + - + +
37C LEU 3.2 17.5 - - - +
39C MET 3.0 17.8 + - - +
41C PRO* 3.7 9.1 - - - +
57C GLN* 2.7 39.3 + - - +
58C ALA* 3.2 11.0 - - - +
59C LEU 3.1 0.2 - - - -
60C THR* 1.3 79.8 + - - +
62C ILE* 1.3 61.2 + - - +
64C GLU* 3.4 4.7 + - - +
65C ILE* 3.2 28.2 + - - +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 4.4 17.7 - - + -
36C GLN* 3.7 17.3 - - + -
58C ALA 3.0 17.8 + - - +
59C LEU* 3.2 17.5 + - + +
61C ASN* 1.3 75.5 - - - +
63C GLY* 1.3 58.6 + - - +
65C ILE* 3.2 9.1 + - - +
66C LEU* 2.9 45.0 + - + +
73C PHE* 4.1 9.2 - - + -
76C VAL* 5.3 2.2 - - + -
123C ILE* 3.7 43.7 - - + +
124C GLU 5.2 0.2 - - - -
125C ALA* 4.8 13.7 - - + -
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Residues in contact with GLY 63 (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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59C LEU 2.8 15.4 + - - -
60C THR* 3.1 5.3 + - - -
62C ILE* 1.3 77.4 - - - +
64C GLU* 1.3 58.3 + - - +
66C LEU* 3.3 8.0 + - - +
67C LYS* 3.0 27.7 + - - +
71C CYS 5.0 0.3 - - - +
72C ASP* 5.8 0.5 - - - -
73C PHE* 3.7 21.3 - - - -
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Residues in contact with GLU 64 (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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11C THR* 4.1 7.1 + - + +
13C LYS* 3.3 59.6 - - + +
14C ALA* 4.6 2.2 - - + -
60C THR* 3.0 20.1 + - - +
61C ASN* 3.8 6.7 - - - +
63C GLY* 1.3 76.3 - - - +
65C ILE* 1.3 62.9 + - - +
67C LYS* 3.3 23.4 + - - +
68C ALA* 3.0 23.7 + - - +
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Residues in contact with ILE 65 (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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9C ILE* 3.8 10.1 - - + +
11C THR* 4.8 2.7 - - - -
14C ALA* 3.8 16.2 - - + -
23C GLN* 4.0 26.7 - - + +
24C ALA* 3.7 28.7 - - + -
31C ILE* 5.6 1.1 - - + -
33C ILE* 4.2 17.9 - - + -
36C GLN* 3.5 38.8 - - + +
61C ASN 3.2 12.9 + - - +
62C ILE* 3.5 9.0 - - - +
63C GLY 3.2 0.2 - - - -
64C GLU* 1.3 77.0 - - - +
66C LEU* 1.3 63.8 - - - +
68C ALA* 3.3 9.3 + - - +
69C ALA* 3.3 15.0 + - + +
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Residues in contact with LEU 66 (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 ILE* 5.2 4.7 - - + -
33C ILE* 3.6 24.5 - - + -
62C ILE* 2.9 30.4 + - + +
63C GLY* 3.3 8.0 + - - +
65C ILE* 1.3 75.7 - - - +
67C LYS* 1.3 54.9 + - - +
69C ALA* 2.8 26.0 + - - +
70C GLY 3.1 0.2 + - - -
71C CYS* 2.8 38.6 + - + +
72C ASP* 3.6 24.2 - - - +
73C PHE* 3.9 12.1 - - + +
76C VAL* 3.9 18.2 - - + -
127C ALA* 3.8 22.0 - - + -
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Residues in contact with LYS 67 (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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13C LYS* 5.8 6.0 - - - +
63C GLY 3.0 13.9 + - - +
64C GLU* 3.5 27.1 - - - +
66C LEU* 1.3 76.5 - - - +
68C ALA* 1.3 58.0 + - - +
70C GLY* 2.8 19.8 + - - -
71C CYS 3.3 13.6 + - - +
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Residues in contact with ALA 68 (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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9C ILE* 4.0 16.4 - - + +
10C SER 4.5 4.0 - - - +
11C THR* 2.7 31.6 - - + +
64C GLU 3.0 9.3 + - - +
65C ILE 3.6 9.2 - - - +
66C LEU 3.2 0.2 - - - -
67C LYS* 1.3 76.5 - - - +
69C ALA* 1.3 58.4 + - - +
70C GLY 3.2 1.0 + - - -
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Residues in contact with ALA 69 (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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7C ARG* 5.4 5.1 + - - +
9C ILE* 3.8 26.2 - - + -
26C LEU* 5.4 2.0 - - + -
31C ILE* 3.6 28.3 - - + -
65C ILE* 3.3 8.6 + - + +
66C LEU* 2.8 10.5 + - - +
68C ALA* 1.3 78.9 - - - +
70C GLY* 1.3 63.1 + - - +
71C CYS* 3.2 5.7 + - - -
129C GLN* 3.6 21.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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