Contacts of the helix formed by residues 50 - 68 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL 4.6 0.2 + - - -
48A PRO* 3.6 2.6 - - - +
49A GLY* 1.3 78.1 - - - +
51A VAL* 1.3 60.6 + - - -
52A VAL 3.3 2.9 - - - -
53A GLU 3.2 2.3 + - - -
54A GLU* 2.9 45.3 + - - +
120A ARG* 5.0 3.4 - - - -
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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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50A GLY* 1.3 70.9 - - - -
52A VAL* 1.3 73.1 + - + +
54A GLU* 3.8 4.4 + - - +
55A ALA* 2.9 31.7 + - - +
83A LEU* 5.2 0.2 - - + -
88A ASP* 3.9 33.9 - - + +
91A ALA* 4.7 5.6 - - + -
92A VAL* 3.7 24.9 - - + -
120A ARG* 3.9 37.6 - - + +
121A VAL* 4.0 5.3 - - + +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 5.1 2.6 + - - +
50A GLY 3.3 0.8 - - - -
51A VAL* 1.3 86.9 - - + +
53A GLU* 1.3 67.2 + - + +
55A ALA* 3.5 6.1 + - - +
56A LYS* 3.2 30.4 + - + +
91A ALA* 4.0 31.6 - - + +
92A VAL* 5.9 0.2 - - - -
95A VAL* 4.0 18.6 - - + +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.9 15.3 - - + +
48A PRO 3.4 26.4 - - - +
49A GLY* 3.9 14.1 + - - +
50A GLY 3.2 8.1 + - - +
52A VAL* 1.3 81.3 - - + +
54A GLU* 1.3 65.8 + - - +
56A LYS* 3.2 30.6 + - - +
57A GLN* 3.1 22.0 + - - +
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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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38A GLY* 3.3 14.9 + - - +
46A LEU* 4.1 23.5 - - + +
47A VAL* 3.9 28.7 - - + +
50A GLY* 2.9 25.9 + - - +
51A VAL 3.8 1.1 - - - +
53A GLU* 1.3 75.4 - - - +
55A ALA* 1.3 53.6 + - - +
57A GLN 3.2 0.9 + - - -
58A ALA* 2.8 33.6 + - - +
119A GLY* 3.6 5.4 - - - -
120A ARG* 2.6 50.0 + - - +
121A VAL* 3.7 16.6 + - + +
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Residues in contact with ALA 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 2.9 19.3 + - - +
52A VAL* 3.6 7.9 - - - +
53A GLU 3.2 0.2 - - - -
54A GLU* 1.3 78.0 - - - +
56A LYS* 1.3 61.8 + - - +
58A ALA* 3.8 3.6 - - - +
59A LEU* 3.1 31.8 + - + +
92A VAL* 4.4 23.3 - - + -
95A VAL* 4.3 15.7 - - + -
121A VAL* 3.7 15.4 - - + +
123A ILE* 4.9 2.6 - - + +
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Residues in contact with LYS 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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52A VAL* 3.2 18.6 + - + +
53A GLU* 3.2 29.6 + - - +
55A ALA* 1.3 77.9 - - - +
57A GLN* 1.3 58.6 + - - +
59A LEU* 3.4 2.3 + - - +
60A THR* 2.9 34.1 + - - +
95A VAL* 3.6 24.9 - - + -
98A GLN* 5.6 7.4 - - - +
99A TYR* 3.9 12.3 + - - +
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Residues in contact with GLN 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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38A GLY* 3.6 18.2 - - - +
39A MET 3.3 21.1 - - - +
40A ASP* 4.4 4.0 - - - +
41A PRO* 3.6 21.1 - - - +
47A VAL* 4.1 12.8 - - + +
53A GLU 3.1 12.9 + - - +
54A GLU 3.7 6.3 - - - +
56A LYS* 1.3 74.9 - - - +
58A ALA* 1.3 59.2 + - - +
60A THR* 3.1 15.0 + - - +
61A ASN* 2.8 62.4 + - - +
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Residues in contact with ALA 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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36A GLN* 3.8 19.5 - - + +
37A LEU* 3.4 23.3 - - - +
38A GLY* 3.8 1.2 - - - +
54A GLU 2.8 20.5 + - - +
55A ALA* 3.8 7.4 - - - +
57A GLN* 1.3 72.1 - - - +
59A LEU* 1.3 57.0 + - - +
61A ASN* 3.2 6.9 + - - +
62A ILE* 3.0 31.3 + - - +
121A VAL* 5.3 4.5 - - + +
122A GLU* 5.6 0.2 - - - -
123A ILE* 4.6 13.7 - - + -
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Residues in contact with LEU 59 (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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55A ALA* 3.1 22.4 + - + +
56A LYS 3.9 3.4 - - - +
58A ALA* 1.3 74.4 - - - +
60A THR* 1.3 61.3 + - - +
62A ILE* 3.2 13.0 + - + +
63A GLY 2.9 23.4 + - - -
73A PHE* 3.3 28.3 - - + -
92A VAL* 5.6 0.9 - - + +
95A VAL* 3.9 8.1 - - + -
96A TYR* 3.8 35.7 - - + +
99A TYR* 3.5 40.2 - - + -
100A PHE* 5.3 2.7 - - + -
123A ILE* 4.0 24.2 - - + -
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Residues in contact with THR 60 (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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13A LYS 5.7 0.7 - - - +
41A PRO* 6.2 0.7 - - + -
56A LYS* 2.9 24.4 + - - +
57A GLN* 3.1 20.6 + - - +
59A LEU* 1.3 76.0 - - - +
61A ASN* 1.3 67.1 + - - +
63A GLY* 3.1 11.6 + - - +
64A GLU* 3.1 25.2 + - + +
73A PHE* 5.9 0.2 - - - -
99A TYR* 4.0 12.6 + - - -
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Residues in contact with ASN 61 (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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13A LYS 4.3 2.2 + - - -
14A ALA* 3.8 4.8 - - - +
15A PRO* 3.1 29.3 - - + +
36A GLN* 3.4 17.7 + - + +
37A LEU 3.5 13.5 - - - +
39A MET 3.0 17.5 - - - +
41A PRO* 3.8 9.1 - - - +
57A GLN* 2.8 39.7 + - - +
58A ALA* 3.3 9.6 - - - +
60A THR* 1.3 78.8 - - - +
62A ILE* 1.3 61.4 + - - +
64A GLU* 3.4 5.4 + - - +
65A ILE* 3.0 27.8 + - - +
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Residues in contact with ILE 62 (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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33A ILE* 4.2 15.9 - - + -
36A GLN* 3.7 16.6 - - + -
58A ALA 3.0 18.4 + - - +
59A LEU* 3.4 17.0 - - + +
60A THR 3.2 0.2 - - - -
61A ASN* 1.3 75.2 - - - +
63A GLY* 1.3 66.9 + - - +
65A ILE* 3.1 9.3 + - - +
66A LEU* 2.9 41.6 + - + +
73A PHE* 4.0 10.3 - - + -
76A VAL* 5.4 1.8 - - + -
123A ILE* 3.7 44.6 - - + +
124A GLU* 5.1 0.7 - - - -
125A ALA* 4.8 13.9 - - + +
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Residues in contact with GLY 63 (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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59A LEU 2.9 11.3 + - - -
60A THR* 3.1 4.4 + - - -
62A ILE* 1.3 78.2 - - - +
64A GLU* 1.3 57.4 + - - +
66A LEU* 3.5 7.0 + - - +
67A LYS* 3.0 27.3 + - - +
71A CYS 4.8 0.5 - - - +
72A ASP* 5.6 1.3 - - - -
73A PHE* 3.6 26.0 - - - -
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Residues in contact with GLU 64 (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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11A THR* 4.0 5.2 + - + +
13A LYS* 3.0 58.2 - - + +
14A ALA* 4.5 2.0 - - + -
60A THR* 3.1 25.5 + - + +
61A ASN 3.7 7.0 - - - +
63A GLY* 1.3 74.1 - - - +
65A ILE* 1.3 67.5 + - - +
67A LYS* 3.1 25.3 + - - +
68A ALA* 2.9 24.8 + - - +
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Residues in contact with ILE 65 (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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9A ILE* 3.9 8.1 - - + +
11A THR* 4.6 6.3 - - - +
14A ALA* 3.5 22.0 - - + -
23A GLN* 3.5 37.5 - - + +
24A ALA* 3.6 30.5 - - + -
31A ILE* 5.7 1.8 - - + -
33A ILE* 4.0 22.2 - - + -
36A GLN* 4.9 8.3 - - - +
61A ASN 3.0 17.3 + - - +
62A ILE* 3.5 10.1 - - - +
64A GLU* 1.3 75.1 - - - +
66A LEU* 1.3 64.6 + - - +
68A ALA* 3.2 13.2 + - - +
69A ALA* 3.3 12.4 + - + +
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Residues in contact with LEU 66 (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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31A ILE* 5.1 3.6 - - + -
33A ILE* 3.7 23.8 - - + -
62A ILE* 2.9 33.7 + - + +
63A GLY* 3.6 5.8 - - - +
65A ILE* 1.3 78.3 - - - +
67A LYS* 1.3 57.6 + - - +
69A ALA* 3.0 10.8 + - - -
71A CYS* 2.7 53.5 + - + +
72A ASP* 3.8 22.9 - - - +
73A PHE* 4.0 12.1 - - + +
76A VAL* 3.9 15.3 - - + -
127A ALA* 3.7 24.9 - - + -
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Residues in contact with LYS 67 (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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63A GLY 3.0 15.2 + - - +
64A GLU* 3.2 33.2 - - - +
66A LEU* 1.3 71.3 - - - +
68A ALA* 1.3 58.2 + - - +
69A ALA 2.9 4.3 - - - -
70A GLY* 2.8 21.5 + - - -
71A CYS 3.3 10.5 + - - +
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Residues in contact with ALA 68 (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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9A ILE* 4.0 18.2 - - + +
10A SER 4.2 4.9 - - - +
11A THR* 2.7 34.3 - - + +
64A GLU 2.9 6.9 + - - +
65A ILE 3.2 8.5 + - - +
67A LYS* 1.3 75.5 - - - +
69A ALA* 1.3 57.1 + - - +
70A GLY 3.4 0.4 - - - -
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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