Contacts of the helix formed by residues 50 - 69 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D VAL 4.8 0.2 + - - -
48D PRO* 3.6 2.0 - - - +
49D GLY* 1.3 78.1 - - - +
51D VAL* 1.3 66.7 + - - -
52D VAL 3.2 4.0 + - - -
53D GLU* 3.2 3.1 + - - -
54D GLU* 3.0 36.7 + - - +
120D ARG* 5.1 2.7 - - - -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLY* 1.3 70.2 - - - -
52D VAL* 1.3 70.8 + - + +
54D GLU* 3.8 3.2 - - - +
55D ALA* 2.9 28.2 + - - +
83D LEU* 5.2 0.4 - - + -
88D ASP* 3.8 37.5 - - + +
91D ALA* 4.9 5.8 - - + -
92D VAL* 3.6 25.6 - - + -
120D ARG* 4.0 30.7 - - + +
121D VAL* 4.0 9.8 - - + +
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLY 5.2 2.0 + - - +
50D GLY 3.3 1.0 - - - -
51D VAL* 1.3 82.2 - - + +
53D GLU* 1.3 71.8 + - + +
55D ALA* 3.3 7.9 + - - +
56D LYS* 3.1 36.1 + - - +
91D ALA* 4.1 31.0 - - + +
92D VAL* 6.0 0.2 - - - -
95D VAL* 4.1 16.8 - - + +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 4.3 13.0 - - + +
48D PRO 3.5 25.8 - - - +
49D GLY* 4.0 14.4 - - - +
50D GLY 3.2 6.1 + - - +
52D VAL* 1.3 86.6 - - + +
54D GLU* 1.3 62.3 + - - +
56D LYS* 3.3 22.8 + - - +
57D GLN* 3.0 23.0 + - - +
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLY* 3.2 23.8 + - - +
46D LEU* 4.0 25.2 - - + +
47D VAL* 3.9 18.9 - - - +
50D GLY* 3.0 24.6 + - - +
51D VAL 3.8 3.8 - - - +
53D GLU* 1.3 75.3 - - - +
55D ALA* 1.3 59.4 + - - +
57D GLN* 3.2 1.0 + - - -
58D ALA* 2.8 28.2 + - - +
119D GLY* 3.5 6.2 - - - -
120D ARG* 2.8 46.7 + - - +
121D VAL* 3.9 13.3 + - + +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL 2.9 19.6 + - - +
52D VAL* 3.5 6.7 - - - +
53D GLU 3.3 0.2 - - - -
54D GLU* 1.3 74.9 - - - +
56D LYS* 1.3 65.0 + - - +
58D ALA* 3.2 5.1 + - - +
59D LEU* 3.0 29.5 + - + +
92D VAL* 4.3 21.3 - - + -
95D VAL* 4.1 19.7 - - + -
121D VAL* 3.7 15.8 - - + +
123D ILE* 4.9 2.2 - - + +
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 3.1 31.3 + - - +
53D GLU* 3.5 26.7 - - - +
54D GLU 3.2 0.2 - - - -
55D ALA* 1.3 80.1 - - - +
57D GLN* 1.3 57.3 + - - +
59D LEU* 3.4 0.4 + - - -
60D THR* 2.9 36.5 + - + +
95D VAL* 3.7 26.1 - - + +
98D GLN* 4.0 23.6 + - - +
99D TYR* 3.6 12.9 + - - +
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Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLY* 3.6 22.7 - - - +
39D MET 3.3 24.2 + - - +
40D ASP* 4.5 0.4 - - - -
41D PRO* 3.5 16.3 - - - +
47D VAL* 3.8 20.2 - - + +
53D GLU 3.0 16.5 + - - +
54D GLU 3.2 0.2 + - - -
56D LYS* 1.3 74.5 - - - +
58D ALA* 1.3 62.0 + - - +
60D THR* 2.9 17.4 + - - +
61D ASN* 2.9 58.5 + - - +
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLN* 3.6 25.1 - - + +
37D LEU 3.6 16.8 - - - +
38D GLY* 3.8 0.8 - - - +
54D GLU 2.8 17.6 + - - +
55D ALA* 3.2 7.8 + - - +
57D GLN* 1.3 76.5 - - - +
59D LEU* 1.3 57.3 + - - +
61D ASN* 3.2 6.0 + - - +
62D ILE* 2.9 32.4 + - - +
121D VAL* 5.2 3.8 - - + +
123D ILE* 4.6 13.9 - - + +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA* 3.0 20.1 + - + +
58D ALA* 1.3 73.5 - - - +
60D THR* 1.3 61.0 + - - +
62D ILE* 3.4 14.7 + - + +
63D GLY 2.9 21.7 + - - -
73D PHE* 3.2 28.4 - - + -
92D VAL* 5.6 1.1 - - + +
95D VAL* 4.0 6.7 - - + -
96D TYR* 3.7 33.4 - - + -
99D TYR* 3.6 41.7 - - + -
100D PHE* 4.7 7.2 - - + -
123D ILE* 3.8 27.8 - - + -
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LYS* 2.9 26.5 + - + +
57D GLN* 2.9 31.8 + - - +
59D LEU* 1.3 73.2 - - - +
61D ASN* 1.3 66.5 + - - +
63D GLY* 3.0 3.9 + - - -
64D GLU* 3.0 27.7 + - - +
73D PHE* 5.4 0.2 - - - -
99D TYR* 3.5 20.6 - - + +
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Residues in contact with ASN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LYS 4.4 2.8 + - - -
14D ALA* 4.1 4.3 - - + +
15D PRO* 3.3 18.7 - - + +
36D GLN* 3.9 16.4 - - + +
37D LEU 3.5 13.3 - - - +
39D MET 2.9 19.4 - - - +
41D PRO* 3.7 16.4 - - - +
57D GLN* 2.9 39.1 + - - +
58D ALA* 3.3 9.0 - - - +
60D THR* 1.3 79.7 + - - +
62D ILE* 1.3 63.6 + - - +
64D GLU* 3.2 6.8 + - - +
65D ILE* 3.1 27.4 + - - +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ILE* 4.2 17.3 - - + -
36D GLN* 3.7 17.7 - - + -
58D ALA 2.9 19.1 + - - +
59D LEU* 3.6 17.7 - - + +
61D ASN* 1.3 74.2 - - - +
63D GLY* 1.3 64.9 + - - +
65D ILE* 3.1 10.6 + - - +
66D LEU* 2.9 33.8 + - + +
73D PHE* 4.0 17.3 - - + -
76D VAL* 5.4 1.3 - - + -
123D ILE* 3.6 44.2 - - + +
125D ALA* 4.7 14.1 - - + +
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Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU 2.9 15.2 + - - -
60D THR* 3.0 6.0 + - - -
62D ILE* 1.3 77.1 - - - +
64D GLU* 1.3 57.1 + - - +
66D LEU* 3.3 8.0 + - - +
67D LYS* 3.0 34.6 + - - +
72D ASP* 5.7 0.7 - - - -
73D PHE* 3.7 21.5 - - - -
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D THR* 4.2 5.3 + - + +
13D LYS* 3.3 56.4 + - + +
14D ALA* 4.6 2.0 - - + -
60D THR* 3.0 17.1 + - - +
61D ASN* 3.2 7.6 + - - +
63D GLY* 1.3 72.7 - - - +
65D ILE* 1.3 66.7 + - - +
67D LYS* 2.9 40.6 + - - +
68D ALA* 3.0 24.3 + - - +
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.9 8.2 - - + +
11D THR* 4.3 8.7 - - + -
14D ALA* 3.9 15.5 - - + -
23D GLN* 4.1 20.0 - - + +
24D ALA* 3.6 29.4 - - + -
31D ILE* 5.7 1.8 - - + -
33D ILE* 4.0 20.6 - - + -
36D GLN* 3.5 40.6 - - + +
61D ASN 3.1 14.6 + - - +
62D ILE* 3.5 7.2 - - - +
64D GLU* 1.3 76.4 - - - +
66D LEU* 1.3 61.4 + - - +
68D ALA* 3.4 5.1 + - - +
69D ALA* 3.4 18.9 + - - +
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 5.1 5.6 - - + -
33D ILE* 3.6 24.5 - - + -
62D ILE* 2.9 27.8 + - + +
63D GLY* 3.5 8.3 - - - +
65D ILE* 1.3 75.3 - - - +
67D LYS* 1.3 60.2 + - - +
69D ALA* 3.0 11.4 + - - +
71D CYS* 2.7 50.0 + - + +
72D ASP* 3.5 26.7 - - - +
73D PHE* 3.9 11.7 - - + +
76D VAL* 4.0 15.7 - - + -
127D ALA* 3.7 23.6 - - + -
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LYS* 4.5 13.5 - - - +
63D GLY 3.0 18.8 + - - +
64D GLU* 2.9 38.2 + - - +
66D LEU* 1.3 75.4 - - - +
68D ALA* 1.3 59.1 + - - +
70D GLY* 2.8 20.5 + - - -
71D CYS 3.5 12.8 - - - +
72D ASP* 5.7 2.9 - - + -
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.9 18.5 - - + +
10D SER 4.6 4.7 - - - +
11D THR* 3.9 24.5 - - + -
64D GLU 3.0 16.8 + - - +
65D ILE 3.6 6.3 - - - +
66D LEU 3.3 0.2 - - - -
67D LYS* 1.3 76.4 - - - +
69D ALA* 1.3 57.7 + - - +
70D GLY 3.3 0.8 + - - -
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.9 26.9 - - + -
26D LEU* 5.2 2.9 - - + -
31D ILE* 4.0 25.4 - - + -
65D ILE 3.4 8.7 + - - +
66D LEU* 3.0 9.0 + - - +
67D LYS 3.0 1.0 - - - -
68D ALA* 1.3 78.5 - - - +
70D GLY* 1.3 62.9 + - - +
71D CYS* 3.4 6.3 + - - -
129D GLN* 3.7 21.5 + - - -
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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