Contacts of the helix formed by residues 50 - 69 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B VAL 4.7 2.4 + - - -
48B PRO 3.7 2.0 - - - -
49B GLY* 1.3 78.0 - - - +
51B VAL* 1.3 66.4 + - - -
52B VAL 3.1 4.1 + - - -
53B GLU* 3.2 2.9 + - - +
54B GLU* 3.0 34.6 + - - +
120B ARG* 5.0 3.6 - - - -
12E ALA* 4.8 8.0 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY* 1.3 70.3 - - - -
52B VAL* 1.3 70.9 + - + +
54B GLU* 3.7 3.4 - - - +
55B ALA* 2.9 27.9 + - - +
83B LEU* 5.0 0.4 - - + -
88B ASP* 3.7 35.7 - - + +
91B ALA* 5.3 3.8 - - + -
92B VAL* 3.6 26.0 - - + -
120B ARG* 3.8 34.9 - - + +
121B VAL* 4.1 13.0 - - + -
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY 4.9 2.9 + - - +
50B GLY 3.1 1.6 + - - -
51B VAL* 1.3 87.2 - - + +
53B GLU* 1.3 69.3 + - + +
55B ALA* 3.4 6.4 + - - +
56B LYS* 3.2 27.6 + - - +
91B ALA* 4.0 27.1 - - + +
92B VAL* 5.8 1.8 - - + -
95B VAL* 3.8 19.0 - - + +
16E ALA* 3.6 26.9 - - + -
17E ALA 3.8 28.7 - - - +
18E ILE* 4.1 5.6 - - + -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 3.6 13.4 - - + +
48B PRO 3.5 17.0 - - - +
49B GLY* 4.1 8.7 + - - +
50B GLY 3.2 6.5 + - - +
52B VAL* 1.3 78.3 - - + +
54B GLU* 1.3 65.6 - - - +
56B LYS* 2.8 42.9 + - - +
57B GLN* 3.1 18.5 + - - +
8E ILE* 4.6 9.2 - - - +
10E SER* 3.4 33.9 + - - +
17E ALA* 4.0 13.9 + - - +
22E SER* 5.1 3.0 + - - -
23E GLN* 5.3 2.9 + - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLY* 3.2 24.6 + - - +
46B LEU* 4.2 21.1 - - + +
47B VAL* 4.0 21.1 - - + +
50B GLY* 3.0 23.9 + - - +
51B VAL 3.7 4.0 - - - +
53B GLU* 1.3 75.8 - - - +
55B ALA* 1.3 57.7 + - - +
57B GLN 3.4 0.2 + - - -
58B ALA* 2.9 27.4 + - - +
118B GLY 4.7 0.7 - - - +
119B GLY* 3.7 6.2 - - - -
120B ARG* 2.8 47.3 + - - +
121B VAL* 3.8 13.7 + - + +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL 2.9 18.3 + - - +
52B VAL* 3.6 7.0 - - - +
54B GLU* 1.3 74.1 - - - +
56B LYS* 1.3 64.5 + - - +
58B ALA* 3.3 4.1 + - - +
59B LEU* 3.0 31.2 + - + +
92B VAL* 4.5 20.0 - - + -
95B VAL* 4.0 20.0 - - + -
121B VAL* 3.8 15.2 - - + +
123B ILE* 4.8 3.3 - - + +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 3.2 16.3 + - - +
53B GLU* 2.8 45.5 + - - +
55B ALA* 1.3 79.8 - - - +
57B GLN* 1.3 53.5 + - - +
59B LEU* 3.3 0.7 + - - +
60B THR* 2.7 36.9 + - - +
95B VAL* 3.8 18.6 - - + +
99B TYR* 3.4 20.0 + - + +
104D PHE* 3.8 20.0 - - + -
17E ALA 2.9 20.9 + - - -
19E GLY 3.4 14.6 - - - +
21E TYR 2.8 27.1 + - - -
22E SER* 4.7 1.4 + - - +
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLY* 3.6 18.8 - - - +
39B MET 3.3 17.9 - - - +
40B ASP* 4.3 2.4 - - - +
41B PRO* 3.4 20.1 - - - +
47B VAL* 3.8 19.7 - - + +
53B GLU 3.1 13.3 + - - +
54B GLU 3.7 4.0 - - - +
56B LYS* 1.3 76.3 - - - +
58B ALA* 1.3 55.3 + - - +
60B THR* 2.9 18.3 + - - +
61B ASN* 2.7 65.9 + - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLN* 3.7 20.2 - - + +
37B LEU* 3.4 22.8 + - - +
38B GLY 4.2 0.2 - - - +
54B GLU 2.9 19.6 + - - +
55B ALA* 3.7 8.1 - - - +
57B GLN* 1.3 76.4 - - - +
59B LEU* 1.3 57.8 + - - +
61B ASN* 3.4 4.8 + - - +
62B ILE* 3.0 32.6 + - - +
121B VAL* 5.2 4.3 - - + +
123B ILE* 4.5 14.1 - - + +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 3.0 21.3 + - + +
56B LYS 3.7 4.0 - - - +
58B ALA* 1.3 73.0 - - - +
60B THR* 1.3 60.6 + - - +
62B ILE* 3.2 14.3 + - + +
63B GLY 2.8 24.1 + - - -
73B PHE* 3.2 26.3 - - + -
92B VAL* 6.5 0.4 - - + -
95B VAL* 4.2 6.1 - - + -
96B TYR* 3.9 33.7 - - + +
99B TYR* 3.4 41.7 - - + -
100B PHE* 4.9 6.1 - - + -
123B ILE* 3.9 25.1 - - + -
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS 5.9 0.2 - - - +
56B LYS* 2.7 24.4 + - - +
57B GLN* 2.9 26.7 + - - +
59B LEU* 1.3 77.8 - - - +
61B ASN* 1.3 63.4 + - - +
63B GLY* 3.1 3.8 + - - -
64B GLU* 3.0 33.8 + - + +
73B PHE* 5.3 0.7 - - - -
99B TYR* 4.1 10.6 + - - -
101D GLN 4.6 2.4 + - - +
102D SER* 4.2 28.6 - - - +
104D PHE* 6.0 0.5 - - - -
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS 4.3 3.0 + - - -
14B ALA* 3.9 4.5 - - + +
15B PRO* 3.5 18.7 - - + +
36B GLN* 3.7 17.9 + - + +
37B LEU 3.3 17.0 - - - +
39B MET 2.9 18.2 + - - +
41B PRO* 3.6 17.8 - - - +
57B GLN* 2.7 43.0 + - - +
58B ALA 3.5 6.5 - - - +
60B THR* 1.3 74.4 - - - +
62B ILE* 1.3 61.7 + - - +
64B GLU* 3.4 4.7 + - - +
65B ILE* 3.2 29.6 + - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.3 16.2 - - + -
36B GLN* 3.7 15.7 - - + -
58B ALA 3.0 19.6 + - - +
59B LEU* 3.5 16.4 - - + +
61B ASN* 1.3 76.2 - - - +
63B GLY* 1.3 63.4 + - - +
65B ILE* 3.2 8.6 + - - +
66B LEU* 2.9 42.5 + - + +
73B PHE* 4.1 9.2 - - + -
76B VAL* 5.4 2.2 - - + -
123B ILE* 3.6 42.8 - - + +
124B GLU* 5.1 0.7 - - - -
125B ALA* 4.9 14.4 - - + +
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Residues in contact with GLY 63 (chain B).
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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59B LEU 2.8 11.3 + - - -
60B THR* 3.1 4.9 + - - -
62B ILE* 1.3 77.0 - - - +
64B GLU* 1.3 58.5 + - - +
66B LEU* 3.3 8.5 + - - +
67B LYS* 2.9 28.5 + - - +
71B CYS 5.0 0.3 - - - +
72B ASP* 5.7 0.9 - - - -
73B PHE* 3.7 25.5 - - - -
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 3.8 6.9 + - + +
13B LYS* 3.0 60.6 + - + +
14B ALA* 4.5 1.8 - - + -
60B THR* 3.0 27.2 + - + +
61B ASN 3.7 6.5 - - - +
62B ILE 3.3 0.2 - - - -
63B GLY* 1.3 77.1 - - - +
65B ILE* 1.3 63.3 + - - +
67B LYS* 3.3 16.0 - - - +
68B ALA* 3.0 21.7 + - - +
101D GLN* 5.5 2.8 - - - +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.7 10.8 - - + +
11B THR* 4.6 3.1 - - - +
14B ALA* 3.9 15.7 - - + -
23B GLN* 4.0 23.8 - - + +
24B ALA* 3.5 30.5 - - + -
31B ILE* 5.7 1.1 - - + -
33B ILE* 4.0 21.5 - - + -
36B GLN* 3.4 33.9 - - + +
61B ASN 3.2 16.8 + - - +
62B ILE* 3.6 7.0 - - - +
64B GLU* 1.3 74.0 - - - +
66B LEU* 1.3 67.4 + - - +
68B ALA* 3.2 15.9 + - - +
69B ALA* 3.2 10.2 + - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 5.2 4.0 - - + -
33B ILE* 3.9 16.6 - - + -
62B ILE* 2.9 35.0 + - + +
63B GLY* 3.5 8.7 - - - +
65B ILE* 1.3 76.5 - - - +
67B LYS* 1.3 56.9 + - - +
69B ALA* 3.0 11.3 + - - +
71B CYS* 2.7 53.7 + - + +
72B ASP* 3.9 18.8 - - - +
73B PHE* 4.0 10.3 - - + +
76B VAL* 3.9 19.1 - - + -
127B ALA* 3.7 30.3 - - + -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLY 2.9 13.4 + - - +
64B GLU* 3.3 22.9 - - - +
66B LEU* 1.3 76.4 - - - +
68B ALA* 1.3 58.1 + - - +
70B GLY* 2.8 21.5 + - - -
71B CYS 3.5 10.5 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ARG* 3.6 17.2 + - - -
9B ILE* 3.8 15.5 - - + +
10B SER 4.5 4.5 - - - +
11B THR* 2.6 33.0 - - + +
64B GLU 3.0 6.4 + - - +
65B ILE 3.2 9.6 + - - +
67B LYS* 1.3 76.4 - - - +
69B ALA* 1.3 56.5 + - - +
70B GLY 3.3 1.9 + - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ARG* 3.8 13.2 + - - +
9B ILE* 3.7 20.9 - - + -
26B LEU* 5.1 2.0 - - + -
31B ILE* 3.8 27.6 - - + -
65B ILE* 3.2 9.2 + - + +
66B LEU* 3.0 9.8 + - - +
67B LYS 3.0 1.2 - - - -
68B ALA* 1.3 78.0 - - - +
70B GLY* 1.3 63.0 + - - +
71B CYS* 3.3 5.0 + - - +
129B GLN* 3.5 22.7 + - - -
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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