Contacts of the helix formed by residues 68 - 86 (chain B) in PDB entry 1NNQ
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 LYS 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 4.6 2.7 - - - +
36A GLU* 3.3 22.7 - - - +
67B GLY* 1.3 75.0 - - - -
69B THR* 1.3 66.9 + - - +
70B PRO* 3.3 11.7 - - + -
71B GLU* 3.0 23.9 + - - +
72B ASN* 2.9 20.9 + - - -
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 4.3 0.5 - - - +
33A ALA* 3.5 24.6 + - + +
36A GLU* 2.5 27.3 + - - -
38A PHE* 3.8 15.3 - - + -
41A ILE* 3.9 27.6 - - + -
45A PHE* 4.8 3.1 - - + -
68B LYS* 1.3 70.4 - - - +
70B PRO* 1.3 63.4 - - - +
72B ASN* 3.3 10.4 + - - +
73B LEU* 2.8 48.6 + - + +
128B ALA* 4.2 3.1 - - + -
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Residues in contact with PRO 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 4.6 0.9 - - - +
38A PHE* 5.5 2.7 - - + -
68B LYS* 3.4 13.5 - - + -
69B THR* 1.3 95.4 - - + +
71B GLU* 1.3 56.4 + - - +
73B LEU* 3.4 4.1 + - + -
74B GLN 3.1 21.0 + - - -
125B LYS* 3.4 34.4 - - + +
128B ALA* 3.9 26.5 - - + +
129B GLU* 4.3 10.8 - - - +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY* 3.5 20.0 + - - +
68B LYS* 3.0 41.2 + - - +
70B PRO* 1.3 77.4 - - - +
72B ASN* 1.3 67.2 + - - +
74B GLN* 3.4 8.4 + - + +
75B MET* 3.1 32.0 + - + +
125B LYS* 5.3 0.4 - - - +
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Residues in contact with ASN 72 (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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29A PHE* 3.3 55.3 + - + +
32A LYS* 3.8 11.7 - - - +
45A PHE* 4.5 4.2 - - + -
65B LYS 4.4 1.4 - - - +
66B LEU* 3.6 12.2 - - - +
67B GLY* 2.9 43.2 + - - -
68B LYS 2.9 15.8 + - - -
69B THR* 3.5 10.2 + - - +
71B GLU* 1.3 75.6 - - - +
73B LEU* 1.3 64.2 + - - +
75B MET* 3.4 2.3 + - - +
76B GLY* 3.1 17.7 + - - -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.1 8.3 - - + -
44A LEU* 5.3 0.4 - - + -
45A PHE* 3.5 22.2 - - + -
69B THR* 2.8 40.3 + - + +
70B PRO* 3.6 5.8 - - + +
71B GLU 3.3 0.2 - - - -
72B ASN* 1.3 71.4 - - - +
74B GLN* 1.3 57.3 + - - +
76B GLY* 3.2 4.5 + - - -
77B ILE* 2.8 33.2 + - - +
121B TYR* 3.5 37.6 - - + +
124B ALA* 3.8 20.2 - - + +
125B LYS* 3.7 35.9 - - + +
128B ALA* 3.9 5.8 - - + -
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO 3.1 13.8 + - - +
71B GLU* 3.6 12.1 - - - +
73B LEU* 1.3 75.8 - - - +
75B MET* 1.3 64.5 + - + +
77B ILE* 3.2 20.9 + - - +
78B GLU* 3.0 58.9 + - - +
125B LYS* 3.2 33.9 + - - +
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Residues in contact with MET 75 (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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25A ARG* 5.7 8.6 + - - -
29A PHE* 4.5 14.1 - - + -
65B LYS 5.4 6.3 - - - +
71B GLU* 3.1 25.4 + - + +
72B ASN* 3.8 6.3 - - - +
73B LEU 3.3 0.2 - - - -
74B GLN* 1.3 86.6 - - + +
76B GLY* 1.3 57.3 + - - +
78B GLU* 3.3 28.6 + - - +
79B GLY* 3.0 26.0 + - - -
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Residues in contact with GLY 76 (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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25A ARG* 6.3 1.1 - - - -
26A TYR* 3.7 26.0 + - - -
29A PHE* 4.6 2.1 - - - -
45A PHE* 5.8 0.9 - - - -
72B ASN 3.1 13.6 + - - -
73B LEU* 3.4 4.9 - - - -
75B MET* 1.3 75.8 - - - +
77B ILE* 1.3 55.5 + - - +
79B GLY* 3.3 2.4 + - - -
80B GLU* 2.9 34.0 + - - +
121B TYR* 4.1 11.9 - - - -
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Residues in contact with ILE 77 (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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73B LEU 2.8 20.4 + - - +
74B GLN* 3.2 35.0 + - - +
76B GLY* 1.3 71.2 - - - +
78B GLU* 1.3 57.9 + - + +
80B GLU* 3.5 6.9 + - - +
81B THR* 2.7 40.6 + - - +
118B ALA* 4.0 7.6 - - + +
121B TYR* 3.6 23.8 - - + +
122B ARG* 3.6 55.9 - - + +
125B LYS* 4.4 9.4 - - + -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLN* 3.0 36.8 + - - +
75B MET* 3.3 38.1 - - - +
77B ILE* 1.3 74.7 - - + +
79B GLY* 1.3 59.1 + - - +
81B THR* 3.3 6.5 + - - -
82B PHE* 3.0 29.6 + - - +
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 5.2 11.7 - - - -
26A TYR* 5.4 2.0 - - - -
75B MET 3.0 14.5 + - - -
76B GLY 3.7 2.9 - - - -
78B GLU* 1.3 74.1 - - - +
80B GLU* 1.3 63.4 + - - +
82B PHE* 3.3 9.6 + - - +
83B GLU* 3.1 28.7 + - - +
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Residues in contact with GLU 80 (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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22A ALA* 5.6 0.3 - - - +
26A TYR* 2.6 24.6 + - - +
52A GLU* 3.0 2.8 - - - +
76B GLY 2.9 24.7 + - - +
77B ILE 3.9 1.6 - - - +
79B GLY* 1.3 71.3 - - - +
81B THR* 1.3 58.1 + - - +
83B GLU* 3.1 14.1 + - - +
84B VAL* 3.0 33.9 + - - +
114B GLU* 3.1 15.0 - - - +
117B HIS* 3.4 19.3 - - + +
118B ALA* 3.8 25.1 - - + +
121B TYR* 3.9 7.6 - - + -
201B ZN 2.2 36.4 - - - -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 2.7 30.7 + - - +
78B GLU* 3.6 7.4 - - - -
79B GLY 3.2 0.2 - - - -
80B GLU* 1.3 74.6 - - - +
82B PHE* 1.3 65.7 + - - +
84B VAL* 4.5 5.2 - - - -
85B GLU* 3.0 52.5 + - - +
118B ALA* 4.5 8.7 - - - +
122B ARG* 4.5 6.8 + - - -
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Residues in contact with PHE 82 (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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78B GLU 3.0 16.9 + - - +
79B GLY* 3.7 8.3 - - - +
81B THR* 1.3 78.4 - - - +
83B GLU* 1.3 61.7 + - + +
86B GLU* 2.9 53.5 + - + +
87B MET* 2.9 54.5 + - + -
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Residues in contact with GLU 83 (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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18A GLY* 4.8 10.0 - - - +
19A GLU* 3.5 19.6 - - - +
22A ALA* 4.9 8.5 - - - +
202A ZN 3.8 2.3 - - - -
79B GLY 3.1 18.3 + - - +
80B GLU* 3.1 20.2 - - - +
82B PHE* 1.3 82.4 - - + +
84B VAL* 1.3 61.4 + - - +
87B MET* 4.1 16.4 - - - +
88B TYR* 3.1 48.0 + - + +
89B PRO* 3.6 0.2 - - - +
114B GLU* 2.9 34.0 - - + +
201B ZN 3.3 3.4 - - - -
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Residues in contact with VAL 84 (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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80B GLU 3.0 20.2 + - - +
81B THR* 4.0 6.1 - - - +
82B PHE 3.4 0.2 - - - -
83B GLU* 1.3 76.5 - - - +
85B GLU* 1.3 71.5 + - + +
89B PRO* 3.0 23.0 - - - +
111B LEU* 3.5 12.1 - - + +
114B GLU* 3.6 25.6 - - + +
115B LYS* 3.6 37.0 - - + +
118B ALA* 5.5 2.7 - - + -
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Residues in contact with GLU 85 (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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81B THR* 3.0 37.3 + - + +
84B VAL* 1.3 88.8 - - + +
86B GLU* 1.3 73.0 + - + +
89B PRO* 3.9 10.9 - - - +
90B VAL* 5.9 0.2 - - - +
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Residues in contact with GLU 86 (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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82B PHE* 2.9 35.8 + - + +
84B VAL 3.5 0.4 - - - -
85B GLU* 1.3 91.4 - - + +
87B MET* 1.3 67.9 + - - +
88B TYR 3.7 0.4 - - - -
89B PRO* 3.8 1.6 - - - +
90B VAL* 3.4 32.3 + - - +
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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
------------------------------------------------------------
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