Contacts of the helix formed by residues 94 - 111 (chain N) in PDB entry 5NO6
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 THR 94 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N ALA* 4.6 2.5 - - - -
92N THR* 5.2 8.1 - - + -
93N ARG* 1.4 74.3 - - - +
95N ARG* 1.3 57.3 + - - +
96N LYS* 4.1 9.5 + - - +
97N GLN* 2.8 54.5 + - - +
98N VAL* 3.3 5.2 + - - +
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Residues in contact with ARG 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F T 3.6 42.2 + - - +
4F G 2.5 61.0 + - - +
78N ASN* 3.7 14.1 + - + +
79N GLU* 3.2 39.0 + - + -
82N ALA* 4.8 3.3 - - - +
94N THR* 1.3 75.4 - - - +
96N LYS* 1.3 87.6 + - + +
97N GLN 3.3 0.2 - - - -
98N VAL* 3.5 7.2 + - - +
99N SER* 2.8 29.0 + - - +
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Residues in contact with LYS 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C A 4.6 1.3 + - + -
31C T 3.6 31.7 - - + +
32C T 3.5 28.4 + - + +
33C C 4.3 2.4 - - - +
4F G 4.2 4.0 + - - -
5F G 2.9 31.5 + - - -
6F A 5.2 0.2 - - - +
94N THR* 3.2 7.8 + - - +
95N ARG* 1.3 120.2 - - + +
97N GLN* 1.3 61.8 + - + +
99N SER* 3.5 9.9 + - - +
100N SER* 2.8 29.5 + - - -
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Residues in contact with GLN 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C A 3.2 37.7 + - - +
43N TRP* 3.2 23.2 + - + +
93N ARG* 2.8 57.8 + - + +
94N THR* 2.8 26.3 + - - +
96N LYS* 1.3 77.4 - - + +
98N VAL* 1.3 54.9 + - - +
100N SER* 3.2 1.9 + - - -
101N HIS 2.8 31.0 + - - -
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Residues in contact with VAL 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N TRP* 4.1 18.4 - - + -
51N PHE* 4.2 4.5 - - + -
78N ASN* 3.6 44.0 - - + +
81N ILE* 4.0 22.0 - - + -
82N ALA* 4.1 18.8 - - + +
85N ILE* 4.5 2.9 - - + -
93N ARG 4.8 1.8 - - - +
94N THR 3.3 8.9 + - - +
95N ARG* 3.7 7.2 - - - +
97N GLN* 1.3 73.5 - - - +
99N SER* 1.3 66.3 + - - +
101N HIS* 4.1 0.8 - - - +
102N ILE* 3.3 32.6 + - + +
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Residues in contact with SER 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C T 5.5 3.6 - - - -
4F G 4.8 0.7 - - - -
5F G 3.3 28.3 + - - -
6F A 5.5 5.6 - - - -
78N ASN* 3.2 23.3 + - - +
95N ARG* 2.8 17.0 + - - -
96N LYS* 3.5 21.6 + - - +
98N VAL* 1.3 75.2 - - - +
100N SER* 1.3 66.3 + - - +
102N ILE* 3.5 4.9 + - - +
103N GLN* 3.3 17.8 + - - +
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Residues in contact with SER 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C C 3.9 18.9 - - - -
30C A 2.7 45.6 + - - +
31C T 4.7 4.5 - - - -
43N TRP* 6.1 0.2 - - - -
96N LYS 2.8 21.3 + - - -
97N GLN 3.8 2.9 - - - -
99N SER* 1.3 70.5 - - - +
101N HIS* 1.3 65.6 + - - +
103N GLN* 2.8 15.0 + - - +
104N VAL* 2.8 24.6 + - - +
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Residues in contact with HIS 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C C 4.7 6.5 + - - -
43N TRP* 3.1 67.8 + + + +
48N GLU* 2.4 37.5 + - - -
51N PHE* 3.6 31.4 - + - -
97N GLN 2.8 9.7 + - - +
98N VAL 4.1 2.9 - - - +
100N SER* 1.3 70.8 - - - +
102N ILE* 1.3 51.1 + - - +
104N VAL* 3.0 12.6 + - - +
105N LEU* 2.8 57.8 + - + +
108N ARG* 5.6 4.2 + - - -
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Residues in contact with ILE 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F G 4.0 15.9 - - - +
6F A 6.1 0.9 - - - +
51N PHE* 3.6 21.3 - - + -
55N LEU* 5.0 4.9 - - + -
77N ARG* 4.8 16.4 - - - +
78N ASN* 3.9 19.7 - - - +
81N ILE* 5.5 1.1 - - + -
98N VAL* 3.3 26.7 + - + +
99N SER* 3.8 4.5 - - - +
100N SER 3.2 0.2 + - - -
101N HIS* 1.3 76.6 - - - +
103N GLN* 1.3 59.3 + - - +
105N LEU* 3.2 9.8 + - - +
106N ALA* 2.8 32.2 + - + +
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Residues in contact with GLN 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C C 6.1 0.9 - - - -
30C A 4.0 4.9 + - - -
5F G 6.2 1.6 - - + -
6F A 3.7 28.6 - - - +
7F A 2.8 49.1 + - - +
8F T 3.6 15.9 + - - +
99N SER 3.3 9.5 + - - +
100N SER* 2.8 17.1 + - - +
102N ILE* 1.3 76.1 - - - +
104N VAL* 1.3 61.9 + - + +
106N ALA* 3.4 6.3 + - + +
107N ARG* 3.0 27.6 + - + +
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Residues in contact with VAL 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C T 5.7 0.2 - - + -
28C G 3.7 43.7 - - + +
29C C 3.8 34.3 - - + +
100N SER* 2.8 32.3 + - - +
101N HIS* 3.5 9.6 - - - +
103N GLN* 1.3 74.0 - - + +
105N LEU* 1.3 61.9 + - + +
107N ARG* 3.5 10.2 - - + +
108N ARG* 3.0 39.6 + - - +
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Residues in contact with LEU 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N GLU* 4.4 7.9 - - - +
51N PHE* 3.8 24.0 - - + -
52N GLN* 4.8 6.3 - - - +
55N LEU* 6.1 0.2 - - + -
101N HIS* 2.8 49.1 + - + +
102N ILE* 3.5 7.6 - - - +
103N GLN 3.2 0.2 - - - -
104N VAL* 1.3 74.5 - - + +
106N ALA* 1.3 68.3 + - - +
108N ARG* 2.8 35.4 + - + +
109N LYS* 2.8 23.5 + - - +
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Residues in contact with ALA 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F A 6.1 1.3 - - - +
102N ILE* 2.8 22.5 + - + +
103N GLN* 3.5 9.9 - - + +
105N LEU* 1.3 72.0 - - - +
107N ARG* 1.3 53.4 + - - +
109N LYS* 3.1 10.2 + - - +
110N ALA* 2.8 36.6 + - - +
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Residues in contact with ARG 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 4.3 28.3 - - - +
26C T 6.1 0.8 - - - +
27C T 4.5 23.6 + - + +
28C G 5.6 2.5 - - - +
8F T 5.4 9.9 - - - +
103N GLN* 3.0 15.2 + - + +
104N VAL* 3.5 17.0 - - + +
106N ALA* 1.3 73.5 - - - +
108N ARG* 1.3 62.8 + - + +
110N ALA* 3.4 5.2 + - - +
111N ARG* 2.8 78.4 + - + +
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Residues in contact with ARG 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C T 5.7 0.4 - - - -
28C G 3.1 40.4 + - - +
29C C 4.2 16.6 + - - -
48N GLU* 5.8 2.2 + - - -
101N HIS* 5.6 4.4 + - - -
104N VAL* 3.0 27.3 - - - +
105N LEU* 2.8 40.9 + - + +
107N ARG* 1.3 75.0 - - + +
109N LYS* 1.3 62.0 + - - +
111N ARG* 2.6 30.3 - - - +
112N GLU* 4.0 1.6 - - - -
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Residues in contact with LYS 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105N LEU 2.8 11.3 + - - +
106N ALA* 3.4 12.3 - - - +
108N ARG* 1.3 78.2 - - - +
110N ALA* 1.3 62.7 + - - +
112N GLU* 3.1 24.5 - - - +
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Residues in contact with ALA 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N ALA 2.8 19.9 + - - +
107N ARG* 3.8 4.9 - - - +
109N LYS* 1.3 70.5 - - - +
111N ARG* 1.3 77.6 + - - +
112N GLU* 2.8 24.5 + - - +
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Residues in contact with ARG 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C T 4.8 18.4 - - - +
107N ARG* 2.8 67.3 + - + +
108N ARG* 2.6 17.2 - - - +
110N ALA* 1.3 83.3 - - - +
112N GLU* 1.3 61.8 + - - +
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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