Contacts of the helix formed by residues 94 - 110 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I THR* 4.7 11.7 - - + +
93I ARG* 1.3 75.5 - - - +
95I ARG* 1.3 69.1 + - - +
96I LYS* 3.5 9.9 + - - +
97I GLN* 2.8 48.7 + - - +
98I VAL* 3.4 4.2 + - - +
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Residues in contact with ARG 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E C 4.9 2.8 + - - -
3E T 4.0 35.1 - - - +
4E G 2.9 50.2 + - - -
78I ASN* 4.2 16.8 - - + +
79I GLU* 4.3 23.2 + - + -
82I ALA* 4.7 4.9 - - + +
93I ARG 3.8 1.0 + - - -
94I THR* 1.3 72.9 - - - +
96I LYS* 1.3 91.0 + - + +
98I VAL* 2.8 35.7 + - - +
99I SER* 2.8 13.6 + - - -
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Residues in contact with LYS 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D T 3.6 27.3 - - + +
32D T 3.3 35.5 + - + +
33D C 3.9 5.3 - - - +
4E G 4.4 1.8 + - - -
5E G 2.8 33.7 + - - -
6E A 4.6 0.4 - - - +
94I THR* 3.1 9.0 + - - +
95I ARG* 1.3 112.5 - - + +
97I GLN* 1.3 64.6 + - - +
99I SER* 3.8 13.4 + - - +
100I SER* 3.4 14.4 + - - -
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Residues in contact with GLN 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D C 5.0 0.7 - - - +
30D A 3.4 37.7 + - - +
43I TRP* 4.2 17.6 - - - -
92I THR* 5.0 4.9 - - - +
93I ARG* 3.6 38.5 + - - +
94I THR* 2.8 46.4 + - - +
96I LYS* 1.3 76.1 - - - +
98I VAL* 1.3 57.8 + - - +
100I SER* 3.4 5.5 + - - -
101I HIS* 2.8 29.0 + - - +
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Residues in contact with VAL 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I PHE* 4.3 17.9 - - + -
78I ASN* 3.5 36.6 - - + +
81I ILE* 4.1 13.9 - - + -
82I ALA* 5.0 3.8 - - + -
85I ILE* 4.5 8.3 - - + -
93I ARG* 4.2 27.1 - - + +
94I THR 3.4 5.6 + - - +
95I ARG* 2.8 29.5 + - - +
97I GLN* 1.3 75.0 - - - +
99I SER* 1.3 64.9 + - - +
101I HIS* 3.6 5.3 - - - +
102I ILE* 2.8 29.8 + - - +
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Residues in contact with SER 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D T 5.5 2.2 - - - -
5E G 4.4 21.1 + - - -
6E A 5.3 5.8 - - - -
78I ASN* 3.3 25.3 + - - +
95I ARG* 2.8 22.7 + - - -
96I LYS* 3.8 24.4 - - - +
98I VAL* 1.3 73.2 - - - +
100I SER* 1.3 52.0 + - - +
102I ILE* 3.1 7.5 + - - +
103I GLN* 2.8 35.1 + - - +
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Residues in contact with SER 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D C 3.9 17.2 - - - -
30D A 3.1 39.9 + - - -
31D T 4.4 5.8 + - - -
96I LYS 3.4 10.6 + - - -
97I GLN 3.4 9.2 + - - -
98I VAL 3.3 0.2 - - - -
99I SER* 1.3 78.4 - - - +
101I HIS* 1.3 58.0 + - - +
103I GLN* 3.2 13.8 + - - +
104I VAL* 2.8 34.0 + - - +
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Residues in contact with HIS 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D C 4.3 14.7 + - - -
43I TRP 3.7 15.9 + - - -
48I GLU* 2.9 27.6 + - - -
51I PHE* 3.8 26.2 - + + -
93I ARG* 3.2 38.9 + - - +
97I GLN 2.8 16.2 + - - +
98I VAL* 3.1 7.4 + - - +
100I SER* 1.3 72.1 + - - +
102I ILE* 1.3 66.5 + - - +
104I VAL* 4.1 8.2 - - + +
105I LEU* 3.1 46.5 + - + +
108I ARG* 5.2 3.6 - - - -
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Residues in contact with ILE 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E G 3.9 17.0 - - - +
51I PHE* 4.7 14.8 - - + -
55I LEU* 5.4 4.3 - - + -
77I ARG* 4.7 15.7 - - - +
78I ASN* 3.3 25.4 - - - +
81I ILE* 4.2 14.6 - - + -
98I VAL 2.8 32.0 + - - +
99I SER* 3.5 5.6 - - - +
101I HIS* 1.3 69.2 - - - +
103I GLN* 1.3 67.6 + - - +
105I LEU* 2.8 8.6 + - + +
106I ALA* 2.8 30.9 + - + +
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Residues in contact with GLN 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D A 3.6 11.8 + - - -
5E G 6.5 0.4 - - + -
6E A 3.3 33.9 + - - +
7E A 2.8 50.6 + - - -
8E T 4.0 4.8 - - - +
99I SER 2.8 13.9 + - - +
100I SER* 3.3 13.0 - - - +
102I ILE* 1.3 75.7 - - - +
104I VAL* 1.3 55.9 + - + +
106I ALA* 3.5 7.5 + - - +
107I ARG* 2.8 39.3 + - + +
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Residues in contact with VAL 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D G 4.2 25.6 - - + +
29D C 4.2 22.4 - - + +
100I SER* 2.8 40.2 + - - +
101I HIS* 3.7 13.9 - - - +
102I ILE 3.0 0.4 + - - -
103I GLN* 1.3 71.7 - - + +
105I LEU* 1.3 60.9 + - + +
107I ARG* 2.9 9.1 + - - +
108I ARG* 2.8 58.8 + - + +
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Residues in contact with LEU 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I GLU* 4.2 16.6 - - - +
51I PHE* 4.2 24.7 - - + -
52I GLN* 4.4 15.3 - - - +
101I HIS* 3.1 36.2 + - + +
102I ILE* 2.8 9.6 + - + +
104I VAL* 1.3 77.2 - - + +
106I ALA* 1.3 53.9 + - - +
108I ARG* 3.8 29.4 - - + +
109I LYS* 2.8 37.4 + - - +
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Residues in contact with ALA 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E A 5.9 2.5 - - - +
102I ILE* 2.8 23.8 + - + +
103I GLN* 3.6 7.6 - - - +
105I LEU* 1.3 76.5 - - - +
107I ARG* 1.3 56.5 + - + +
109I LYS* 3.7 6.4 - - - +
110I ALA* 3.0 29.2 + - - +
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Residues in contact with ARG 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I GLN* 2.8 28.9 + - + +
104I VAL* 2.9 5.5 + - - +
106I ALA* 1.3 72.8 - - - +
108I ARG* 1.3 58.1 + - + +
110I ALA* 2.8 52.9 + - - +
111I ARG* 4.1 0.9 + - - +
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Residues in contact with ARG 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D G 3.3 46.1 + - - +
29D C 5.1 5.3 + - - -
48I GLU* 5.4 2.6 + - - -
101I HIS* 5.2 3.0 - - - -
104I VAL* 2.8 36.4 + - + +
105I LEU* 3.8 25.3 - - + +
107I ARG* 1.3 70.9 - - - +
109I LYS* 1.3 61.6 + - - +
111I ARG* 3.4 22.7 + - - +
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Residues in contact with LYS 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I LEU 2.8 23.7 + - - +
106I ALA* 3.7 6.1 - - - +
108I ARG* 1.3 72.9 - - - +
110I ALA* 1.3 54.9 + - - +
111I ARG* 2.7 26.6 + - - +
112I GLU 4.6 2.3 - - - +
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Residues in contact with ALA 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I ALA 3.0 17.2 + - - +
107I ARG* 2.8 42.8 + - - +
109I LYS* 1.3 68.9 - - - +
111I ARG* 1.3 55.5 + - - -
112I GLU 4.2 2.8 + - - -
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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
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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