Contacts of the helix formed by residues 97 - 114 (chain B) in PDB entry 4NAC
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 ASP 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ARG* 3.3 32.5 - - - +
49A ARG* 5.7 5.8 - - + +
50A LYS* 5.0 16.2 - - + +
96B THR* 1.3 79.6 - - - +
98B GLU* 1.3 61.4 + - - +
99B SER* 3.3 11.7 + - - -
100B CYS* 2.7 31.8 + - - +
101B LYS* 3.0 25.1 + - - +
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Residues in contact with GLU 98 (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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97B ASP* 1.3 72.9 - - - +
99B SER* 1.3 65.9 + - - +
101B LYS* 3.2 29.0 + - - +
102B LYS* 3.0 23.2 + - - +
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Residues in contact with SER 99 (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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42A THR* 5.9 2.4 - - - +
46A ARG* 3.7 26.8 - - - +
97B ASP* 3.3 17.1 + - - -
98B GLU* 1.3 77.6 - - - +
100B CYS* 1.3 64.7 + - - +
102B LYS* 3.2 15.8 + - - +
103B HIS* 3.2 24.1 + - - -
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Residues in contact with CYS 100 (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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46A ARG* 5.2 1.8 - - - +
53B PRO 5.4 4.5 - - - -
57B LEU* 4.2 24.7 - - + -
92B VAL* 4.2 18.8 - - - -
95B GLU 5.4 1.1 - - - -
96B THR* 2.7 28.7 - - - +
97B ASP* 2.7 23.7 + - - +
99B SER* 1.3 72.2 - - - +
101B LYS* 1.3 63.3 + - - +
103B HIS* 3.1 11.3 + - - +
104B LEU* 3.1 21.6 + - - +
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Residues in contact with LYS 101 (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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93B SER* 3.5 21.6 + - - +
96B THR* 3.5 27.0 + - + +
97B ASP 3.0 9.6 + - - +
98B GLU* 3.2 33.9 + - - +
100B CYS* 1.3 76.1 - - - +
102B LYS* 1.3 57.6 + - - +
104B LEU* 3.3 4.7 + - - +
105B GLY* 2.9 24.9 + - - -
129B LEU* 3.5 38.5 - - + +
130B TYR* 5.0 20.5 + - + +
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Residues in contact with LYS 102 (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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98B GLU 3.0 12.3 + - - +
99B SER* 3.2 9.6 + - - +
101B LYS* 1.3 79.8 - - - +
103B HIS* 1.3 58.8 + - + +
105B GLY* 3.6 2.7 - - - +
106B ARG* 2.9 30.0 + - + +
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Residues in contact with HIS 103 (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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46A ARG* 5.0 13.3 + - - -
57B LEU* 3.8 24.2 - - + -
61B TYR* 3.5 21.5 + - - +
99B SER* 3.2 29.0 + - - -
100B CYS* 3.1 8.4 + - - +
102B LYS* 1.3 76.7 - - + +
104B LEU* 1.3 63.4 + - - +
106B ARG* 3.0 45.6 + - - +
107B VAL* 3.2 17.2 + - - +
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Residues in contact with LEU 104 (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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57B LEU* 3.5 22.4 - - + -
60B LEU* 3.4 31.4 - - + -
89B PHE* 3.8 19.6 - - + +
92B VAL* 3.7 26.5 - - + -
93B SER* 4.3 11.0 - - - +
96B THR* 4.8 0.9 - - - +
100B CYS* 3.1 16.6 + - - +
101B LYS* 3.6 6.7 - - - +
103B HIS* 1.3 74.8 - - - +
105B GLY* 1.3 62.8 + - - +
107B VAL* 3.1 9.7 + - + +
108B LEU* 3.0 25.1 + - - +
129B LEU* 3.7 27.1 - - + -
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Residues in contact with GLY 105 (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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101B LYS 2.9 14.2 + - - -
102B LYS* 3.2 5.1 + - - -
103B HIS 3.2 0.2 - - - -
104B LEU* 1.3 75.9 - - - +
106B ARG* 1.3 56.6 + - - +
108B LEU* 3.7 2.4 - - - +
109B SER* 2.9 31.9 + - - -
129B LEU* 3.6 18.1 - - - +
130B TYR* 3.8 12.8 + - - -
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Residues in contact with ARG 106 (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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61B TYR* 3.0 40.4 + - - -
102B LYS* 2.9 13.3 + - + +
103B HIS* 3.0 39.1 + - - +
105B GLY* 1.3 77.2 - - - +
107B VAL* 1.3 65.0 + - - +
109B SER* 3.3 6.1 + - - -
110B ILE* 2.9 46.5 + - + +
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Residues in contact with VAL 107 (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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57B LEU* 5.9 0.2 - - + -
60B LEU* 5.1 7.2 - - + +
61B TYR* 4.1 27.6 - - + -
64B ASN* 4.2 18.2 - - + +
89B PHE* 4.3 12.6 - - + -
103B HIS 3.2 12.3 + - - +
104B LEU* 3.1 12.6 + - + +
106B ARG* 1.3 81.4 - - + +
108B LEU* 1.3 56.2 + - - +
110B ILE* 3.1 11.6 + - + +
111B TRP* 2.8 62.5 + - + +
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Residues in contact with LEU 108 (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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89B PHE* 3.3 29.8 - - + -
104B LEU 3.0 15.7 + - - +
105B GLY* 3.7 7.2 - - - +
107B VAL* 1.3 76.6 - - - +
109B SER* 1.3 51.5 + - - +
111B TRP* 3.1 11.2 + - + +
112B GLU* 2.8 35.4 + - - +
122B LEU* 4.7 5.2 - - + +
125B LEU* 3.8 50.5 - - + +
126B LYS* 4.1 11.9 - - + +
129B LEU* 3.4 30.3 - - + -
130B TYR* 4.9 3.6 - - + +
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Residues in contact with SER 109 (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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105B GLY 2.9 19.0 + - - -
106B ARG* 3.7 6.1 - - - -
108B LEU* 1.3 72.7 - - - +
110B ILE* 1.3 61.2 + - - +
112B GLU* 3.4 10.9 + - - +
113B GLU* 2.9 30.5 + - - +
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Residues in contact with ILE 110 (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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64B ASN* 4.9 9.6 - - - +
68B GLN* 3.7 23.8 - - - +
106B ARG* 2.9 40.7 + - + +
107B VAL* 3.4 12.6 - - + +
109B SER* 1.3 77.5 - - - +
111B TRP* 1.3 59.3 + - + +
113B GLU* 3.3 4.8 + - - +
114B ARG* 2.9 45.3 + - - +
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Residues in contact with TRP 111 (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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60B LEU* 5.4 1.1 - - + -
63B ALA* 5.3 1.3 - - + -
64B ASN* 2.8 39.5 + - - +
67B ILE* 3.9 24.9 - - + -
68B GLN* 4.2 4.5 + - - +
85B ILE* 3.8 31.4 - - + -
89B PHE* 4.0 10.5 - + - -
107B VAL* 2.8 31.7 + - + +
108B LEU* 3.1 14.1 + - + +
110B ILE* 1.3 74.3 - - + +
112B GLU* 1.3 60.8 + - - +
115B SER* 2.9 8.5 + - - -
116B VAL* 2.9 60.0 + - + +
117B TYR* 3.9 14.8 - + - -
122B LEU* 4.0 12.8 - - + +
125B LEU* 3.8 31.4 - - + -
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Residues in contact with GLU 112 (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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108B LEU 2.8 16.3 + - - +
109B SER* 3.7 9.7 - - - +
110B ILE 3.3 0.2 - - - -
111B TRP* 1.3 76.9 - - - +
113B GLU* 1.3 64.3 + - - +
115B SER* 3.1 16.5 + - - -
119B ASN* 5.7 3.7 + - - +
122B LEU* 3.8 27.6 - - + +
126B LYS* 3.3 36.8 + - - -
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Residues in contact with GLU 113 (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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109B SER 2.9 18.2 + - - +
110B ILE* 3.7 6.7 - - - +
112B GLU* 1.3 78.5 - - - +
114B ARG* 1.3 65.7 + - + +
115B SER* 3.4 2.6 + - - -
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Residues in contact with ARG 114 (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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68B GLN* 2.9 29.1 - - - +
110B ILE* 2.9 31.8 + - - +
113B GLU* 1.3 83.7 - - + +
115B SER* 1.3 71.2 + - - +
116B VAL* 3.3 13.1 + - + +
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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