Contacts of the helix formed by residues 96 - 114 (chain B) in PDB entry 2NP5
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B PRO 3.3 1.7 + - - -
95B LEU* 1.3 77.4 - - - +
97B GLU* 1.3 66.9 + - - +
98B ALA* 3.5 9.5 + - - +
99B ARG* 2.6 62.2 + - - +
100B SER* 2.9 24.6 + - - -
173B PRO* 5.5 0.2 - - - -
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Residues in contact with GLU 97 (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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96B ASP* 1.3 76.2 - - - +
98B ALA* 1.3 63.0 + - - +
100B SER* 3.2 6.1 + - - -
101B ARG* 2.9 46.1 + - + +
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Residues in contact with ALA 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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19B PHE* 4.9 0.5 - - - -
96B ASP* 3.3 11.0 + - - +
97B GLU* 1.3 80.4 - - - +
99B ARG* 1.3 60.9 + - + +
101B ARG* 3.4 10.8 + - - +
102B GLU* 3.1 32.9 + - - +
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Residues in contact with ARG 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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71B ARG* 3.8 9.6 - - - +
90B SER* 3.1 19.8 + - - -
91B GLN* 3.7 39.5 - - - +
92B LEU 5.8 0.2 - - - -
93B LEU 3.3 25.1 + - - +
94B PRO* 3.9 6.6 - - + +
95B LEU* 3.7 26.2 + - - +
96B ASP* 2.6 44.4 + - - +
98B ALA* 1.3 75.7 - - + +
100B SER* 1.3 59.2 + - - +
102B GLU* 3.6 21.3 - - - +
103B ALA* 2.8 30.1 + - - +
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Residues in contact with SER 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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94B PRO* 3.7 20.5 - - - +
96B ASP 2.9 19.3 + - - -
97B GLU* 3.4 10.1 - - - -
99B ARG* 1.3 73.3 - - - +
101B ARG* 1.3 67.0 + - - +
103B ALA* 3.3 2.8 + - - +
104B HIS* 3.1 23.1 + - - +
165B ILE* 4.3 7.8 - - - +
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Residues in contact with ARG 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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19B PHE* 3.7 20.5 - - + -
20B ASP* 3.4 31.5 + - - +
23B ALA* 4.0 18.1 - - + +
24B GLU* 2.7 41.0 + - - +
38B ARG* 4.6 0.6 - - - +
97B GLU* 2.9 39.5 + - + +
98B ALA* 3.6 11.0 - - - +
100B SER* 1.3 76.4 - - - +
102B GLU* 1.3 60.9 + - - +
104B HIS* 3.3 5.8 + - - +
105B VAL* 3.1 28.8 + - - +
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Residues in contact with GLU 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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19B PHE* 3.7 22.4 - - + -
64B LEU* 4.1 11.7 - - + +
67B LYS* 5.3 4.7 - - - +
68B LEU* 3.3 16.0 - - + +
71B ARG* 2.7 45.7 + - - -
91B GLN 4.3 0.9 - - - +
98B ALA* 3.1 21.8 + - - +
99B ARG* 3.6 16.8 - - - +
100B SER 3.3 0.2 - - - -
101B ARG* 1.3 73.9 - - - +
103B ALA* 1.3 54.2 + - - +
105B VAL* 3.3 2.1 + - - +
106B MSE 2.8 42.1 + - + +
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Residues in contact with ALA 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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92B LEU 5.5 2.0 - - - +
94B PRO* 4.2 13.0 - - + -
99B ARG 2.8 21.4 + - - +
100B SER 3.7 1.8 - - - +
102B GLU* 1.3 73.3 - - - +
104B HIS* 1.3 57.4 + - - +
106B MSE 4.0 4.8 - - - +
107B ALA* 2.9 33.6 + - - +
161B ALA* 4.2 19.3 - - + +
165B ILE* 3.6 22.9 - - + +
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Residues in contact with HIS 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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22B ALA 3.3 15.7 + - - -
23B ALA 2.8 30.8 + - - -
26B GLY* 3.9 9.9 - - - -
100B SER 3.1 12.9 + - - +
101B ARG* 3.6 10.8 - - - +
102B GLU 3.2 0.2 - - - -
103B ALA* 1.3 77.2 - - - +
105B VAL* 1.3 64.1 + - - +
107B ALA* 3.9 1.2 - - - +
108B ALA* 3.1 21.7 + - + +
165B ILE* 4.0 16.6 - - + +
111D VAL* 4.2 15.0 + - + +
114D ALA* 3.6 27.5 - - + +
115D THR* 3.5 28.2 + - + +
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Residues in contact with VAL 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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19B PHE* 3.5 45.5 - - + +
22B ALA* 4.0 12.6 - - + -
23B ALA* 3.6 20.2 - - + +
64B LEU* 3.8 13.7 - - + -
101B ARG 3.1 17.6 + - - +
102B GLU 3.9 0.4 - - - +
104B HIS* 1.3 77.9 - - - +
106B MSE 1.3 57.8 + - - +
108B ALA* 3.3 5.5 + - - +
109B PHE* 2.9 53.7 + - + -
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Residues in contact with MSE 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 LEU* 3.8 19.3 - - + -
64B LEU* 3.7 25.1 - - + -
65B VAL* 4.0 21.1 - - + -
68B LEU* 3.9 24.7 - - + -
102B GLU 2.8 27.1 + - - +
103B ALA* 4.0 4.7 - - - +
105B VAL* 1.3 72.0 - - - +
107B ALA* 1.3 59.2 + - - +
109B PHE* 3.2 6.1 + - - +
110B ALA* 2.9 28.1 + - - +
123B ARG* 3.8 29.0 + - + +
126B THR* 4.9 10.1 - - + -
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Residues in contact with ALA 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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103B ALA 2.9 19.7 + - - +
104B HIS 3.9 0.9 - - - +
106B MSE 1.3 78.4 - - - +
108B ALA* 1.3 61.1 + - - +
110B ALA* 3.1 9.8 + - - +
111B VAL* 3.1 26.5 + - - +
162B LEU* 3.9 21.5 - - + -
165B ILE* 3.8 22.0 - - + -
111D VAL* 3.8 6.3 - - + -
162D LEU* 4.4 8.0 - - + +
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Residues in contact with ALA 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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22B ALA* 5.7 0.9 - - + +
27B LEU* 3.6 34.4 - - + +
28B GLU* 5.6 1.1 - - + +
104B HIS* 3.1 20.2 + - + +
105B VAL* 3.5 7.0 - - - +
107B ALA* 1.3 76.0 - - - +
109B PHE* 1.3 62.8 + - - +
111B VAL* 3.3 4.1 + - - +
112B ARG* 3.0 23.9 + - - +
111D VAL* 3.9 24.4 - - + +
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Residues in contact with PHE 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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18B LEU* 3.9 25.8 - - + -
27B LEU* 3.7 21.8 - - + -
57B PHE* 3.5 38.1 - + - -
60B ALA* 4.7 1.8 - - + -
61B LEU* 3.8 42.2 - - + -
64B LEU* 4.9 2.0 - - + -
105B VAL* 2.9 44.2 + - + +
106B MSE 3.6 7.9 - - - +
108B ALA* 1.3 77.2 - - - +
110B ALA* 1.3 55.7 + - - +
112B ARG* 3.3 2.0 + - - +
113B ALA* 2.8 29.8 + - - +
119B LEU* 3.8 28.8 - - + +
123B ARG* 4.2 4.2 - - - -
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Residues in contact with ALA 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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106B MSE 2.9 8.8 + - - +
107B ALA 3.1 10.1 + - - +
109B PHE* 1.3 77.4 - - - +
111B VAL* 1.3 61.6 + - - +
113B ALA* 3.3 15.2 + - - +
114B ALA 3.7 1.2 + - - -
123B ARG* 3.4 39.9 - - - +
162D LEU* 3.7 29.6 - - + +
165D ILE* 4.3 1.6 - - - +
166D GLY* 3.5 13.2 + - - -
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Residues in contact with VAL 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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28B GLU* 5.8 2.7 - - + +
107B ALA 3.1 13.6 + - - +
108B ALA* 3.9 5.6 - - - +
109B PHE 3.3 0.2 - - - -
110B ALA* 1.3 75.9 - - - +
112B ARG* 1.3 64.8 + - - +
114B ALA* 3.1 19.8 + - - +
115B THR* 4.4 1.0 + - - +
104D HIS* 4.0 26.3 + - + +
107D ALA* 3.8 26.7 - - + +
108D ALA* 4.1 18.6 - - + -
111D VAL* 3.6 21.3 - - + -
162D LEU* 3.9 7.2 - - + -
165D ILE* 4.7 5.6 - - + -
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Residues in contact with ARG 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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27B LEU* 3.8 22.1 + - + +
28B GLU* 4.3 14.8 + - - +
53B LYS* 4.5 18.6 - - - +
54B ASP* 5.9 0.4 + - - -
57B PHE* 3.3 43.2 - - - +
108B ALA 3.0 16.8 + - - +
109B PHE 3.3 4.7 + - - +
111B VAL* 1.3 79.3 - - - +
113B ALA* 1.3 60.5 + - - +
114B ALA 3.0 0.2 - - - -
115B THR* 3.1 20.7 + - - +
116B SER* 3.2 13.4 + - - -
119B LEU* 3.5 24.2 - - + +
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Residues in contact with ALA 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 PHE 2.8 14.2 + - - +
110B ALA 3.3 13.0 - - - +
111B VAL 3.2 0.4 - - - -
112B ARG* 1.3 70.0 - - - +
114B ALA* 1.3 62.4 + - - +
115B THR 3.0 6.7 + - - -
116B SER 3.3 15.2 + - - +
119B LEU* 3.9 15.7 - - - +
120B ALA* 3.7 23.6 - - - +
123B ARG* 4.0 5.8 - - - -
165D ILE 4.7 0.3 - - - +
166D GLY* 3.5 25.4 - - - +
168D PRO* 6.0 0.2 - - - +
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Residues in contact with ALA 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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110B ALA 3.7 2.0 + - - -
111B VAL 3.1 14.8 + - - +
112B ARG 3.0 1.2 - - - -
113B ALA* 1.3 79.4 - - - +
115B THR* 1.3 61.8 + - - +
104D HIS* 4.0 21.0 - - + +
165D ILE* 3.4 39.2 + - + +
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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