Contacts of the helix formed by residues 78 - 89 (chain B) in PDB entry 3NT2
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 ALA 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B SER* 3.8 6.6 + - - +
75B TRP* 3.0 16.9 + - + +
77B PRO* 1.3 78.4 - - + +
79B HIS* 1.3 61.3 + - - +
81B SER* 4.6 8.3 - - - -
82B SER* 3.5 22.2 + - - -
400B NAI 3.1 41.9 + - - +
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Residues in contact with HIS 79 (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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72B VAL* 3.2 30.7 + - + -
73B THR 4.3 0.6 - - - -
74B SER* 2.6 31.9 + - - -
75B TRP 3.3 10.8 - - - -
76B GLY* 3.3 15.7 + - - +
77B PRO 3.1 2.6 - - - -
78B ALA* 1.3 75.7 - - - +
80B GLU* 1.3 71.0 + - - +
81B SER 3.2 2.0 - - - -
82B SER* 3.1 3.3 + - - -
83B VAL* 2.8 27.1 + - - +
95B CYS* 4.1 3.4 - - - -
96B GLU* 3.3 17.4 + - + -
97B LYS 3.8 0.7 - - - -
98B PRO* 2.9 20.4 + - - +
99B LEU 3.6 14.6 - - - +
100B ALA* 5.1 0.2 - - - -
400B NAI 3.0 28.0 - - - -
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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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76B GLY 4.8 0.4 + - - -
77B PRO 4.2 6.5 + - - +
79B HIS* 1.3 76.7 - - - +
81B SER* 1.3 64.2 + - - +
83B VAL* 3.2 1.0 + - - +
84B LEU* 2.9 43.5 + - + +
99B LEU 3.9 2.5 + - - -
100B ALA* 4.0 12.5 - - + +
102B THR* 4.3 4.5 + - - -
105B GLY* 3.4 28.1 - - - +
108B ARG* 2.8 42.9 + - - -
109B ILE* 4.1 14.1 - - + -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASP* 4.5 2.8 + - - -
77B PRO 5.0 1.9 + - - -
78B ALA* 4.6 9.6 - - - -
79B HIS 3.2 0.8 - - - +
80B GLU* 1.3 82.8 - - - +
82B SER* 1.3 63.2 + - - +
84B LEU* 3.2 5.8 + - - +
85B LYS* 3.0 48.5 + - - +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.7 32.4 - - - +
58B ASP* 3.0 24.8 + - - -
62B LEU* 4.6 3.3 - - - +
72B VAL* 4.2 15.1 - - - +
74B SER* 5.2 0.3 + - - -
78B ALA 3.5 14.0 + - - -
79B HIS 3.1 7.2 + - - -
81B SER* 1.3 78.8 + - - +
83B VAL* 1.3 62.0 + - - +
85B LYS* 3.9 4.6 - - - +
86B ALA* 3.0 24.8 + - - +
400B NAI 4.8 3.8 + - - -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.1 11.0 - - + -
79B HIS 2.8 21.9 + - - +
80B GLU 3.6 3.6 - - - +
82B SER* 1.3 74.4 - - - +
84B LEU* 1.3 66.1 + - - +
86B ALA* 3.1 7.9 + - - +
87B ILE* 2.9 26.8 + - + +
93B VAL* 4.6 7.0 - - + -
95B CYS* 3.6 35.0 - - + -
99B LEU* 4.4 8.7 - - + +
109B ILE* 3.7 35.9 - - + -
121B VAL* 4.5 9.0 - - + -
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Residues in contact with LEU 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* 2.9 49.5 + - + +
81B SER* 3.7 5.2 - - - +
83B VAL* 1.3 70.4 - - - +
85B LYS* 1.3 66.3 + - + +
87B ILE* 3.1 7.8 + - + +
88B LYS* 2.9 44.3 + - - +
108B ARG* 4.1 13.7 - - + +
109B ILE* 3.8 27.8 - - + +
112B GLU* 3.6 31.6 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASP* 3.3 30.2 + - - +
59B ASP* 2.9 32.3 + - - +
62B LEU* 3.8 16.6 - - + -
81B SER* 3.0 35.4 + - - +
82B SER* 3.9 1.8 - - - +
84B LEU* 1.3 74.6 - - + +
86B ALA* 1.3 54.6 + - - +
88B LYS* 3.0 14.5 + - + +
89B ALA* 2.6 37.8 + - + +
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Residues in contact with ALA 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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62B LEU* 3.9 19.0 - - + +
70B VAL* 4.1 26.0 - - + -
82B SER 3.0 18.1 + - - +
83B VAL* 3.1 8.0 + - - +
85B LYS* 1.3 77.6 - - - +
87B ILE* 1.3 56.9 + - - +
89B ALA* 3.5 1.3 - - - -
90B GLN 3.0 6.2 + - - -
91B LYS* 2.9 32.7 + - + +
93B VAL* 4.4 11.0 - - + -
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Residues in contact with ILE 87 (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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83B VAL* 2.9 19.4 + - + +
84B LEU* 3.1 9.2 + - - +
86B ALA* 1.3 73.7 - - - +
88B LYS* 1.3 60.0 + - - +
90B GLN* 2.7 31.0 + - - +
91B LYS 5.0 0.7 - - - +
93B VAL* 5.0 2.9 - - + -
109B ILE* 3.8 31.4 - - + +
112B GLU* 3.9 27.1 - - + +
113B GLU* 4.2 6.7 - - + +
116B VAL* 3.7 25.3 - - + +
120B LEU* 4.3 13.6 - - + +
121B VAL* 3.7 30.7 - - + -
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Residues in contact with LYS 88 (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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84B LEU* 2.9 40.0 + - - +
85B LYS* 3.5 10.0 - - + +
87B ILE* 1.3 76.4 - - - +
89B ALA* 1.3 59.4 + - - +
90B GLN* 3.1 14.6 + - - +
112B GLU* 3.5 32.3 - - - +
116B VAL* 6.0 0.4 - - - -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 4.5 17.7 - - + +
85B LYS* 2.6 21.8 + - + +
86B ALA* 3.9 6.7 - - - +
88B LYS* 1.3 70.9 - - - +
90B GLN* 1.3 69.4 + - - +
91B LYS* 3.4 21.6 + - + +
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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