Contacts of the helix formed by residues 75 - 95 (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 PRO 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS* 6.4 0.4 - - + -
74B GLY* 1.3 83.3 - - - +
76B GLU* 1.3 74.3 + - + +
77B PHE 3.4 1.6 - - - -
78B THR* 3.2 11.5 + - - +
79B LYS* 2.9 45.2 + - + +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 3.8 49.5 + - + +
35B LYS* 5.1 3.3 + - - -
37B SER* 3.4 18.6 - - - +
70B SER* 6.0 0.3 - - - -
73B LYS 5.0 0.5 - - - +
74B GLY* 3.2 21.7 - - - +
75B PRO* 1.3 87.2 - - + +
77B PHE* 1.3 59.1 + - - +
79B LYS* 3.8 3.2 - - - +
80B ASP* 2.8 35.7 + - - +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.2 37.9 - - + -
31B ILE* 3.9 3.6 - - - -
34B ARG* 3.6 22.7 - - + -
37B SER* 3.6 27.4 - - - -
40B ILE* 3.6 34.3 - - + -
41B VAL* 4.5 3.4 - - + -
66B VAL* 3.5 26.9 - - + +
67B ILE* 4.7 3.6 - - - -
70B SER* 3.6 28.5 + - - +
74B GLY 4.8 0.4 + - - -
75B PRO 3.4 0.2 - - - -
76B GLU* 1.3 77.4 + - - +
78B THR* 1.3 67.7 + - - +
80B ASP* 4.4 0.4 - - - +
81B PHE* 2.9 46.9 + + + +
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.9 12.0 + - - +
70B SER* 4.5 3.1 + - - -
71B LYS* 2.9 41.6 + - - +
74B GLY 5.1 0.3 + - - -
75B PRO* 3.2 15.8 + - + +
77B PHE* 1.3 79.0 - - - +
79B LYS* 1.3 70.0 + - + +
82B ALA* 3.3 5.9 + - - +
116B VAL 4.3 1.3 - - - +
117B TYR* 2.8 49.5 + - + -
118B GLU* 5.9 0.4 - - - +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 2.9 38.9 + - + +
76B GLU* 3.9 3.8 - - - +
78B THR* 1.3 83.8 - - + +
80B ASP* 1.3 65.1 + - - +
82B ALA* 3.4 7.9 + - + +
83B PRO* 3.1 23.7 - - - +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 2.5 29.5 + - - +
38B ARG* 3.4 33.3 + - - +
41B VAL* 3.4 33.2 - - + +
76B GLU* 2.8 21.3 + - - +
77B PHE 4.6 0.4 - - - +
79B LYS* 1.3 77.2 - - - +
81B PHE* 1.3 62.5 + - - +
83B PRO* 3.3 12.6 - - - +
84B VAL* 4.4 1.7 - - - +
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 6.4 1.3 - - + -
40B ILE* 5.5 3.4 - - + -
41B VAL* 3.9 17.0 - - + -
44B TRP* 3.6 53.2 - + + -
62B LEU* 6.4 0.4 - - + -
63B ALA* 3.9 18.6 - - + -
66B VAL* 4.2 11.9 - - + -
67B ILE* 3.6 27.4 - - + -
77B PHE* 2.9 47.8 + + - +
80B ASP* 1.3 78.0 - - - +
82B ALA* 1.3 64.6 + - - +
83B PRO 3.3 0.2 - - - -
84B VAL* 3.0 9.3 + - + +
85B ILE* 2.9 30.8 + - + +
117B TYR* 3.4 12.6 - - - +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR 3.3 14.7 + - - +
79B LYS* 3.4 11.2 - - + +
81B PHE* 1.3 76.6 - - - +
83B PRO* 1.3 68.1 - - + +
84B VAL 3.3 1.0 + - - -
85B ILE* 3.7 15.3 + - - +
86B VAL* 4.7 6.1 + - - +
117B TYR* 3.7 18.6 - - + -
118B GLU* 6.1 0.4 - - - +
121B VAL* 5.4 10.1 - - + +
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Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS 3.1 17.5 - - - +
80B ASP* 3.3 14.4 - - - +
82B ALA* 1.3 92.9 - - + +
84B VAL* 1.3 64.9 + - + +
86B VAL* 5.4 1.2 - - - +
87B GLU* 5.5 2.4 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 3.6 31.0 - - + -
44B TRP* 4.3 11.0 - - + -
45B GLU* 3.2 34.9 - - + +
80B ASP 4.8 1.3 - - - +
81B PHE* 3.0 19.5 + - + +
83B PRO* 1.3 88.4 - - + +
85B ILE* 1.3 65.2 + - - +
86B VAL 3.3 2.7 - - - -
87B GLU* 3.4 9.0 + - - +
88B ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 4.3 11.9 - - + -
60B LEU* 3.9 17.7 - - + -
63B ALA* 4.7 4.0 - - + -
67B ILE* 4.9 1.6 - - + -
81B PHE* 2.9 30.5 + - + +
82B ALA* 3.7 16.4 - - - +
83B PRO 3.8 0.4 - - - -
84B VAL* 1.3 77.2 - - - +
86B VAL* 1.3 74.5 + - + +
88B ALA* 3.2 2.7 + - - +
89B PHE* 2.9 41.3 + - + -
111B TRP* 3.8 29.4 - - + -
117B TYR* 4.5 14.6 - - + +
121B VAL* 4.6 6.1 - - + -
125B LEU* 4.1 8.1 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA 4.7 4.9 + - - +
83B PRO 6.1 1.1 - - - +
84B VAL 3.3 0.8 - - - -
85B ILE* 1.3 83.6 - - + +
87B GLU* 1.3 58.7 + - - +
89B PHE* 3.1 6.1 + - - +
90B LYS* 3.0 24.5 + - + +
121B VAL* 4.5 7.0 - - + -
124B GLN* 3.7 55.4 - - + +
125B LEU* 3.8 20.6 - - + -
128B ALA* 3.6 10.1 - - + +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU* 5.4 7.0 - - - +
49B ARG* 6.5 0.9 - - - -
83B PRO 5.7 0.2 + - - -
84B VAL* 3.4 12.1 + - - +
85B ILE 3.4 0.2 - - - -
86B VAL* 1.3 80.3 - - - +
88B ALA* 1.3 58.6 + - - +
90B LYS* 4.0 27.7 + - - +
91B HIS* 2.9 35.4 + - + +
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Residues in contact with ALA 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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44B TRP* 3.7 32.8 - - + -
45B GLU* 6.3 1.8 - - + -
48B LEU* 3.8 15.0 - - + -
60B LEU* 4.3 5.6 - - + -
84B VAL 2.9 17.7 + - - +
85B ILE* 3.4 7.4 - - - +
86B VAL 3.2 0.2 - - - -
87B GLU* 1.3 77.6 - - - +
89B PHE* 1.3 57.7 + - - +
91B HIS* 3.2 3.8 + - - +
92B VAL* 3.0 35.2 + - - +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.0 22.7 - - + -
85B ILE* 2.9 47.0 + - + +
86B VAL 3.5 7.4 - - - +
88B ALA* 1.3 76.1 - - - +
90B LYS* 1.3 56.0 + - - +
92B VAL* 4.1 0.9 - - - +
93B SER* 3.0 31.8 + - - -
104B LEU* 3.8 37.8 - - + +
107B VAL* 4.3 19.3 - - + -
108B LEU* 3.3 41.5 - - + -
111B TRP* 4.0 7.6 - + - -
125B LEU* 3.4 19.7 - - + +
128B ALA* 4.3 8.5 - - + -
129B LEU* 4.6 6.6 - - + +
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Residues in contact with LYS 90 (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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86B VAL* 3.0 16.5 + - + +
87B GLU* 3.8 28.5 + - - +
88B ALA 3.3 0.2 - - - -
89B PHE* 1.3 75.7 - - - +
91B HIS* 1.3 63.0 + - - +
93B SER* 3.4 1.9 + - - -
94B SER* 3.1 35.7 + - - +
128B ALA* 3.8 30.4 - - + +
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Residues in contact with HIS 91 (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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48B LEU* 4.1 21.3 - - + -
49B ARG* 3.7 29.8 - - + +
56B LYS* 2.9 40.0 + - + -
87B GLU* 2.9 26.8 + - + +
88B ALA* 3.6 5.4 - - - +
90B LYS* 1.3 74.7 - - - +
92B VAL* 1.3 67.7 + - - +
94B SER* 3.2 7.8 + - - -
95B GLU* 3.0 46.6 + - - +
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Residues in contact with VAL 92 (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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48B LEU* 4.1 16.2 - - + -
53B PRO 5.4 0.9 - - - +
56B LYS* 4.1 33.2 - - + +
57B LEU 4.6 4.3 - - - +
60B LEU* 3.4 27.1 - - + -
88B ALA 3.0 18.1 + - - +
89B PHE 4.1 2.2 - - - +
91B HIS* 1.3 78.7 - - + +
93B SER* 1.3 58.9 + - - +
95B GLU* 3.4 10.7 + - - +
96B THR* 3.0 22.5 + - - -
100B CYS* 4.2 14.8 - - - -
104B LEU* 3.7 19.1 - - + -
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE 3.0 18.9 + - - -
90B LYS 3.7 4.9 - - - -
92B VAL* 1.3 79.9 - - - +
94B SER* 1.3 61.6 + - - +
96B THR* 3.1 26.6 + - - +
101B LYS* 3.5 19.4 + - - +
104B LEU* 4.3 3.5 - - - +
128B ALA 4.1 7.6 - - - -
129B LEU* 3.0 38.1 + - - +
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Residues in contact with SER 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS* 3.1 26.2 + - - +
91B HIS* 3.2 7.1 + - - -
93B SER* 1.3 78.2 - - - +
95B GLU* 1.3 71.0 + - - +
96B THR 3.1 7.5 + - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PRO* 3.9 29.5 - - + +
56B LYS* 4.0 25.2 - - + -
91B HIS* 3.0 34.2 + - - +
92B VAL* 3.4 7.8 + - - +
93B SER 3.4 0.4 - - - -
94B SER* 1.3 84.0 - - - +
96B THR* 1.3 58.6 + - - +
100B CYS* 5.4 0.5 - - - -
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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