Contacts of the helix formed by residues 75 - 96 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLY* 1.3 84.6 - - - +
76A GLU* 1.3 75.1 + - + +
77A PHE 3.3 2.2 + - - -
78A THR* 3.3 9.4 + - - +
79A LYS* 2.9 53.8 + - + +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 3.8 47.5 + - + +
35A LYS* 5.6 1.3 - - - -
37A SER* 3.5 18.8 - - - +
70A SER* 5.2 1.0 - - - +
73A LYS 4.8 1.0 - - - +
74A GLY* 3.1 23.6 + - - +
75A PRO* 1.3 88.2 - - + +
77A PHE* 1.3 58.3 + - + +
79A LYS* 3.8 2.8 - - - -
80A ASP* 2.9 37.2 + - - +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.4 37.7 - - + -
31A ILE* 4.0 3.4 - - + -
34A ARG* 3.7 23.6 - - + -
37A SER* 3.7 26.2 - - - -
40A ILE* 3.8 31.9 - - + -
41A VAL* 4.3 3.4 - - + -
66A VAL* 3.6 21.8 - - + +
67A ILE* 4.6 3.1 - - - -
70A SER* 3.5 28.8 + - - +
74A GLY 4.8 0.4 + - - -
75A PRO 3.4 0.4 - - - -
76A GLU* 1.3 77.2 + - - +
78A THR* 1.3 66.1 + - - +
80A ASP* 4.3 1.3 - - - +
81A PHE* 2.9 53.3 + + + +
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.9 9.8 + - + +
70A SER* 4.3 2.2 + - - -
71A LYS* 3.0 44.4 + - - +
75A PRO* 3.3 14.0 + - - +
77A PHE* 1.3 76.9 - - - +
79A LYS* 1.3 68.2 + - + +
82A ALA* 3.3 3.5 + - - +
116A VAL 4.1 1.6 - - - +
117A TYR* 2.8 54.1 + - + -
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO* 2.9 47.0 + - + +
76A GLU* 3.9 3.1 - - - +
78A THR* 1.3 83.1 - - + +
80A ASP* 1.3 62.9 - - - +
82A ALA* 3.4 7.7 + - - +
83A PRO* 3.2 21.1 - - - +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.5 32.4 + - - +
38A ARG* 3.4 30.7 + - + +
41A VAL* 3.5 31.6 - - + +
76A GLU* 2.9 19.6 + - - +
77A PHE 3.3 0.6 + - - +
79A LYS* 1.3 81.7 - - - +
81A PHE* 1.3 63.1 + - - +
83A PRO* 3.5 14.9 - - - +
84A VAL* 4.6 0.7 - - - +
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 6.2 2.0 - - + -
40A ILE* 5.6 2.9 - - + -
41A VAL* 3.9 22.0 - - + -
44A TRP* 3.7 47.8 - + + -
62A LEU* 6.5 0.2 - - + -
63A ALA* 3.9 22.4 - - + -
66A VAL* 4.1 11.9 - - + -
67A ILE* 3.4 27.4 - - + -
77A PHE* 2.9 45.9 + + - +
80A ASP* 1.3 76.6 - - - +
82A ALA* 1.3 65.2 + - - +
83A PRO* 3.3 0.4 - - - -
84A VAL* 3.0 8.6 + - + +
85A ILE* 2.9 28.9 + - + +
117A TYR* 3.3 17.9 - - - +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A THR 3.3 13.7 + - - +
79A LYS* 3.5 11.2 - - - +
81A PHE* 1.3 79.8 - - - +
83A PRO* 1.3 69.1 - - + +
84A VAL 3.2 1.4 + - - -
85A ILE* 3.7 16.9 + - - +
86A VAL* 4.6 6.6 + - - +
117A TYR* 3.8 16.6 - - + -
121A VAL* 5.4 11.8 - - + +
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Residues in contact with PRO 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LYS 3.2 16.2 - - - +
80A ASP* 3.5 11.2 - - - +
81A PHE 3.4 3.6 - - - -
82A ALA* 1.3 92.1 - - + +
84A VAL* 1.3 64.9 + - + +
86A VAL* 5.4 1.1 - - - +
87A GLU* 5.5 3.3 - - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.6 31.0 - - + -
44A TRP* 4.3 17.3 - - + -
45A GLU* 3.5 34.5 - - - +
80A ASP 4.7 0.2 - - - +
81A PHE* 3.0 13.9 + - + +
83A PRO* 1.3 92.4 - - + +
85A ILE* 1.3 65.3 + - - +
86A VAL 3.4 2.5 - - - -
87A GLU* 3.4 10.8 + - - +
88A ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 4.3 14.4 - - + -
60A LEU* 4.3 14.1 - - + -
63A ALA* 4.7 4.9 - - + -
67A ILE* 4.8 1.3 - - + -
81A PHE* 2.9 30.2 + - + +
82A ALA* 3.7 15.2 + - - +
84A VAL* 1.3 76.6 - - - +
86A VAL* 1.3 68.9 + - + +
88A ALA* 3.2 2.0 + - + +
89A PHE* 3.0 35.3 + - + -
111A TRP* 3.6 34.8 - - + -
117A TYR* 4.4 14.6 - - + -
121A VAL* 4.5 12.3 - - + -
125A LEU* 4.1 8.1 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 4.6 5.1 + - - +
83A PRO 5.4 0.8 - - - +
84A VAL 3.4 0.4 - - - -
85A ILE* 1.3 83.0 - - + +
87A GLU* 1.3 64.4 + - - +
89A PHE* 3.2 2.1 + - - +
90A LYS* 3.0 23.6 + - + +
121A VAL* 4.4 8.3 - - + +
124A GLN* 3.6 56.8 - - + +
125A LEU* 3.8 19.5 - - + -
128A ALA* 3.7 10.0 - - + +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 4.0 11.0 - - - +
49A ARG* 2.7 38.8 + - - +
83A PRO 5.5 2.8 + - - +
84A VAL* 3.4 13.1 + - - +
85A ILE 3.4 0.2 - - - -
86A VAL* 1.3 81.0 - - - +
88A ALA* 1.3 56.5 - - - +
90A LYS* 3.4 9.2 + - + +
91A HIS* 2.8 28.1 + - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.8 31.4 - - + -
45A GLU* 6.0 0.7 - - + +
48A LEU* 3.9 13.5 - - + -
49A ARG* 4.5 5.4 - - - +
60A LEU* 4.4 3.4 - - + -
84A VAL 3.0 14.2 + - - +
85A ILE* 3.4 13.0 - - + +
86A VAL 3.1 0.2 - - - -
87A GLU* 1.3 76.2 - - - +
89A PHE* 1.3 60.8 + - - +
91A HIS* 3.2 5.1 + - - +
92A VAL* 2.9 35.2 + - - +
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.0 24.0 - - + -
85A ILE* 3.0 22.9 + - + +
86A VAL 3.2 6.9 + - - +
88A ALA* 1.3 75.4 - - - +
90A LYS* 1.3 58.1 + - - +
92A VAL* 4.0 4.2 - - - +
93A SER* 2.8 34.3 + - - -
104A LEU* 3.8 42.5 - - + +
107A VAL* 4.1 24.7 - - + -
108A LEU* 4.4 11.2 - - + -
111A TRP* 3.9 31.0 - + - -
125A LEU* 3.6 19.7 - - + -
128A ALA* 4.2 10.1 - - + -
129A LEU* 4.6 12.5 - - + +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 3.0 17.7 + - + +
87A GLU* 3.7 9.2 - - + +
89A PHE* 1.3 77.0 - - - +
91A HIS* 1.3 64.0 + - - +
93A SER* 3.7 1.2 - - - -
94A SER* 3.0 34.3 + - - +
127A GLN 6.0 0.4 - - - -
128A ALA* 3.8 30.0 - - + +
133A GLU* 3.7 39.8 + - - +
134A HIS* 4.4 15.0 + - + -
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Residues in contact with HIS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.1 12.0 - - - +
49A ARG* 3.7 48.9 + - + +
56A LYS* 2.9 43.9 + - + +
87A GLU 2.8 18.5 + - - +
88A ALA* 3.5 4.7 - - - +
90A LYS* 1.3 77.2 - - - +
92A VAL* 1.3 64.5 + - - +
94A SER* 3.2 5.3 + - - -
95A GLU* 3.1 45.7 + - + +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.0 28.7 - - + -
56A LYS* 4.1 22.4 - - + +
57A LEU* 4.0 18.4 - - + +
60A LEU* 3.8 21.8 - - + -
88A ALA 2.9 20.7 + - - +
89A PHE 4.0 1.8 - - - +
91A HIS* 1.3 78.8 - - - +
93A SER* 1.3 56.6 + - - +
95A GLU 3.2 0.7 + - - -
96A THR* 2.6 43.2 + - + +
104A LEU* 3.8 18.8 - - + -
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE 2.8 19.5 + - - -
90A LYS 3.7 0.4 - - - -
92A VAL* 1.3 79.6 - - - +
94A SER* 1.3 60.7 + - - +
95A GLU 3.5 0.2 + - - -
96A THR* 3.5 18.1 + - - +
98A GLU* 6.2 0.2 - - - -
101A LYS* 3.2 29.5 + - - +
104A LEU* 4.0 8.0 - - - +
128A ALA 3.9 4.7 - - - -
129A LEU* 3.3 18.4 + - - +
134A HIS* 3.3 23.8 + - - -
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 3.0 26.4 + - - +
91A HIS* 3.2 5.4 + - - -
93A SER* 1.3 76.4 - - - +
95A GLU* 1.3 70.5 + - - +
96A THR 3.4 3.5 + - - +
134A HIS* 3.1 22.1 + - - -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PRO* 3.4 26.1 - - + +
56A LYS* 3.9 23.7 - - + -
91A HIS* 3.1 42.5 + - + +
92A VAL 3.2 0.8 + - - +
94A SER* 1.3 85.8 - - - +
96A THR* 1.3 60.6 + - - +
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Residues in contact with THR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PRO* 3.6 29.6 - - + +
56A LYS* 4.9 1.6 - - + -
57A LEU* 5.2 4.7 - - + -
92A VAL* 2.6 38.5 + - + +
93A SER* 3.5 15.8 + - - +
94A SER 4.3 3.5 - - - +
95A GLU* 1.3 84.3 - - + +
97A ASP* 1.3 65.2 + - - +
98A GLU* 3.7 1.4 + - - -
100A CYS* 3.8 27.3 - - + +
104A LEU* 4.4 2.6 - - - +
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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
------------------------------------------------------------
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