Contacts of the helix formed by residues 70 - 87 (chain A) in PDB entry 4IJ3
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 CYS 70 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA* 2.9 12.8 + - + +
69A TRP* 1.3 99.9 - - + +
71A GLY* 1.3 64.4 + - - +
72A HIS* 3.8 3.4 - - - -
73A CYS* 2.1 54.5 + - - +
74A ILE* 3.0 23.4 + - - +
118A PHE* 3.6 22.9 - - + -
31C GLY 3.5 5.4 - - - +
32C TYR* 6.3 0.2 - - - -
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP 3.4 3.8 + - - -
70A CYS* 1.3 70.3 - - - +
72A HIS* 1.3 60.7 + - - +
74A ILE* 3.1 15.1 + - - +
75A ALA* 3.1 20.4 + - - +
30C THR 5.8 0.2 - - - -
31C GLY* 2.9 16.9 + - - -
32C TYR* 3.5 28.8 + - - -
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Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A CYS* 3.5 2.9 - - - -
71A GLY* 1.3 75.1 - - - +
73A CYS* 1.3 52.0 - - - +
75A ALA* 3.1 8.8 + - + +
76A PHE* 2.7 36.0 + - - +
118A PHE 4.2 5.2 + - - +
119A PRO* 3.6 19.7 - - + -
32C TYR* 3.4 37.1 - + - -
97C SER* 6.0 0.9 - - - -
98C ASP* 4.6 9.4 + - - -
100C TYR* 3.4 59.8 + + + -
101C GLY 4.1 2.7 + - - -
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Residues in contact with CYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.2 9.8 - - + +
36A TYR* 4.8 0.5 + - - -
64A GLU* 4.8 3.1 - - - +
66A PHE* 3.8 14.6 - - + -
67A ALA 3.5 20.2 - - - +
70A CYS* 2.1 53.4 - - - +
72A HIS* 1.3 73.8 - - - +
74A ILE* 1.3 64.1 + - - +
76A PHE* 3.2 7.2 + - - +
77A ALA* 3.0 24.3 + - - +
118A PHE* 3.3 20.0 - - - -
119A PRO* 3.7 10.8 - - - -
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.1 22.3 - - + +
68A SER 3.7 21.1 - - - +
69A TRP* 4.3 6.3 - - - +
70A CYS 3.0 21.2 + - - +
71A GLY* 3.5 10.5 - - - +
73A CYS* 1.3 77.0 - - - +
75A ALA* 1.3 62.2 + - - +
76A PHE 3.4 0.2 + - - -
77A ALA* 3.6 4.3 + - - +
78A PRO* 3.5 16.5 - - - +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY 3.1 13.1 + - - +
72A HIS* 3.4 13.7 - - + +
74A ILE* 1.3 79.8 - - - +
76A PHE* 1.3 58.8 + - - +
78A PRO* 3.4 12.2 - - - +
79A THR* 4.9 4.2 + - - -
32C TYR* 5.7 0.9 - - - +
100C TYR* 4.1 9.1 + - + +
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 3.4 24.2 - - + -
72A HIS 2.7 19.4 + - - +
73A CYS* 3.2 5.8 + - - +
75A ALA* 1.3 74.2 - - - +
77A ALA* 1.3 67.0 + - - +
78A PRO 3.3 0.9 - - - -
79A THR* 2.8 36.8 + - + -
80A TRP* 3.0 51.8 + + + -
119A PRO* 4.3 11.7 - - + -
121A VAL* 4.4 5.8 - - + -
138A VAL* 3.7 41.5 - - + -
141A ALA 5.4 1.8 - - - -
146A LEU* 4.1 7.6 - - + -
100C TYR* 3.3 20.6 - + + +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.6 18.6 - - + +
36A TYR* 3.4 29.5 + - + +
73A CYS 3.0 12.4 + - - +
74A ILE 3.7 9.2 - - - +
76A PHE* 1.3 75.1 - - - +
78A PRO* 1.3 64.4 - - + +
80A TRP* 3.2 1.3 + - - +
81A LYS* 2.8 45.8 + - - +
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Residues in contact with PRO 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE 3.5 8.7 - - - +
75A ALA* 3.4 14.4 - - - +
76A PHE 3.3 4.9 - - - -
77A ALA* 1.3 94.3 - - + +
79A THR* 1.3 55.7 + - - +
81A LYS* 3.8 14.1 - - - +
82A ALA* 3.0 29.3 + - - +
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Residues in contact with THR 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 ALA 4.9 4.9 + - - -
76A PHE* 2.8 28.0 + - + -
78A PRO* 1.3 73.6 - - - +
80A TRP* 1.3 60.8 + - - +
82A ALA* 3.2 6.5 + - - +
83A LEU* 2.9 28.1 + - - +
141A ALA 4.5 9.1 + - - +
142A ASP* 5.4 0.2 - - - -
143A VAL* 4.1 17.7 - - + +
146A LEU* 3.5 29.2 - - + -
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.6 17.3 - + - +
42A LEU* 3.4 26.9 - - + +
62A ALA* 3.6 28.3 - - + -
64A GLU* 3.4 27.3 - - + +
76A PHE* 3.0 37.9 + + + +
77A ALA 3.8 1.6 - - - +
79A THR* 1.3 77.5 - - - +
81A LYS* 1.3 57.5 + - - +
83A LEU* 3.4 28.6 + - + +
84A ALA* 2.9 27.7 + - - +
96A LEU* 3.7 22.9 - - + +
97A ALA 3.2 19.9 + - - -
121A VAL* 3.8 27.8 - - + -
136A PHE* 4.7 10.8 - + - -
138A VAL* 5.0 0.2 - - + -
146A LEU* 4.8 1.8 - - + -
150A LEU* 5.4 0.4 - - + -
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU 3.8 13.7 + - - -
36A TYR* 3.6 21.3 - - + -
40A ASP* 3.1 37.1 + - + +
41A PRO* 4.0 6.2 - - + +
42A LEU* 4.4 4.3 - - + -
77A ALA* 2.8 35.2 + - - +
78A PRO* 3.8 12.6 - - - +
80A TRP* 1.3 70.6 - - - +
82A ALA* 1.3 65.4 + - - +
84A ALA* 3.2 8.5 + - - +
85A GLU* 3.2 22.5 + - - +
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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
----------------------------------------------------------
78A PRO 3.0 18.2 + - - +
79A THR* 3.5 5.4 - - - +
81A LYS* 1.3 76.4 - - - +
83A LEU* 1.3 57.9 + - - +
85A GLU* 3.4 7.4 + - - +
86A ASP* 2.9 27.8 + - - +
143A VAL* 4.1 18.8 - - + +
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Residues in contact with LEU 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 THR 2.9 16.1 + - - +
80A TRP* 3.6 35.7 - - + +
82A ALA* 1.3 74.2 - - - +
84A ALA* 1.3 66.7 + - - +
86A ASP* 3.0 13.6 + - - +
87A VAL* 3.0 22.4 + - + +
96A LEU* 3.7 12.6 - - + -
136A PHE* 5.6 0.2 - - + -
143A VAL* 3.8 36.9 - - + +
146A LEU* 3.7 21.5 - - + -
147A ARG* 3.9 19.5 - - + +
150A LEU* 4.0 16.6 - - + -
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Residues in contact with ALA 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 PRO* 3.6 32.3 - - + +
42A LEU* 4.0 14.1 - - + -
80A TRP 2.9 17.1 + - - +
81A LYS* 3.2 8.5 + - - +
83A LEU* 1.3 75.5 - - - +
85A GLU* 1.3 57.5 + - - +
87A VAL* 3.5 3.4 + - - +
88A LYS* 3.1 30.0 + - - +
96A LEU* 4.1 18.3 - - + +
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Residues in contact with GLU 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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41A PRO* 3.5 33.2 - - + +
81A LYS 3.2 7.3 + - - +
82A ALA* 3.6 10.1 - - - +
83A LEU 3.1 0.4 - - - -
84A ALA* 1.3 77.5 - - - +
86A ASP* 1.3 65.8 + - - +
87A VAL 3.0 1.7 + - - -
88A LYS* 2.6 53.3 + - - +
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Residues in contact with ASP 86 (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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82A ALA 2.9 15.2 + - - +
83A LEU* 3.0 13.4 + - - +
85A GLU* 1.3 77.3 - - - +
87A VAL* 1.3 57.8 + - + +
89A ALA* 5.4 1.6 + - - +
143A VAL* 4.2 10.3 - - + +
147A ARG* 2.7 42.3 + - - +
206A ASP* 4.6 1.0 - - - +
256A ARG* 3.0 47.0 + - - -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.0 25.9 + - + +
84A ALA 4.0 3.8 - - - +
86A ASP* 1.3 87.5 - - - +
88A LYS* 1.3 57.9 + - - +
89A ALA 3.1 3.4 - - - +
90A TRP* 2.9 70.8 + - + +
91A ARG* 4.2 2.3 + - - +
94A LEU* 4.7 4.3 - - + +
96A LEU* 4.3 23.1 - - + -
147A ARG* 4.0 13.9 - - + -
150A LEU* 4.4 10.8 - - + -
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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