Contacts of the helix formed by residues 73 - 87 (chain A) in PDB entry 4XJO
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 HIS 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A HIS* 3.6 26.5 - - + +
70A GLY 4.4 2.0 - - - +
71A HIS 3.2 3.3 + - - -
72A GLY* 1.3 76.1 - - - +
74A PRO* 1.4 81.3 - - + +
75A ALA* 3.1 36.8 + - + +
76A LEU* 3.0 18.4 + - + -
77A ASP* 2.9 21.5 + - - -
289A TYR* 2.9 4.8 + - - +
335A LEU* 3.5 40.1 - - + +
413A ILE* 5.1 8.8 - - + +
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Residues in contact with PRO 74 (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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72A GLY 3.5 6.7 - - - +
73A HIS* 1.4 99.2 - - + +
75A ALA* 1.3 56.9 + - - +
77A ASP* 3.8 6.5 - - + +
78A GLN* 2.9 41.2 + - + +
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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
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73A HIS* 3.1 22.9 + - + +
74A PRO* 1.3 79.1 - - - +
76A LEU* 1.3 65.7 + - + +
78A GLN* 4.1 4.5 - - - +
79A ALA* 3.1 26.3 + - - +
331A ALA* 4.1 5.4 - - + +
335A LEU* 4.7 11.2 - - + -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 3.9 31.2 - - + -
70A GLY 5.2 0.4 - - - +
73A HIS* 3.0 14.4 + - + +
75A ALA* 1.3 77.7 - - + +
77A ASP* 1.3 64.9 + - - +
78A GLN 3.3 0.2 - - - -
79A ALA* 3.3 4.7 + - - +
80A LEU* 3.1 19.9 + - - +
286A THR 4.5 0.9 - - - +
287A GLY* 4.4 5.8 - - - +
289A TYR* 3.5 39.0 - - + +
328A VAL* 3.6 17.6 - - + +
331A ALA* 3.6 13.7 - - + +
332A SER* 3.5 38.4 - - - +
335A LEU* 4.1 9.6 - - + -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY* 3.5 23.0 - - - +
73A HIS 2.9 15.6 + - - +
74A PRO* 3.8 7.9 - - + +
76A LEU* 1.3 76.5 - - - +
78A GLN* 1.3 61.3 + - + +
80A LEU* 3.3 5.5 + - - +
81A THR* 3.1 25.6 + - - -
289A TYR* 2.7 33.8 + - - -
84B LEU* 3.6 35.2 - - + +
85B ARG* 5.7 1.0 - - - -
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Residues in contact with GLN 78 (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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74A PRO* 2.9 30.5 + - + +
75A ALA* 4.1 5.4 - - - +
77A ASP* 1.3 75.7 - - + +
79A ALA* 1.3 61.0 + - - +
81A THR* 3.3 11.7 + - - -
82A THR* 2.8 39.6 + - - +
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Residues in contact with ALA 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 3.1 11.8 + - - +
76A LEU* 3.3 6.2 + - - +
78A GLN* 1.3 75.7 - - - +
80A LEU* 1.3 61.9 - - - +
82A THR* 3.6 4.8 + - - -
83A GLN* 3.1 23.7 + - - +
327A ALA* 3.9 19.0 - - + +
328A VAL* 4.3 3.1 - - - -
331A ALA* 3.4 32.5 - - + -
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Residues in contact with LEU 80 (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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76A LEU 3.1 11.7 + - - +
77A ASP* 3.5 9.2 - - - +
78A GLN 3.2 0.2 - - - -
79A ALA* 1.3 77.0 - - - +
81A THR* 1.3 58.1 + - + +
83A GLN* 3.3 4.1 + - - +
84A LEU* 2.9 29.5 + - + +
289A TYR* 4.4 6.7 - - + -
290A LEU* 4.2 14.1 - - + -
324A LEU* 3.5 50.9 - - + +
328A VAL* 4.9 7.8 - - + +
80B LEU* 4.7 19.1 - - + -
84B LEU* 3.8 29.2 - - + -
324B LEU* 4.1 18.2 - - + -
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Residues in contact with THR 81 (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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77A ASP 3.1 9.8 + - - +
78A GLN* 3.3 19.9 + - - -
80A LEU* 1.3 73.1 - - + +
82A THR* 1.3 65.0 + - - +
84A LEU* 3.6 9.7 - - + +
85A ARG* 3.2 22.5 + - - +
81B THR* 3.9 25.6 - - + -
84B LEU* 3.7 26.5 - - + -
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Residues in contact with THR 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 GLN* 2.8 27.7 + - - +
79A ALA* 3.9 5.8 - - - -
81A THR* 1.3 76.7 + - - +
83A GLN* 1.3 61.4 + - - +
85A ARG* 3.3 21.6 + - - +
86A VAL* 3.7 11.5 + - + +
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Residues in contact with GLN 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 ALA 3.1 17.8 + - - +
80A LEU* 3.7 3.8 - - - +
82A THR* 1.3 74.7 - - - +
84A LEU* 1.3 61.6 + - - +
86A VAL* 3.0 22.6 + - - +
87A MET* 2.9 63.9 + - - +
99A PRO* 3.4 25.9 - - - +
323A PRO* 3.7 26.5 - - - +
324A LEU* 3.9 11.0 - - + -
327A ALA* 3.6 12.9 - - + +
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Residues in contact with LEU 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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80A LEU* 2.9 18.0 + - + +
81A THR* 3.6 11.4 - - + +
82A THR 3.3 0.2 - - - -
83A GLN* 1.3 77.2 - - - +
85A ARG* 1.3 61.4 + - - +
86A VAL 3.4 1.0 + - - -
87A MET 4.2 5.0 + - - -
88A ASN* 4.5 6.9 + - + +
324A LEU* 3.7 15.1 - - + +
42B HIS* 5.6 0.5 - - - -
72B GLY* 5.3 4.0 - - - -
77B ASP* 3.7 35.5 - - + +
80B LEU* 3.7 26.0 - - + -
81B THR* 3.7 30.3 - - + -
289B TYR* 3.7 31.9 - - + -
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Residues in contact with ARG 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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81A THR 3.2 12.6 + - - +
82A THR* 3.4 15.9 - - - +
83A GLN 3.1 0.6 - - - -
84A LEU* 1.3 78.1 - - - +
86A VAL* 1.3 64.0 + - + +
42B HIS* 3.2 20.8 - - - -
77B ASP* 5.5 1.3 - - - -
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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 THR* 3.9 13.0 - - + +
83A GLN* 3.0 30.9 + - - +
84A LEU 4.5 0.4 - - - -
85A ARG* 1.3 87.6 - - + +
87A MET* 1.3 64.2 + - + +
39B VAL 4.4 13.7 - - - +
40B ALA* 3.4 5.1 - - + -
41B ALA 3.0 22.5 + - - +
42B HIS* 3.3 16.5 + - - +
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Residues in contact with MET 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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83A GLN* 2.9 47.2 + - - +
84A LEU 4.2 1.2 + - - -
86A VAL* 1.3 77.8 - - + +
88A ASN* 1.3 65.7 + - - +
89A HIS* 4.2 5.4 - - - +
90A VAL* 3.6 26.7 - - + -
97A HIS* 3.6 35.4 - - + -
99A PRO* 5.1 2.9 - - + -
323A PRO* 3.6 14.9 - - + +
38B ALA* 3.7 14.6 - - - +
39B VAL 4.7 3.6 - - - +
40B ALA* 3.8 24.2 - - - +
41B ALA* 3.6 21.5 - - + +
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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
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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