Contacts of the helix formed by residues 72 - 86 (chain M) in PDB entry 2QJK
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 72 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70M THR* 2.9 15.3 + - + -
71M PRO* 1.3 77.4 - - - +
73M VAL* 1.3 60.9 + - + +
74M ASP* 2.8 42.8 + - + +
75M LEU 2.6 33.4 + - - -
76M ALA* 3.0 9.8 + - - -
188M ASN* 3.2 27.7 + - - +
191M LEU* 3.8 5.9 - - - +
70P THR* 4.1 19.7 - - + +
75P LEU* 3.8 33.0 - - + +
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Residues in contact with VAL 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72M HIS* 1.3 80.9 - - + +
74M ASP* 1.3 78.1 + - - +
75M LEU 3.3 1.2 + - - -
76M ALA* 4.1 5.7 + - - +
77M PHE* 4.7 3.6 + - - +
151M TRP* 3.4 53.5 - - + +
187M ASP* 4.4 6.1 - - - +
188M ASN* 2.9 43.3 + - + +
191M LEU* 3.4 12.0 - - + +
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Residues in contact with ASP 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72M HIS* 2.8 30.0 + - + -
73M VAL* 1.3 86.7 - - - +
75M LEU* 1.3 70.9 + - + +
78M ALA* 4.9 4.5 - - - +
75P LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70M THR* 3.5 32.8 - - + +
72M HIS* 2.6 12.6 + - - +
73M VAL 4.2 0.2 - - - -
74M ASP* 1.3 86.6 - - + +
76M ALA* 1.3 66.2 + - - +
77M PHE* 3.2 2.2 - - - -
78M ALA* 2.7 27.3 + - + +
79M SER* 2.8 10.5 + - - +
72P HIS* 3.8 27.1 - - + +
75P LEU* 3.7 27.1 - - + -
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Residues in contact with ALA 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M TYR* 3.8 18.7 - - - +
70M THR 3.0 22.5 + - - +
72M HIS 3.0 18.1 + - - +
73M VAL 4.2 2.9 - - - +
75M LEU* 1.3 74.4 - - - +
77M PHE* 1.3 59.4 + - - +
79M SER* 2.8 20.6 - - - -
80M VAL* 3.1 14.2 + - - +
149M LEU 3.9 8.1 - - - +
150M PRO 4.3 1.8 - - - -
151M TRP* 4.1 7.2 - - + -
191M LEU* 4.0 9.2 - - + -
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Residues in contact with PHE 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M VAL 4.7 4.1 + - - +
75M LEU 2.8 4.8 + - - +
76M ALA* 1.3 73.4 - - - +
78M ALA* 1.3 64.6 + - - +
80M VAL* 2.9 18.5 + - + +
81M GLU* 3.1 16.1 + - + +
94M ARG* 6.2 1.6 - - - -
150M PRO* 3.1 30.0 + - + +
151M TRP* 4.0 16.2 - - + +
152M GLY* 4.5 0.7 - - - -
279M ASN 3.7 20.9 - - - -
280M TYR* 3.8 20.0 - + - -
281M ILE 4.5 4.0 - - - -
282M GLU* 3.3 35.9 - - + +
44N PHE* 3.6 30.1 - + - -
102N LEU* 3.8 24.2 - - + -
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Residues in contact with ALA 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74M ASP 4.9 4.0 - - - +
75M LEU* 2.7 20.5 + - + +
77M PHE* 1.3 73.7 - - - +
79M SER* 1.3 54.8 + - - +
81M GLU* 2.8 4.9 + - - +
82M HIS* 2.7 36.7 + - - +
44N PHE* 3.9 28.2 - - + -
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Residues in contact with SER 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68M HIS 3.5 3.9 + - - +
69M TYR* 3.1 16.3 - - - -
70M THR* 2.8 36.8 + - - -
75M LEU* 2.8 11.7 + - - +
76M ALA* 2.8 22.2 - - - -
78M ALA* 1.3 74.5 - - - +
80M VAL* 1.3 55.1 + - - -
82M HIS* 3.1 24.7 - - - +
83M ILE* 3.1 13.7 + - - +
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Residues in contact with VAL 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M TYR* 3.9 23.6 - - + -
76M ALA 3.1 13.2 + - - +
77M PHE* 2.9 12.9 + - + +
79M SER* 1.3 74.3 - - - +
81M GLU* 1.3 67.1 + - - +
82M HIS 3.0 1.3 - - - -
83M ILE* 3.2 13.2 + - + +
84M MET* 3.0 20.9 + - + +
94M ARG* 3.8 43.1 - - + +
150M PRO* 4.2 14.6 - - + -
502M HEM 4.1 17.0 - - + +
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Residues in contact with GLU 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M PHE* 3.1 15.5 + - + +
78M ALA 2.8 10.5 + - - +
80M VAL* 1.3 71.6 - - + +
82M HIS* 1.3 68.3 + - - +
84M MET* 2.8 21.9 + - - +
85M ARG* 2.7 73.9 + - - +
94M ARG* 5.3 0.9 + - - -
280M TYR* 4.6 11.1 - - - -
44N PHE* 4.3 21.3 - - + -
102N LEU* 3.8 38.8 - - + +
105N LYS* 4.9 2.1 + - - -
219N ALA 4.5 2.9 - - - +
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Residues in contact with HIS 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M HIS* 4.5 13.7 + - + -
78M ALA 2.7 11.3 + - - +
79M SER* 3.1 17.3 - - - +
81M GLU* 1.3 76.1 - - - +
83M ILE* 1.3 62.1 + - + +
85M ARG* 5.0 1.8 - - - +
86M ASN* 2.6 67.8 + - + +
87M VAL* 4.0 20.0 - - + +
41O SER* 4.4 4.7 + - - -
43O ASP* 3.5 33.8 + - - -
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Residues in contact with ILE 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65M LEU* 3.6 42.0 - - + +
68M HIS* 3.7 36.8 - - + +
69M TYR* 4.2 7.6 - - + +
79M SER 3.1 14.5 + - - +
80M VAL* 3.2 18.8 + - + +
82M HIS* 1.3 77.6 - - + +
84M MET* 1.3 63.3 + - - +
87M VAL* 3.7 20.9 + - + +
90M GLY* 3.1 43.4 - - - +
93M LEU* 6.2 0.2 - - + -
94M ARG* 4.8 5.6 - - + -
502M HEM 5.3 2.2 - - + -
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Residues in contact with MET 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M VAL* 3.0 19.4 + - + +
81M GLU* 2.8 30.3 + - - +
83M ILE* 1.3 80.7 - - - +
85M ARG* 1.3 60.8 + - + +
87M VAL 4.8 1.9 - - - +
91M PHE* 3.5 36.6 + - + +
94M ARG* 3.5 44.6 - - + +
95M TYR* 3.5 44.9 - - + +
280M TYR* 5.3 0.2 - - + -
105N LYS* 3.9 12.8 - - - +
220N GLU* 5.0 3.4 - - - +
221N PRO* 5.8 1.1 - - - -
222N LYS* 4.2 10.4 - - - +
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Residues in contact with ARG 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M GLU* 2.7 49.4 + - - +
82M HIS* 4.1 1.1 - - - +
84M MET* 1.3 76.2 - - + +
86M ASN* 1.3 71.9 + - - +
87M VAL 5.1 0.2 - - - -
44N PHE* 2.9 36.0 + - - +
45N VAL* 3.9 18.2 - - - +
46N PRO* 4.3 13.0 - - + +
49N SER* 5.5 1.4 + - - -
52N GLU* 4.8 3.8 - - - +
88N HIS* 6.0 0.2 - - - -
101N SER 3.8 8.5 + - - -
102N LEU* 4.4 3.2 - - - +
218N ALA 2.8 29.3 + - - -
219N ALA* 3.8 12.5 + - - +
221N PRO* 3.7 25.6 - - + +
222N LYS* 3.8 27.6 + - - -
42O ALA* 4.6 3.8 - - - +
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Residues in contact with ASN 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M HIS* 2.6 54.2 + - + +
84M MET 3.6 0.6 - - - -
85M ARG* 1.3 88.4 - - - +
87M VAL* 1.3 69.2 + - - +
88M ASN* 3.3 4.9 + - - +
46N PRO* 4.7 4.6 - - - +
48N ARG* 3.1 32.2 + - - +
52N GLU* 5.2 0.9 - - - +
88N HIS* 5.6 7.7 - - - -
222N LYS* 6.1 0.3 - - - -
41O SER* 4.1 0.8 - - - -
42O ALA* 3.5 27.4 + - - +
43O ASP* 4.0 13.6 - - - +
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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