Contacts of the helix formed by residues 72 - 86 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A THR* 2.9 14.5 + - + -
71A PRO* 1.3 77.8 - - - +
73A VAL* 1.3 62.2 + - + +
74A ASP* 3.0 40.7 + - + +
75A LEU* 2.6 33.9 + - - +
76A ALA 3.0 7.9 + - - -
188A ASN* 3.3 27.7 + - - +
191A LEU* 3.8 6.8 - - - +
70D THR* 4.1 20.4 - - + -
75D LEU* 4.0 31.5 - - + +
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Residues in contact with VAL 73 (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 HIS* 1.3 80.7 - - + +
74A ASP* 1.3 78.1 + - - +
75A LEU 3.3 2.1 + - - -
76A ALA* 4.1 5.2 + - - +
77A PHE* 4.7 4.0 + - - +
151A TRP* 3.6 51.1 - - + +
187A ASP* 4.3 6.5 - - - +
188A ASN* 2.8 43.2 + - + +
191A LEU* 3.4 12.0 - - + +
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Residues in contact with ASP 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 HIS* 2.8 30.0 + - + -
73A VAL* 1.3 86.4 - - - +
75A LEU* 1.3 69.0 + - + +
78A ALA* 4.9 5.4 - - - +
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Residues in contact with LEU 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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70A THR* 3.5 30.5 - - + +
72A HIS* 2.6 12.5 + - - +
74A ASP* 1.3 88.2 - - + +
76A ALA* 1.3 67.2 + - - +
77A PHE 3.3 2.0 - - - -
78A ALA* 2.7 25.1 + - + +
79A SER* 2.7 11.2 + - - +
72D HIS* 4.0 26.7 - - + +
75D LEU* 3.4 32.8 - - + -
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Residues in contact with ALA 76 (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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69A TYR* 3.7 19.0 - - - +
70A THR 3.0 21.9 + - - +
72A HIS 3.0 19.4 + - - +
73A VAL 4.3 3.1 - - - +
75A LEU* 1.3 73.3 - - - +
77A PHE* 1.3 59.2 + - - +
79A SER* 2.8 20.0 + - - -
80A VAL* 3.1 14.7 + - - +
149A LEU 3.9 7.6 - - - +
150A PRO 4.3 2.0 - - - -
151A TRP* 4.1 7.4 - - + -
191A LEU* 4.1 7.6 - - + -
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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
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73A VAL 4.7 5.1 + - - +
75A LEU 2.8 5.1 + - - -
76A ALA* 1.3 73.9 - - - +
78A ALA* 1.3 65.4 + - - +
80A VAL* 2.9 18.3 + - + +
81A GLU* 3.1 16.5 + - + +
94A ARG* 6.0 3.6 - - - -
150A PRO* 3.1 30.6 + - + +
151A TRP* 3.9 15.7 - - + +
152A GLY* 4.8 0.2 - - - -
279A ASN 3.7 20.0 - - - -
280A TYR* 3.8 19.5 - + - -
281A ILE 4.6 3.1 - - - -
282A GLU* 3.4 36.1 - - + +
44B PHE* 3.7 28.7 - + - -
102B LEU* 3.6 24.5 - - + -
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Residues in contact with ALA 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 ASP 4.9 3.8 + - - +
75A LEU* 2.7 19.0 + - + +
77A PHE* 1.3 74.8 - - - +
79A SER* 1.3 66.3 + - - +
81A GLU* 2.8 4.0 + - - +
82A HIS* 2.7 25.8 + - - +
44B PHE* 3.8 30.0 - - + -
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Residues in contact with SER 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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68A HIS 3.6 3.7 + - - +
69A TYR* 3.0 14.9 - - - -
70A THR* 2.7 38.6 + - - -
75A LEU* 2.7 11.9 + - - +
76A ALA* 2.8 22.9 + - - -
78A ALA* 1.3 75.5 - - - +
80A VAL* 1.3 55.6 + - - -
82A HIS* 3.1 24.4 - - - +
83A ILE* 3.2 13.9 + - - +
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Residues in contact with VAL 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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69A TYR* 3.9 23.1 - - + -
76A ALA 3.5 12.8 - - - +
77A PHE* 2.9 12.7 + - + +
79A SER* 1.3 73.1 - - - +
81A GLU* 1.3 67.8 + - + +
82A HIS 3.1 1.8 - - - -
83A ILE* 3.2 10.3 + - + +
84A MET* 3.0 20.4 + - + +
94A ARG* 3.5 46.4 - - + +
150A PRO* 4.2 12.3 - - + -
502A HEM 4.0 18.8 - - + +
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Residues in contact with GLU 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 PHE* 3.1 17.0 + - + +
78A ALA 2.8 9.4 + - - +
80A VAL* 1.3 72.8 - - + +
82A HIS* 1.3 68.4 + - - +
84A MET* 2.9 21.3 + - - +
85A ARG* 2.7 73.0 + - - +
94A ARG* 4.9 1.7 + - - -
280A TYR* 4.6 6.4 - - - -
44B PHE* 4.4 21.1 - - + -
102B LEU* 3.4 40.0 - - + +
105B LYS* 4.5 6.8 + - - -
219B ALA 4.5 2.8 - - - +
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Residues in contact with HIS 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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68A HIS* 4.5 13.9 + - + -
78A ALA 2.7 11.1 + - - +
79A SER* 3.1 17.5 - - - +
81A GLU* 1.3 77.3 - - - +
83A ILE* 1.3 66.8 + - + +
85A ARG* 5.0 1.8 - - - +
86A ASN* 2.6 70.4 + - + +
87A VAL* 4.0 16.9 - - + +
41C SER* 4.5 4.3 + - - -
43C ASP* 3.6 27.8 - - - -
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Residues in contact with ILE 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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65A LEU* 3.7 41.7 - - + +
68A HIS* 3.6 38.1 - - + +
69A TYR* 4.1 7.2 - - + +
79A SER 3.3 13.9 - - - +
80A VAL* 3.2 16.6 + - + +
82A HIS* 1.3 78.2 - - + +
84A MET* 1.3 63.1 + - - +
87A VAL* 3.6 22.2 + - + +
90A GLY* 3.2 37.3 - - - +
93A LEU* 6.2 0.2 - - + -
94A ARG* 4.9 6.1 - - + -
502A HEM 5.2 2.5 - - + -
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Residues in contact with MET 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 VAL* 3.0 17.4 + - + +
81A GLU* 2.9 30.5 + - - +
83A ILE* 1.3 78.1 - - - +
85A ARG* 1.3 60.2 + - + +
86A ASN 3.9 0.2 + - - -
87A VAL 4.9 1.4 - - - +
91A PHE* 3.5 36.8 + - + +
94A ARG* 3.6 44.2 - - + +
95A TYR* 3.5 41.3 - - + +
280A TYR* 4.5 0.2 - - - +
105B LYS* 3.6 18.2 - - - +
220B GLU* 5.0 2.9 - - - +
221B PRO* 5.6 0.8 - - - +
222B LYS* 4.2 10.7 - - - +
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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 GLU* 2.7 49.4 + - - +
82A HIS* 4.1 1.6 - - - +
84A MET* 1.3 75.0 - - + +
86A ASN* 1.3 72.4 + - - +
44B PHE* 3.0 34.9 + - - +
45B VAL* 4.0 16.1 - - - +
46B PRO* 4.3 12.4 - - + +
49B SER* 5.5 1.4 + - - -
88B HIS* 6.1 0.4 - - - -
101B SER 3.7 15.0 + - - -
102B LEU* 4.6 1.4 - - - +
217B TRP* 6.4 0.2 - - - -
218B ALA 2.9 29.1 + - - -
219B ALA* 3.7 8.7 + - - +
221B PRO* 3.6 25.3 - - + +
222B LYS* 3.0 33.7 + - - +
42C ALA* 4.8 2.8 - - - +
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Residues in contact with ASN 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 HIS* 2.6 54.7 + - + +
84A MET 3.6 0.4 - - - -
85A ARG* 1.3 88.5 - - - +
87A VAL* 1.3 69.9 + - - +
88A ASN* 3.3 5.0 + - - +
46B PRO* 4.8 4.5 - - - +
48B ARG* 3.2 29.7 + - - +
88B HIS* 5.7 6.5 - - - -
222B LYS* 6.0 0.5 - - - -
41C SER* 4.2 1.0 - - - -
42C ALA* 3.7 26.9 + - - +
43C ASP* 4.0 15.3 - - - +
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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