Contacts of the helix formed by residues 72 - 86 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A THR* 4.2 20.6 - - + -
75A LEU* 4.0 31.8 - - + +
70D THR* 2.8 13.6 + - + -
71D PRO* 1.3 78.5 - - - +
73D VAL* 1.3 60.6 + - + +
74D ASP* 2.8 41.5 + - + +
75D LEU* 2.6 33.4 + - - -
76D ALA 3.0 7.7 + - - -
188D ASN* 3.3 28.3 + - - -
191D LEU* 3.7 7.9 - - - +
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D HIS* 1.3 79.3 - - + +
74D ASP* 1.3 76.5 + - - +
75D LEU 3.2 1.4 + - - -
76D ALA* 4.1 6.1 + - - +
77D PHE* 4.7 3.8 + - - +
151D TRP* 3.4 53.0 - - + +
187D ASP* 4.2 6.7 - - - +
188D ASN* 2.9 47.0 + - + +
191D LEU* 3.4 10.9 - - + +
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Residues in contact with ASP 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D HIS* 2.8 29.5 + - + +
73D VAL* 1.3 83.1 - - - +
75D LEU* 1.3 69.6 + - + +
78D ALA* 4.9 5.0 + - - +
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Residues in contact with LEU 75 (chain D).
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* 4.0 25.8 - - + +
75A LEU* 3.4 33.4 - - + -
70D THR* 3.5 30.3 - - + +
72D HIS* 2.6 13.2 + - - +
74D ASP* 1.3 88.0 - - + +
76D ALA* 1.3 66.6 + - - +
77D PHE 3.3 2.0 - - - -
78D ALA* 2.7 25.8 + - + +
79D SER* 2.8 11.9 + - - +
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TYR* 3.7 18.7 - - - +
70D THR 3.1 22.8 + - - +
72D HIS 3.0 20.1 + - - +
73D VAL 4.3 3.1 - - - +
75D LEU* 1.3 74.8 - - - +
77D PHE* 1.3 58.8 + - - +
79D SER* 2.8 19.9 + - - -
80D VAL* 3.1 15.1 + - - +
149D LEU 3.9 7.6 - - - +
150D PRO 4.3 2.0 - - - -
151D TRP* 4.1 11.4 - - + -
191D LEU* 4.1 3.4 - - + -
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Residues in contact with PHE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL 4.7 4.9 + - - +
75D LEU 2.8 4.9 + - - -
76D ALA* 1.3 73.3 - - - +
78D ALA* 1.3 64.5 + - - +
80D VAL* 2.9 18.6 + - + +
81D GLU* 3.0 17.0 + - + +
94D ARG* 6.0 2.7 - - - -
150D PRO* 3.2 28.0 + - + +
151D TRP* 4.0 15.2 - - + +
152D GLY* 4.7 0.2 - - - -
279D ASN 3.7 20.4 - - - -
280D TYR* 3.9 28.9 - + - -
281D ILE 4.6 2.9 - - - -
282D GLU* 3.2 37.7 - - + +
44E PHE* 3.6 29.2 - + - -
102E LEU* 4.0 15.3 - - + -
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ASP 4.9 4.3 - - - +
75D LEU* 2.7 19.2 + - + +
77D PHE* 1.3 74.8 - - - +
79D SER* 1.3 66.9 + - - +
81D GLU* 2.8 3.5 + - - +
82D HIS* 2.7 26.3 + - - +
44E PHE* 3.8 29.3 - - + -
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Residues in contact with SER 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D HIS 3.5 3.1 + - - +
69D TYR* 3.0 15.1 - - - -
70D THR* 2.7 38.2 + - - -
75D LEU* 2.8 11.0 + - - +
76D ALA* 2.8 24.1 + - - -
78D ALA* 1.3 75.9 - - - +
80D VAL* 1.3 54.3 + - - -
82D HIS* 3.1 23.8 - - - +
83D ILE* 3.1 16.0 + - - +
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TYR* 3.9 22.7 - - + -
76D ALA 3.4 13.7 - - - +
77D PHE* 2.9 12.2 + - + +
79D SER* 1.3 73.0 - - - +
81D GLU* 1.3 67.3 + - + +
82D HIS 3.1 1.6 - - - -
83D ILE* 3.1 10.7 + - + +
84D MET* 3.0 21.2 + - + +
94D ARG* 3.3 48.2 - - + +
150D PRO* 4.2 13.7 - - + +
502D HEM 4.0 14.8 - - + -
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D PHE* 3.0 16.6 + - + +
78D ALA 2.8 7.1 + - - +
80D VAL* 1.3 74.8 - - + +
82D HIS* 1.3 67.4 + - - +
84D MET* 2.9 22.5 + - - +
85D ARG* 2.7 70.1 + - - +
94D ARG* 5.3 1.0 + - - -
280D TYR* 4.6 10.0 - - - -
44E PHE* 4.3 22.4 - - + -
102E LEU* 3.6 40.4 - - + +
105E LYS* 5.0 1.4 + - - -
219E ALA 4.5 2.6 - - - +
221E PRO* 5.8 0.2 - - - +
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Residues in contact with HIS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D HIS* 4.6 13.5 + - + -
78D ALA 2.7 12.3 + - - +
79D SER* 3.1 17.3 - - - +
81D GLU* 1.3 76.5 - - - +
83D ILE* 1.3 65.0 + - + +
85D ARG* 5.0 2.0 - - - +
86D ASN* 2.6 70.3 + - + +
87D VAL* 4.0 17.7 - - + +
41F SER* 4.4 5.1 + - - -
43F ASP* 3.6 26.2 - - - -
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LEU* 3.7 41.3 - - + +
68D HIS* 3.6 36.3 - - + +
69D TYR* 4.1 7.9 - - + +
79D SER 3.1 15.2 + - - +
80D VAL* 3.1 17.9 + - + +
82D HIS* 1.3 78.2 - - + +
84D MET* 1.3 63.1 + - - +
87D VAL* 3.6 21.9 + - + +
90D GLY* 3.1 36.6 - - - +
93D LEU* 6.2 0.2 - - + -
94D ARG* 4.9 5.4 - - + -
502D HEM 5.3 2.7 - - + -
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Residues in contact with MET 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D VAL* 3.0 17.4 + - + +
81D GLU* 2.9 31.3 + - - +
83D ILE* 1.3 79.1 - - - +
85D ARG* 1.3 59.8 + - + +
87D VAL 4.9 1.4 - - - +
91D PHE* 3.5 36.5 + - + +
94D ARG* 3.6 45.8 - - + +
95D TYR* 3.5 44.0 - - + +
105E LYS* 3.8 12.8 - - - +
220E GLU* 4.9 3.4 - - - +
221E PRO* 5.8 1.1 - - - -
222E LYS* 4.0 10.7 - - - +
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Residues in contact with ARG 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLU* 2.7 49.8 + - - +
82D HIS* 4.1 1.8 - - - +
84D MET* 1.3 77.4 - - + +
86D ASN* 1.3 72.0 + - - +
44E PHE* 2.9 35.4 + - - +
45E VAL* 3.9 16.5 - - - +
46E PRO* 4.2 13.9 - - + +
49E SER* 5.4 2.0 + - - -
52E GLU* 4.6 2.4 - - - +
88E HIS* 6.0 0.2 - - - -
101E SER 3.8 12.7 + - - -
102E LEU* 4.5 1.8 - - - +
217E TRP* 6.3 0.4 - - - -
218E ALA 2.9 29.5 + - - -
219E ALA* 3.8 8.3 + - - +
221E PRO* 3.6 25.1 - - + +
222E LYS* 3.1 32.3 + - - +
42F ALA* 4.6 2.3 - - - +
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Residues in contact with ASN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D HIS* 2.6 54.0 + - + +
84D MET 3.6 0.4 - - - -
85D ARG* 1.3 91.5 - - - +
87D VAL* 1.3 70.1 + - - +
88D ASN* 3.3 4.9 + - - +
46E PRO* 4.8 3.8 - - - +
48E ARG* 3.0 31.7 + - - +
52E GLU* 5.5 0.2 - - - +
88E HIS* 5.6 6.3 - - - -
222E LYS* 5.8 1.4 - - - -
41F SER* 3.9 3.3 - - - -
42F ALA* 3.5 23.3 + - - +
43F ASP* 3.8 16.6 - - - +
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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