Contacts of the helix formed by residues 72 - 86 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70M THR* 4.1 20.2 - - + -
75M LEU* 3.8 30.9 - - + +
70P THR* 2.9 14.2 + - + -
71P PRO* 1.3 77.6 - - - +
73P VAL* 1.3 59.3 + - + +
74P ASP* 2.7 41.9 + - + +
75P LEU* 2.6 34.3 + - + +
76P ALA* 3.0 9.8 + - - -
188P ASN* 3.2 29.7 + - - +
191P LEU* 3.8 6.3 - - - +
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Residues in contact with VAL 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72P HIS* 1.3 79.6 - - + +
74P ASP* 1.3 77.1 + - - +
75P LEU 3.3 1.9 + - - -
76P ALA* 4.1 6.2 + - - +
77P PHE* 4.7 3.6 + - - +
151P TRP* 3.5 51.6 - - + +
187P ASP* 4.6 5.6 - - - +
188P ASN* 2.9 40.1 + - + +
191P LEU* 3.4 12.2 - - + +
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Residues in contact with ASP 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M LEU* 6.1 0.2 - - + -
72P HIS* 2.7 31.0 + - + +
73P VAL* 1.3 86.2 - - - +
75P LEU* 1.3 69.5 + - + +
78P ALA* 4.9 4.7 - - - +
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Residues in contact with LEU 75 (chain P).
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* 3.8 28.0 - - + +
74M ASP* 6.1 0.2 - - + -
75M LEU* 3.7 27.8 - - + -
70P THR* 3.4 33.7 - - + -
72P HIS* 2.6 11.4 + - - +
73P VAL 4.2 0.2 - - - -
74P ASP* 1.3 87.7 - - + +
76P ALA* 1.3 67.2 + - - +
77P PHE 2.7 2.0 + - - -
78P ALA* 2.7 25.9 + - + +
79P SER* 2.9 10.4 + - - +
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Residues in contact with ALA 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P TYR* 3.8 19.5 - - - +
70P THR 3.1 21.4 + - - +
72P HIS 3.0 19.4 + - - +
73P VAL 4.2 2.9 - - - +
75P LEU* 1.3 73.4 - - - +
77P PHE* 1.3 59.6 + - - +
79P SER* 2.8 20.8 - - - -
80P VAL* 3.1 14.0 + - - +
149P LEU 3.9 7.9 - - - +
150P PRO 4.3 2.5 - - - -
151P TRP* 4.1 7.2 - - + -
191P LEU* 4.0 8.3 - - + -
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Residues in contact with PHE 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P VAL 4.7 4.5 + - - +
75P LEU 2.7 4.9 + - - -
76P ALA* 1.3 73.7 - - - +
78P ALA* 1.3 64.3 + - - +
80P VAL* 2.9 18.9 + - + +
81P GLU* 3.1 15.2 + - + +
94P ARG* 6.2 1.1 - - - -
150P PRO* 3.2 29.8 + - + +
151P TRP* 4.0 16.5 - - + +
152P GLY* 4.5 0.2 - - - -
279P ASN 3.6 21.1 - - - -
280P TYR* 3.8 28.5 - + - -
281P ILE 4.5 4.5 - - - -
282P GLU* 3.3 35.7 - - + +
44Q PHE* 3.4 29.8 - + - -
102Q LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74P ASP 4.9 3.8 - - - +
75P LEU* 2.7 21.0 + - + +
77P PHE* 1.3 74.6 - - - +
79P SER* 1.3 54.5 + - - +
81P GLU* 2.8 4.0 + - - +
82P HIS* 2.7 36.3 + - - +
44Q PHE* 3.8 29.1 - - + -
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Residues in contact with SER 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P HIS 3.5 4.4 + - - +
69P TYR* 3.1 16.3 - - - -
70P THR* 2.8 37.9 + - - -
75P LEU* 2.9 10.4 + - - +
76P ALA* 2.8 22.2 - - - -
78P ALA* 1.3 75.6 - - - +
80P VAL* 1.3 55.3 + - - +
82P HIS* 3.1 24.9 - - - +
83P ILE* 3.1 13.9 + - - +
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Residues in contact with VAL 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P TYR* 3.9 13.7 - - + -
76P ALA 3.1 12.8 + - - +
77P PHE* 2.9 11.8 + - + +
79P SER* 1.3 74.4 - - - +
81P GLU* 1.3 68.6 + - - +
82P HIS 3.0 1.3 - - - -
83P ILE* 3.1 11.5 + - + +
84P MET* 3.0 20.1 + - + +
94P ARG* 3.6 44.6 - - + +
150P PRO* 4.1 13.5 - - + -
502P HEM 3.9 28.0 - - + +
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Residues in contact with GLU 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77P PHE* 3.1 16.8 + - + +
78P ALA 2.8 9.5 + - - +
80P VAL* 1.3 71.9 - - + +
82P HIS* 1.3 68.0 + - - +
84P MET* 2.9 22.7 + - - +
85P ARG* 2.7 71.7 + - - +
94P ARG* 5.1 0.9 + - - -
280P TYR* 4.6 9.4 - - - -
44Q PHE* 4.2 23.8 - - + +
102Q LEU* 3.6 40.5 - - + +
105Q LYS* 4.8 1.4 + - - -
219Q ALA 4.5 2.8 - - - +
221Q PRO* 5.7 0.2 - - - +
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Residues in contact with HIS 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P HIS* 4.6 13.3 + - + -
78P ALA 2.7 12.4 + - - +
79P SER* 3.1 17.3 - - - +
81P GLU* 1.3 76.7 - - - +
83P ILE* 1.3 61.9 + - + +
85P ARG* 5.0 2.5 - - - +
86P ASN* 2.6 66.4 + - + +
87P VAL* 4.0 20.9 - - + +
41R SER* 4.4 4.9 + - - -
43R ASP* 3.5 32.5 - - - -
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Residues in contact with ILE 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P LEU* 3.6 42.4 - - + +
68P HIS* 3.6 36.3 - - + +
69P TYR* 4.2 7.6 - - + +
79P SER 3.2 15.0 - - - +
80P VAL* 3.1 18.6 + - + +
82P HIS* 1.3 77.7 - - + +
84P MET* 1.3 64.1 + - - +
87P VAL* 3.7 20.7 + - + +
90P GLY* 3.0 42.8 - - - +
93P LEU* 5.6 0.4 - - + -
94P ARG* 4.8 5.8 - - + -
502P HEM 5.4 2.2 - - + -
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Residues in contact with MET 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P VAL* 3.0 17.4 + - + +
81P GLU* 2.9 29.0 + - - +
83P ILE* 1.3 79.7 - - - +
85P ARG* 1.3 60.6 + - + +
87P VAL 4.8 1.7 - - - +
91P PHE* 3.5 36.4 + - + +
94P ARG* 3.5 46.9 - - + +
95P TYR* 3.5 40.6 - - + +
105Q LYS* 3.6 17.7 - - - +
220Q GLU* 5.0 3.6 - - - +
221Q PRO* 5.9 1.1 - - - -
222Q LYS* 4.1 9.5 - - - +
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Residues in contact with ARG 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P GLU* 2.7 50.2 + - - +
82P HIS* 4.1 1.6 - - - +
84P MET* 1.3 76.2 - - + +
86P ASN* 1.3 73.1 + - - +
44Q PHE* 2.9 34.1 + - - +
45Q VAL* 3.9 20.0 - - - +
46Q PRO* 4.2 14.4 - - + +
49Q SER* 5.4 1.6 + - - -
52Q GLU* 4.9 1.0 - - - +
101Q SER 3.9 6.3 + - - -
102Q LEU* 4.6 1.4 - - - +
217Q TRP* 6.3 0.4 - - - -
218Q ALA 2.8 30.3 + - - -
219Q ALA* 3.8 11.9 + - - +
221Q PRO* 3.6 25.2 - - + +
222Q LYS* 2.6 35.9 + - - +
42R ALA* 4.6 1.7 - - - +
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Residues in contact with ASN 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P HIS* 2.6 54.8 + - + +
84P MET 3.6 0.2 - - - -
85P ARG* 1.3 88.6 - - - +
87P VAL* 1.3 70.4 + - - +
88P ASN* 3.3 4.3 + - - +
46Q PRO* 4.7 4.3 - - - +
48Q ARG* 3.1 32.2 + - - +
52Q GLU* 5.4 0.3 - - - +
88Q HIS* 5.6 6.9 - - - -
222Q LYS* 5.4 1.6 + - - -
41R SER* 3.9 2.7 - - - -
42R ALA* 3.4 25.9 + - - +
43R ASP* 3.8 15.9 - - - +
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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