Contacts of the helix formed by residues 46 - 67 (chain G) 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 ILE 46 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ASN 4.7 1.6 - - - +
43G TRP* 3.3 48.5 - - + +
45G TRP* 1.3 79.6 - - - +
47G TRP* 1.3 95.0 + - + +
48G GLY 3.2 0.2 - - - -
49G VAL* 3.0 18.5 + - + +
50G VAL* 3.1 20.8 + - + +
251G LYS* 4.9 4.7 - - - +
252G ASP* 4.6 7.6 - - - +
255G ALA* 3.7 30.5 - - + -
259G VAL* 4.7 6.3 - - + -
505G ANJ 4.5 13.7 - - - -
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Residues in contact with TRP 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G TRP 3.8 5.6 + - - -
44G MET* 3.5 50.3 - - + +
45G TRP 3.3 0.4 - - - -
46G ILE* 1.3 93.7 - - + +
48G GLY* 1.3 63.7 + - - +
50G VAL* 3.1 30.4 + - + +
51G LEU* 2.8 27.3 + - - +
103G LEU* 6.0 2.0 - - + -
106G ILE* 5.7 2.0 - - + -
107G ALA* 4.3 14.8 - - - +
110G LEU* 3.4 41.6 - - + +
111G HIS* 4.2 24.2 - - + +
259G VAL* 5.1 7.9 - - + -
504G LOP 3.2 47.8 - - + -
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Residues in contact with GLY 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ILE 3.1 0.6 + - - -
47G TRP* 1.3 71.8 - - - +
49G VAL* 1.3 58.2 + - - +
51G LEU* 3.1 8.0 + - - +
52G ALA* 3.0 22.7 + - - +
111G HIS* 3.8 5.8 + - - -
501G HEM 2.8 62.9 + - - +
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Residues in contact with VAL 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G TRP 4.9 0.4 + - - -
46G ILE* 3.0 10.4 + - + +
48G GLY* 1.3 71.0 - - - +
50G VAL* 1.3 71.4 + - + +
51G LEU 2.9 1.8 - - - -
52G ALA* 2.7 17.9 + - + +
53G PHE* 2.9 12.6 + - + +
252G ASP* 3.3 41.5 - - + +
256G LEU* 3.3 31.4 - - + -
501G HEM 4.3 0.8 - - - +
505G ANJ 3.3 39.7 + - + +
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Residues in contact with VAL 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ILE* 3.1 27.5 + - + +
47G TRP* 3.1 37.2 + - + +
49G VAL* 1.3 75.2 - - + +
51G LEU* 1.3 60.7 + - - +
53G PHE* 3.6 4.4 - - + +
54G CYS* 3.2 23.0 + - - -
103G LEU* 4.6 14.4 - - + -
107G ALA* 4.5 9.2 - - + -
255G ALA* 5.9 0.2 - - + -
256G LEU* 4.0 17.5 - - + +
259G VAL* 3.9 32.8 - - + -
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G TRP 2.8 14.2 + - - +
48G GLY* 3.1 7.2 - - - +
49G VAL 2.9 0.2 - - - -
50G VAL* 1.3 74.8 - - - +
52G ALA* 1.3 67.2 + - - +
54G CYS* 2.9 16.8 + - - +
55G LEU* 2.9 11.3 + - - +
104G PHE* 3.5 45.0 - - + +
107G ALA* 3.5 13.5 - - + -
108G VAL* 3.7 13.5 - - + +
111G HIS* 3.4 43.5 - - + +
501G HEM 3.5 31.4 - - + +
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Residues in contact with ALA 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G GLY 3.0 9.8 + - - +
49G VAL* 2.7 20.0 + - + +
51G LEU* 1.3 69.7 - - - +
53G PHE* 1.3 64.9 + - - +
55G LEU* 2.8 19.0 + - - +
56G VAL* 3.1 17.7 + - + +
501G HEM 3.6 10.4 - - - +
505G ANJ 3.1 39.4 - - + +
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Residues in contact with PHE 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G VAL* 2.9 8.7 + - + +
50G VAL* 3.6 12.1 - - + +
52G ALA* 1.3 76.4 - - - +
54G CYS* 1.3 57.6 + - - +
56G VAL* 3.1 10.2 + - + +
57G LEU* 2.7 68.1 + - + +
103G LEU* 4.9 7.6 - - + -
256G LEU* 4.1 32.1 - - + -
260G LEU* 3.3 45.3 - - + -
263G PHE* 5.2 0.2 - + - -
264G PHE* 5.6 4.3 - + - -
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Residues in contact with CYS 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G VAL* 3.2 19.0 + - - -
51G LEU* 2.9 10.2 + - - +
53G PHE* 1.3 83.0 - - - +
55G LEU* 1.3 63.6 + - - +
57G LEU* 3.5 5.6 - - - +
58G GLN* 2.8 31.1 + - + +
100G GLY* 4.2 3.8 - - - +
103G LEU* 3.4 41.1 - - - -
104G PHE* 3.6 39.3 - - + -
107G ALA* 5.2 0.4 - - - -
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Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU 2.9 9.0 + - - +
52G ALA* 2.8 19.9 + - - +
54G CYS* 1.3 72.3 - - - +
56G VAL* 1.3 65.3 + - + +
58G GLN* 3.6 1.3 - - - +
59G ILE* 2.9 44.7 + - + +
104G PHE* 4.3 20.8 - - + -
202G PRO* 4.5 5.4 - - + +
205G ILE* 4.1 13.9 - - + -
206G ALA* 3.7 34.1 - - + +
209G VAL* 3.9 18.2 - - + -
501G HEM 5.1 3.8 - - + -
502G HEM 4.5 11.4 - - + -
505G ANJ 4.3 14.4 - - + -
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Residues in contact with VAL 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ALA* 3.1 14.2 + - + +
53G PHE* 3.6 8.1 - - + +
55G LEU* 1.3 75.3 - - + +
57G LEU* 1.3 69.3 + - - +
59G ILE* 2.8 18.1 + - + +
60G VAL* 2.9 31.6 + - + +
505G ANJ 5.1 12.3 - - + -
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Residues in contact with LEU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G PHE* 2.7 47.2 + - + +
54G CYS* 3.5 7.2 - - - +
56G VAL* 1.3 75.0 - - - +
58G GLN* 1.3 59.6 + - - +
60G VAL* 3.3 7.6 + - + +
61G THR* 2.6 54.3 + - + +
96G LEU* 4.4 19.7 - - + +
100G GLY* 4.5 8.5 - - - -
103G LEU* 5.3 2.7 - - + -
263G PHE* 3.8 32.8 - - + -
264G PHE* 6.6 0.2 - - + -
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Residues in contact with GLN 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G CYS* 2.8 26.2 + - - +
55G LEU* 3.6 2.9 - - - +
57G LEU* 1.3 77.2 - - - +
59G ILE* 1.3 57.5 + - - +
61G THR* 3.5 3.1 - - - -
62G GLY* 2.8 28.1 + - - -
96G LEU 3.9 0.5 - - - +
97G HIS* 2.8 66.7 + - - +
100G GLY* 3.0 21.2 - - - +
101G ALA 3.9 6.2 - - - +
104G PHE* 4.3 7.2 - - + -
502G HEM 3.1 50.5 - - + +
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Residues in contact with ILE 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU* 2.9 44.7 + - + +
56G VAL* 2.8 17.1 + - + +
58G GLN* 1.3 73.6 - - + +
60G VAL* 1.3 61.0 + - + +
62G GLY* 3.6 0.2 - - - -
63G ILE* 2.9 51.9 + - + +
202G PRO* 4.3 26.9 - - + +
203G PHE* 4.6 18.4 - - + -
206G ALA* 4.9 6.7 - - + -
502G HEM 4.0 10.4 - - + +
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Residues in contact with VAL 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G VAL* 2.9 34.6 + - + +
57G LEU* 3.5 12.3 - - + +
59G ILE* 1.3 70.1 - - + +
61G THR* 1.3 90.3 - - + +
62G GLY 2.9 2.4 + - - -
63G ILE* 3.1 8.8 + - - +
64G VAL* 3.0 26.2 + - + +
34I LEU* 4.1 28.0 - - + -
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Residues in contact with THR 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G LEU* 2.6 42.7 + - + +
58G GLN* 3.3 0.5 + - - -
60G VAL* 1.3 88.0 - - + +
62G GLY* 1.3 58.2 + - - +
64G VAL* 3.4 8.9 - - - +
65G LEU* 3.0 34.7 + - - +
93G LEU* 4.1 26.6 - - + +
96G LEU* 4.4 14.1 - - + -
97G HIS* 3.3 27.7 + - - +
34I LEU* 5.2 1.6 - - + -
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Residues in contact with GLY 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G GLN 2.8 20.5 + - - -
59G ILE 3.6 0.2 - - - -
60G VAL 2.9 0.2 - - - -
61G THR* 1.3 75.3 + - - +
63G ILE* 1.3 55.0 + - - +
65G LEU* 2.9 6.7 + - - +
66G ALA 2.8 31.9 + - - -
97G HIS* 3.8 5.6 - - - -
502G HEM 3.1 32.4 - - - +
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ILE* 2.9 33.5 + - + +
60G VAL* 3.7 7.2 - - - +
62G GLY* 1.3 73.1 - - - +
64G VAL* 1.3 64.6 + - + +
66G ALA* 3.2 6.7 - - - +
67G MET* 3.1 17.2 - - + +
199G TYR* 3.6 14.6 - - + +
203G PHE* 4.9 2.2 - - + -
502G HEM 3.3 11.1 - - + +
196J SER* 2.8 33.3 + - - +
197J LEU* 4.8 0.9 - - + -
200J LEU* 3.2 44.2 - - + -
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Residues in contact with VAL 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G VAL* 3.0 15.9 + - + +
61G THR* 3.4 9.2 - - - +
63G ILE* 1.3 74.1 - - + +
65G LEU* 1.3 58.9 + - + +
67G MET* 2.7 39.7 + - - +
68G HIS* 3.4 7.7 - - + -
93G LEU* 3.4 31.2 - - + -
34I LEU* 3.8 26.5 - - + +
37I GLN* 3.7 29.2 - - + +
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Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G THR 3.0 16.0 + - - +
62G GLY* 2.9 6.8 + - - +
64G VAL* 1.3 79.3 - - + +
66G ALA* 1.3 57.9 + - - +
68G HIS* 2.8 25.4 + - + +
69G TYR* 3.0 12.0 + - - +
83G ILE* 3.6 39.8 - - + +
93G LEU* 4.1 18.8 - - + +
94G ARG* 4.2 18.4 - - + +
97G HIS* 3.6 37.7 - - + -
502G HEM 4.0 26.2 - - + +
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Residues in contact with ALA 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G GLY 2.8 15.2 + - - +
63G ILE 3.2 14.1 - - - +
65G LEU* 1.3 72.3 - - - +
67G MET* 1.3 55.2 + - - +
68G HIS 3.2 0.6 + - - -
69G TYR* 3.7 8.1 + - - +
195G PHE* 4.5 14.6 - - + -
199G TYR* 4.3 5.4 - - + -
502G HEM 3.9 33.1 - - + +
192J ASN* 3.2 17.0 + - - +
195J PHE* 5.3 1.9 - - - -
196J SER* 3.3 19.3 + - - +
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Residues in contact with MET 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ILE* 3.1 16.8 - - + +
64G VAL* 2.7 18.3 + - - +
66G ALA* 1.3 73.2 - - - +
68G HIS* 1.3 72.5 + - + +
37I GLN* 3.6 26.7 - - - -
38I MET* 4.3 14.6 - - - +
189J ALA* 4.5 2.3 - - - +
192J ASN* 3.0 30.2 + - - +
193J ARG* 3.7 24.3 + - + +
196J SER* 3.7 13.2 - - - +
197J LEU* 3.4 47.6 - - + -
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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
------------------------------------------------------------
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