Contacts of the helix formed by residues 73 - 90 (chain G) in PDB entry 1Q0K
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 GLU 73 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G TYR* 3.3 27.5 - - - -
72G PRO* 1.3 77.7 - - + +
74G LEU* 1.3 61.6 + - - +
75G HIS 3.5 1.3 - - - -
76G THR* 3.4 11.4 + - - -
77G LEU* 2.9 33.3 + - + +
106G GLN* 6.1 2.2 - - - +
110G ILE* 4.0 16.6 - - + +
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Residues in contact with LEU 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G PHE* 3.6 49.8 - - + -
67G HIS* 4.5 11.9 - - + +
68G PHE* 3.8 22.4 - - + -
71G TYR* 2.9 21.2 + - + +
72G PRO 3.4 0.2 - - - -
73G GLU* 1.3 77.1 - - - +
75G HIS* 1.3 66.5 + - - +
77G LEU* 3.1 11.6 + - + +
78G VAL* 2.9 45.4 + - + +
107G ILE* 5.0 2.5 - - + -
110G ILE* 4.2 27.4 - - + -
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Residues in contact with HIS 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G TRP* 2.9 31.5 + + - +
68G PHE* 3.4 51.1 - + + +
71G TYR 4.8 0.6 + - - -
72G PRO 4.8 7.9 + - - +
73G GLU 3.5 0.6 - - - -
74G LEU* 1.3 77.0 - - - +
76G THR* 1.3 58.5 + - - +
78G VAL* 3.4 0.5 + - - -
79G ASN* 2.9 30.0 + - - +
59L TRP* 3.8 5.0 - - - -
75L HIS* 3.5 53.0 - + + +
76L THR* 4.2 13.7 + - - -
79L ASN* 4.2 5.8 - - + -
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Residues in contact with THR 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G PRO 5.3 2.1 + - - -
73G GLU* 3.4 13.0 + - - -
74G LEU 3.3 0.6 - - - -
75G HIS* 1.3 78.4 - - - +
77G LEU* 1.3 54.0 + - - +
79G ASN* 3.6 5.9 - - + +
80G GLU* 2.7 68.7 + - + +
69L GLU* 5.8 0.2 + - - -
75L HIS* 4.2 14.0 + - - -
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Residues in contact with LEU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G GLU* 2.9 25.0 + - + +
74G LEU* 3.1 7.8 + - + +
76G THR* 1.3 77.1 - - - +
78G VAL* 1.3 62.2 + - - +
80G GLU* 3.4 8.5 + - - +
81G ALA* 3.0 22.3 + - - +
103G TYR* 3.7 26.2 - - + +
106G GLN* 3.4 34.5 - - + +
107G ILE* 3.5 31.6 - - + +
110G ILE* 3.7 30.1 - - + -
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Residues in contact with VAL 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU* 4.1 21.3 - - + +
58G LEU* 6.3 0.7 - - + -
59G TRP* 3.8 29.8 - - + -
63G PHE* 4.8 5.6 - - + -
74G LEU* 2.9 38.7 + - + +
75G HIS 3.9 2.9 - - - +
77G LEU* 1.3 74.6 - - - +
79G ASN* 1.3 65.0 + - - +
81G ALA* 3.1 3.1 + - - +
82G VAL* 3.0 23.1 + - + +
107G ILE* 3.9 23.1 - - + -
59L TRP* 3.6 20.2 - - + -
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Residues in contact with ASN 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G HIS 2.9 19.2 + - - +
76G THR* 3.6 5.2 - - - +
78G VAL* 1.3 77.6 - - - +
80G GLU* 1.3 59.0 + - + +
82G VAL* 2.9 20.4 - - - +
83G LYS* 2.8 40.5 + - - +
59L TRP* 3.0 58.6 + - + +
60L SER* 4.0 1.8 - - - +
65L PRO* 5.8 1.0 - - - +
68L PHE* 3.5 18.4 - - + -
75L HIS* 4.0 5.8 - - + -
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Residues in contact with GLU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G THR* 2.7 47.1 + - + +
77G LEU* 3.8 9.3 - - - +
79G ASN* 1.3 71.7 - - + +
81G ALA* 1.3 61.2 + - - +
83G LYS* 3.8 9.5 - - + +
84G ALA* 2.9 29.5 + - - +
103G TYR* 3.4 39.8 + - + +
65L PRO* 6.4 1.8 - - + -
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Residues in contact with ALA 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU* 3.7 14.6 - - + -
77G LEU 3.0 13.9 + - - +
78G VAL 3.1 8.7 + - - +
80G GLU* 1.3 77.6 - - - +
82G VAL* 1.3 62.3 + - - +
84G ALA* 3.2 4.3 + - - +
85G LEU* 3.1 25.1 + - - +
100G ALA* 4.7 1.7 - - - +
103G TYR* 3.7 24.7 - - + -
104G ILE* 4.9 2.5 - - + +
107G ILE* 3.7 22.0 - - + -
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Residues in contact with VAL 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LYS* 3.9 19.7 - - + +
55G LEU* 4.0 24.5 - - + -
56G ASP* 3.8 19.7 - - - +
78G VAL* 3.0 12.9 + - + +
79G ASN* 2.9 29.4 - - - +
81G ALA* 1.3 72.8 - - - +
83G LYS* 1.3 64.7 + - - +
85G LEU* 3.1 10.7 + - - +
86G SER* 3.0 24.4 + - - -
59L TRP* 4.1 7.2 - - + -
60L SER* 3.4 31.0 - - - -
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Residues in contact with LYS 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G ASN* 2.8 43.9 + - - +
80G GLU* 3.9 10.3 - - + +
82G VAL* 1.3 77.0 - - - +
84G ALA* 1.3 57.0 + - - +
86G SER* 3.3 10.5 + - - -
87G ALA* 3.0 25.8 + - - +
59L TRP 3.7 1.0 + - - -
60L SER 2.7 36.4 + - - +
61L ASP 5.3 0.2 - - - -
63L PHE 2.9 26.8 + - - -
64L LYS* 4.1 17.9 - - - +
65L PRO* 4.2 19.7 - - + -
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Residues in contact with ALA 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G GLU 2.9 18.3 + - - +
81G ALA 3.3 7.2 - - - +
82G VAL 3.2 0.2 - - - -
83G LYS* 1.3 77.0 - - - +
85G LEU* 1.3 60.2 + - - +
87G ALA* 3.3 8.2 + - - +
88G ALA* 3.0 25.5 + - - +
96G THR* 4.4 4.0 - - - +
99G LYS* 4.6 11.7 - - + +
100G ALA* 3.9 26.8 - - - +
103G TYR* 3.9 14.6 - - + -
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Residues in contact with LEU 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ALA* 4.2 13.7 - - + -
21G VAL* 5.0 5.4 - - + -
48G ALA* 4.1 13.0 - - + +
51G ALA* 3.7 35.9 - - + -
52G LYS* 3.6 28.0 - - + +
55G LEU* 3.9 18.2 - - + -
81G ALA 3.1 16.6 + - - +
82G VAL* 3.1 7.4 + - - +
84G ALA* 1.3 76.5 - - - +
86G SER* 1.3 64.2 + - - +
88G ALA* 3.2 7.8 + - + +
89G LYS* 3.1 25.8 + - - +
100G ALA* 3.6 22.0 - - + -
104G ILE* 4.8 4.3 - - + -
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Residues in contact with SER 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LYS* 3.0 27.3 + - - -
82G VAL 3.0 10.3 + - - -
83G LYS* 3.5 12.8 - - - -
84G ALA 3.3 0.4 - - - -
85G LEU* 1.3 76.8 - - - +
87G ALA* 1.3 61.7 + - - +
89G LYS* 3.3 18.3 + - - +
90G ALA* 3.3 9.2 + - - +
39J ARG* 5.1 1.2 + - - -
3L ASP* 3.2 25.3 + - - +
60L SER 5.3 0.2 + - - -
61L ASP* 3.6 5.9 + - - -
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Residues in contact with ALA 87 (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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83G LYS 3.0 14.3 + - - +
84G ALA* 3.5 12.6 - - - +
85G LEU 3.1 0.2 - - - -
86G SER* 1.3 76.1 - - - +
88G ALA* 1.3 62.8 + - - +
90G ALA* 3.2 15.6 + - - +
91G SER* 3.3 17.2 + - - -
96G THR* 4.3 11.3 + - + +
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Residues in contact with ALA 88 (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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21G VAL* 3.8 24.9 - - + -
25G GLN* 3.3 8.7 + - - +
44G LYS* 2.8 21.9 + - - +
48G ALA* 5.5 0.7 - - + -
84G ALA 3.0 12.8 + - - +
85G LEU* 3.2 14.3 + - + +
87G ALA* 1.3 74.3 - - - +
89G LYS* 1.3 62.6 + - - +
91G SER 2.9 11.8 - - - +
96G THR* 3.5 17.0 - - - +
97G GLY* 4.3 9.4 - - - +
100G ALA* 5.3 0.2 - - + -
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Residues in contact with LYS 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LYS* 2.8 24.3 + - - +
45G GLU* 3.1 52.1 + - - +
48G ALA* 3.6 15.4 - - + +
49G GLU* 2.9 36.9 + - - +
52G LYS* 4.3 4.6 - - - +
85G LEU 3.1 16.0 + - - +
86G SER* 3.3 8.7 - - - +
87G ALA 3.2 0.2 - - - -
88G ALA* 1.3 77.1 - - - +
90G ALA* 1.3 57.7 + - - +
91G SER 3.4 0.7 + - - -
39J ARG* 3.2 24.7 + - - +
2L CYS 4.9 1.2 + - - -
3L ASP* 2.5 42.7 + - - +
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Residues in contact with ALA 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G SER 3.3 8.9 + - - +
87G ALA* 3.2 10.8 + - - +
88G ALA 3.2 0.8 - - - -
89G LYS* 1.3 79.0 - - - +
91G SER* 1.3 58.0 + - - -
35J HIS* 6.0 2.6 - - - +
39J ARG* 3.8 26.2 - - - +
4L LEU 5.1 1.8 - - - +
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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
------------------------------------------------------------
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