Contacts of the helix formed by residues 66 - 86 (chain D) in PDB entry 2HQT
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 THR 66 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 3.8 8.7 - - - -
20D VAL* 4.2 17.7 - - + -
22D PHE* 4.2 7.4 - - + -
60D VAL* 4.0 7.8 - - + +
62D THR* 3.8 24.9 - - + +
64D TYR 3.8 9.6 - - - +
65D PRO* 1.3 77.7 - - - +
67D SER* 1.3 66.2 - - - +
68D THR* 3.4 19.2 + - - -
69D ASP* 2.9 26.0 + - - +
70D VAL* 3.2 13.5 + - - +
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Residues in contact with SER 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 6.1 3.1 - - - -
10D PHE* 3.9 16.6 - - - -
66D THR* 1.3 73.9 - - - +
68D THR* 1.3 59.3 + - - +
70D VAL* 3.2 9.1 + - - +
71D HIS* 2.8 56.0 + - - -
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PHE* 5.6 1.0 - - - -
30D ALA* 3.6 27.5 + - - +
33D TRP* 3.8 30.1 - - + -
37D LEU* 6.1 0.2 - - + -
59D ILE* 4.0 10.1 - - + -
60D VAL* 3.7 19.2 - - + +
66D THR* 3.1 12.1 + - - -
67D SER* 1.3 81.1 + - - +
69D ASP* 1.3 61.0 - - - +
71D HIS* 3.3 5.9 + - - -
72D VAL* 2.9 35.5 + - + +
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D PHE* 3.5 15.1 - - - +
59D ILE* 2.9 33.2 + - - +
60D VAL 4.8 1.2 + - - -
62D THR* 4.6 0.3 + - - -
64D TYR 4.5 0.3 - - - +
65D PRO* 3.4 6.7 - - + +
66D THR* 2.9 39.8 + - - +
68D THR* 1.3 76.4 - - - +
70D VAL* 1.3 57.7 + - - +
73D PHE* 3.0 32.4 + - - +
103D TRP* 2.9 28.2 + - - +
107D MET* 3.9 18.3 - - + +
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 4.1 24.4 - - + +
7D VAL* 3.7 28.7 - - + -
10D PHE* 3.5 37.2 - - + -
66D THR 3.5 12.3 - - - +
67D SER* 3.2 9.5 + - - +
69D ASP* 1.3 78.0 - - - +
71D HIS* 1.3 58.0 + - - +
73D PHE* 3.7 4.1 - - - +
74D GLU* 3.0 29.4 + - - +
107D MET* 4.2 16.8 - - + -
111D LEU* 4.5 5.4 - - + -
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Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D SER* 5.5 0.2 - - - -
7D VAL* 3.5 32.9 - - + +
34D GLU* 6.2 2.6 - - - +
37D LEU* 3.7 30.2 - - + +
67D SER* 2.8 43.1 + - - +
68D THR* 3.9 4.8 + - - +
70D VAL* 1.3 73.1 - - - +
72D VAL* 1.3 62.7 + - - +
74D GLU* 3.6 20.7 + - - +
75D VAL* 3.7 6.6 + - - +
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Residues in contact with VAL 72 (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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33D TRP* 4.1 22.2 - - + -
37D LEU* 4.0 18.3 - - + +
42D ILE* 4.3 12.0 - - + +
49D LEU* 3.5 33.2 - - + -
59D ILE* 3.6 24.7 - - + -
68D THR* 2.9 30.6 + - + +
71D HIS* 1.3 71.9 - - - +
73D PHE* 1.3 55.7 + - - +
75D VAL* 3.2 5.5 + - - +
76D ALA* 2.7 36.4 + - + +
103D TRP* 3.8 3.6 - - + -
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Residues in contact with PHE 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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6D LEU* 3.9 20.0 - - + -
69D ASP 3.0 22.4 + - - +
70D VAL* 3.7 3.6 - - - +
72D VAL* 1.3 77.5 - - - +
74D GLU* 1.3 57.4 + - - +
76D ALA* 4.3 1.1 - - - -
77D LEU* 2.9 63.3 + - + +
103D TRP* 3.4 15.6 - + + -
104D ILE* 4.0 28.9 - - + -
107D MET* 3.5 25.4 - - + -
108D GLN* 3.6 25.1 - - + -
111D LEU* 3.8 25.6 - - + -
113D VAL* 4.0 9.2 - - + -
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Residues in contact with GLU 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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4D SER* 2.8 37.3 + - - -
5D ASP* 4.6 1.4 + - - +
6D LEU* 3.8 34.0 + - + +
7D VAL* 4.6 4.3 - - - +
70D VAL 3.0 16.5 + - - +
71D HIS* 3.7 12.8 - - - +
72D VAL 3.3 0.2 - - - -
73D PHE* 1.3 76.2 - - - +
75D VAL* 1.3 61.1 + - + +
77D LEU* 5.4 0.9 - - - -
78D PRO* 3.3 20.4 - - - +
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Residues in contact with VAL 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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37D LEU* 3.9 15.9 - - + -
42D ILE* 4.0 27.4 - - + -
71D HIS 3.9 11.9 - - - +
72D VAL 3.2 6.3 + - - +
73D PHE 3.1 0.4 - - - -
74D GLU* 1.3 82.0 - - + +
76D ALA* 1.3 65.2 + - - +
77D LEU 3.4 0.4 - - - -
78D PRO* 3.3 15.5 - - - +
79D LEU* 3.5 14.6 + - + +
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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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42D ILE* 4.9 6.2 - - + +
46D LEU* 4.8 4.0 - - + -
49D LEU* 4.4 14.4 - - + -
72D VAL* 2.7 25.5 + - + +
73D PHE 4.1 1.6 - - - +
75D VAL* 1.3 72.9 - - - +
77D LEU* 1.3 65.0 + - - +
79D LEU* 3.4 2.9 + - - -
80D ILE* 2.9 40.9 + - + +
100D ILE* 5.0 0.7 - - + -
103D TRP* 4.2 19.3 - - + -
104D ILE* 4.4 3.8 - - + -
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Residues in contact with LEU 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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6D LEU* 6.0 2.0 - - + -
73D PHE* 2.9 50.7 + - + +
74D GLU* 5.2 0.4 - - - -
76D ALA* 1.3 74.7 - - - +
78D PRO* 1.4 67.7 - - + +
80D ILE* 3.8 1.7 - - - +
81D LYS* 3.0 50.6 + - + +
104D ILE* 4.1 15.8 - - + +
108D GLN* 3.8 18.8 - - - +
113D VAL* 4.2 16.2 - - + -
117D ASP* 4.0 13.9 - - + +
119D LEU* 3.9 12.8 - - + +
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Residues in contact with PRO 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 GLU 3.3 21.1 - - - +
75D VAL* 3.3 15.0 - - - +
77D LEU* 1.4 99.2 - - + +
79D LEU* 1.3 53.4 + - - +
81D LYS* 3.7 9.5 - - + +
82D ASP* 2.8 44.2 + - - +
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Residues in contact with LEU 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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42D ILE* 4.2 12.3 - - + -
43D GLN* 3.7 37.9 - - + +
46D LEU* 3.6 36.6 - - + -
75D VAL* 3.5 18.1 + - + +
76D ALA 3.4 3.8 + - - +
77D LEU 3.3 0.4 - - - -
78D PRO* 1.3 76.1 - - - +
80D ILE* 1.3 63.0 + - + +
82D ASP* 3.2 10.0 + - + +
83D LEU* 2.8 51.6 + - + +
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Residues in contact with ILE 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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46D LEU* 4.1 30.1 - - + -
76D ALA* 2.9 25.6 + - + +
77D LEU 3.8 2.7 - - - +
79D LEU* 1.3 83.7 - - + +
81D LYS* 1.3 56.4 + - - +
83D LEU* 3.2 10.1 + - + +
84D VAL* 2.8 38.2 + - + +
93D THR* 6.0 0.7 - - + -
97D TYR* 5.4 14.1 - - + -
100D ILE* 4.1 12.6 - - + -
101D LEU* 4.4 8.1 - - + -
104D ILE* 3.9 16.2 - - + -
119D LEU* 3.4 28.5 - - + -
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Residues in contact with LYS 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 LEU* 3.0 33.2 + - + +
78D PRO* 3.7 9.9 - - + +
80D ILE* 1.3 75.7 - - - +
82D ASP* 1.3 61.3 + - - +
84D VAL* 3.3 2.8 + - - +
85D ALA* 2.9 30.0 + - - +
116D THR 3.6 10.5 + - - -
117D ASP* 3.1 27.5 + - - +
118D LYS 2.8 25.0 + - - +
119D LEU* 3.8 26.7 - - + +
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Residues in contact with ASP 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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78D PRO* 2.8 32.3 + - - +
79D LEU* 3.4 9.8 - - + +
80D ILE 3.1 0.2 - - - -
81D LYS* 1.3 78.3 - - - +
83D LEU* 1.3 61.3 + - + +
85D ALA* 3.3 5.7 + - - +
86D SER* 2.6 35.1 + - - -
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Residues in contact with LEU 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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43D GLN* 3.5 27.4 - - - +
46D LEU* 3.8 28.3 - - + -
79D LEU* 2.8 31.4 + - + +
80D ILE* 3.6 10.8 - - + +
82D ASP* 1.3 76.1 - - + +
84D VAL* 1.3 60.9 + - - +
86D SER* 3.7 5.8 + - - +
87D SER* 3.1 23.7 + - - -
93D THR* 4.3 13.5 + - + +
97D TYR* 4.0 24.7 - - + +
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Residues in contact with VAL 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 ILE* 2.8 36.8 + - + +
81D LYS 3.7 5.4 - - - +
83D LEU* 1.3 73.4 - - - +
85D ALA* 1.3 65.1 + - - +
87D SER* 3.1 21.7 + - - +
90D VAL* 3.8 21.8 - - + +
93D THR* 4.2 14.1 - - + -
94D TYR* 3.8 32.1 - - + +
119D LEU* 4.2 13.7 - - + -
120D GLU* 6.1 0.4 - - + +
115F SER* 5.0 2.5 - - - +
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Residues in contact with ALA 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 LYS 2.9 18.3 + - - +
82D ASP* 3.3 8.7 + - - +
84D VAL* 1.3 79.9 - - - +
86D SER* 1.3 60.2 + - - +
87D SER 3.3 2.3 + - - +
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Residues in contact with SER 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 ASP 2.6 25.3 + - - -
83D LEU* 3.7 7.2 + - - +
84D VAL 3.2 0.2 - - - -
85D ALA* 1.3 76.2 - - - +
87D SER* 1.3 64.8 + - - +
88D LYS* 3.5 13.7 + - - +
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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