Contacts of the helix formed by residues 66 - 87 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I TYR* 6.5 0.7 - - - -
19I PRO* 6.4 1.3 - - + -
22I PHE* 4.9 9.6 - - + -
60I VAL* 3.8 7.6 - - + +
62I THR* 3.6 33.9 - - + +
64I TYR 4.0 1.3 - - - +
65I PRO* 1.3 76.9 - - - +
67I SER* 1.3 66.0 + - - +
68I THR* 3.3 24.3 + - - -
69I ASP* 2.8 24.1 + - - +
70I VAL* 3.2 16.0 + - - +
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Residues in contact with SER 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I GLU* 5.5 0.7 + - - -
66I THR* 1.3 71.2 - - - +
68I THR* 1.3 64.0 + - - +
70I VAL* 3.3 8.6 + - - +
71I HIS* 2.8 57.8 + - - -
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Residues in contact with THR 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ALA* 3.6 19.6 - - - +
33I TRP* 3.8 25.8 - - + -
34I GLU* 3.3 27.7 + - - +
59I ILE* 4.3 10.5 - - + -
60I VAL* 3.8 17.9 - - + +
66I THR* 3.1 13.0 + - - -
67I SER* 1.3 81.6 + - - +
69I ASP* 1.3 62.2 + - - +
71I HIS* 3.2 0.9 + - - +
72I VAL* 3.0 27.5 + - + +
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Residues in contact with ASP 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I PHE* 3.5 15.9 - - - +
59I ILE* 2.9 33.2 + - - +
60I VAL 4.7 0.9 + - - -
62I THR* 4.4 1.2 + - - -
65I PRO* 3.3 9.8 - - + +
66I THR* 2.8 37.9 + - - +
68I THR* 1.3 77.5 - - - +
70I VAL* 1.3 58.6 + - - +
73I PHE* 2.9 31.7 + - - +
103I TRP* 2.8 28.0 + - - +
107I MET* 3.9 17.5 - - + -
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Residues in contact with VAL 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I PRO* 5.5 2.9 - - + -
66I THR 3.2 14.0 + - - +
67I SER* 3.6 11.4 - - - +
69I ASP* 1.3 78.1 - - - +
71I HIS* 1.3 66.9 + - + +
73I PHE* 3.4 4.3 + - + +
74I GLU* 3.0 30.2 + - + +
107I MET* 4.0 18.4 - - + -
110I LEU* 5.6 1.6 - - + -
111I LEU* 4.4 24.9 - - + -
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Residues in contact with HIS 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I GLU* 2.9 31.0 + - + +
37I LEU* 3.5 18.8 - - + +
67I SER* 2.8 47.6 + - - +
68I THR 4.0 0.9 - - - +
70I VAL* 1.3 79.2 - - + +
72I VAL* 1.3 66.9 + - - +
74I GLU* 3.5 13.1 + - + +
75I VAL* 3.7 9.4 + - - +
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Residues in contact with VAL 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I TRP* 4.1 29.2 - - + -
37I LEU* 4.1 24.9 - - + -
42I ILE* 4.0 12.6 - - + +
49I LEU* 3.7 27.4 - - + -
59I ILE* 3.6 26.0 - - + -
68I THR* 3.0 20.0 + - + +
71I HIS* 1.3 74.7 - - - +
73I PHE* 1.3 53.6 + - - +
75I VAL* 3.1 4.7 + - - +
76I ALA* 2.7 33.2 + - + +
103I TRP* 3.8 2.7 - - + -
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Residues in contact with PHE 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I ASP 2.9 21.5 + - - +
70I VAL* 3.6 6.5 - - + +
72I VAL* 1.3 76.8 - - - +
74I GLU* 1.3 66.6 + - + +
76I ALA* 4.4 0.7 - - - +
77I LEU* 3.0 50.4 + - + +
103I TRP* 3.4 17.8 - + + -
104I ILE* 3.9 23.6 - - + -
107I MET* 3.4 26.5 - - + -
108I GLN* 3.6 31.6 - - + -
111I LEU* 3.9 24.5 - - + -
113I VAL* 3.8 18.8 - - + -
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Residues in contact with GLU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I VAL* 3.0 18.6 + - + +
71I HIS* 3.8 8.5 - - + +
72I VAL 3.2 0.6 - - - -
73I PHE* 1.3 83.8 - - + +
75I VAL* 1.3 66.8 + - - +
77I LEU* 5.5 0.2 - - - -
78I PRO* 3.1 22.1 - - - +
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Residues in contact with VAL 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LEU* 4.4 10.1 - - + -
42I ILE* 3.9 29.6 - - + -
71I HIS 3.7 9.8 + - - +
72I VAL 3.1 6.7 + - - +
74I GLU* 1.3 89.3 - - - +
76I ALA* 1.3 64.2 + - - +
77I LEU 3.4 0.2 - - - -
78I PRO* 3.3 15.0 - - + +
79I LEU* 3.4 13.9 + - + +
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Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I ILE* 4.5 6.5 - - + +
46I LEU* 4.5 10.1 - - + -
49I LEU* 4.2 25.1 - - + -
72I VAL* 2.7 25.1 + - + +
75I VAL* 1.3 71.7 - - - +
77I LEU* 1.3 59.1 + - - +
79I LEU* 3.3 6.9 + - - +
80I ILE* 2.8 38.4 + - + +
100I ILE* 5.1 1.3 - - + -
103I TRP* 4.4 11.0 - - + -
104I ILE* 4.5 1.6 - - + -
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Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I PHE* 3.0 44.5 + - + +
74I GLU* 5.5 0.2 - - - -
76I ALA* 1.3 77.3 - - - +
78I PRO* 1.4 66.0 - - + +
80I ILE* 3.8 0.7 - - - +
81I LYS* 2.9 35.5 + - + +
104I ILE* 3.8 19.1 - - + +
108I GLN* 3.6 20.4 - - - +
113I VAL* 4.2 14.6 - - + -
117I ASP* 3.4 21.8 - - + +
119I LEU* 3.7 23.8 - - + +
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Residues in contact with PRO 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I GLU 3.1 27.4 - - - +
75I VAL* 3.3 11.9 - - + +
77I LEU* 1.4 95.7 - - + +
79I LEU* 1.3 57.9 + - - +
81I LYS* 3.8 10.1 - - + +
82I ASP* 3.2 23.2 + - - +
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Residues in contact with LEU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I ILE* 3.8 13.2 - - + -
43I GLN* 3.6 49.6 - - + +
46I LEU* 3.2 42.0 - - + -
75I VAL* 3.4 15.1 + - + +
76I ALA 3.3 8.0 + - - +
77I LEU 3.2 0.2 - - - -
78I PRO* 1.3 75.2 - - - +
80I ILE* 1.3 65.8 + - - +
82I ASP* 3.3 7.3 + - + +
83I LEU* 3.0 26.7 + - + +
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Residues in contact with ILE 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I LEU* 4.3 17.7 - - + -
76I ALA 2.8 24.4 + - - +
77I LEU 3.9 2.2 - - - +
79I LEU* 1.3 73.8 - - - +
81I LYS* 1.3 57.7 + - - +
83I LEU* 3.2 7.3 + - + +
84I VAL* 2.9 36.0 + - + +
97I TYR* 3.9 39.7 - - + -
100I ILE* 4.0 17.7 - - + -
101I LEU* 3.8 27.1 - - + -
104I ILE* 3.9 15.3 - - + -
119I LEU* 3.9 9.4 - - + -
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Residues in contact with LYS 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I LEU* 2.9 23.7 + - + +
78I PRO* 3.8 8.7 - - + +
80I ILE* 1.3 76.7 - - - +
82I ASP* 1.3 51.8 + - - +
84I VAL* 3.7 3.3 - - - +
85I ALA* 2.7 34.6 + - - +
116I THR 2.7 29.9 + - - -
117I ASP* 3.3 22.3 + - - +
118I LYS 3.1 17.1 + - - +
119I LEU* 3.9 29.8 - - + +
120I GLU 5.6 0.2 - - - +
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Residues in contact with ASP 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I PRO 3.2 16.4 + - - +
79I LEU* 3.3 6.7 + - + +
81I LYS* 1.3 75.7 - - - +
83I LEU* 1.3 62.5 + - + +
85I ALA* 3.6 8.3 - - - +
86I SER* 2.9 30.3 + - - -
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Residues in contact with LEU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I GLN* 4.1 20.9 - - - +
46I LEU* 3.8 23.1 - - + -
79I LEU* 3.0 22.9 + - + +
80I ILE* 3.2 12.1 + - + +
82I ASP* 1.3 72.8 - - + +
84I VAL* 1.3 67.7 + - - +
86I SER* 3.3 7.6 + - - +
87I SER* 3.1 26.5 + - - -
93I THR* 4.5 10.3 - - + -
97I TYR* 3.8 32.5 - - + +
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Residues in contact with VAL 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I ILE* 2.9 24.9 + - + +
81I LYS 3.7 4.5 - - - +
83I LEU* 1.3 78.5 - - - +
85I ALA* 1.3 63.8 + - - +
86I SER 3.2 1.0 + - - -
87I SER* 3.4 14.6 + - - -
90I VAL* 3.8 17.6 - - + +
93I THR* 3.7 19.5 - - + -
94I TYR* 3.4 41.5 - - + +
101I LEU* 5.5 1.6 - - + -
119I LEU* 4.2 16.8 - - + -
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Residues in contact with ALA 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H ALA* 5.2 9.9 - - - +
32H GLN* 5.8 0.7 + - - +
81I LYS 2.7 23.2 + - - +
82I ASP* 3.6 11.2 - - - +
83I LEU 3.3 0.2 - - - -
84I VAL* 1.3 75.6 - - - +
86I SER* 1.3 58.2 + - - +
87I SER 3.9 0.2 + - - -
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Residues in contact with SER 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ASP 2.9 18.2 + - - -
83I LEU* 3.6 8.7 + - - +
85I ALA* 1.3 76.6 - - - +
87I SER* 1.3 66.0 + - - +
88I LYS* 3.8 5.7 + - - +
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Residues in contact with SER 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I LEU 3.1 14.2 + - - -
84I VAL 3.4 5.4 + - - -
85I ALA 3.6 0.8 + - - -
86I SER* 1.3 81.8 - - - +
88I LYS* 1.3 63.1 + - - +
89I ASP* 3.1 23.2 + - - -
90I VAL* 3.2 16.3 + - - +
93I THR* 3.1 24.2 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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