Contacts of the helix formed by residues 45 - 56 (chain L) 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 HIS 45 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88K LYS* 3.1 40.3 + - + +
32L GLN* 4.7 1.5 + - - -
33L TRP* 4.1 16.9 - + + -
36L VAL* 3.8 30.3 - - + +
41L GLN* 2.7 38.1 + - + +
42L ILE 3.1 8.8 + - - +
44L PRO* 1.3 76.4 - - - +
46L LEU* 1.3 58.3 + - - +
47L ASP 3.4 2.2 - - - -
48L GLN* 3.1 32.5 + - - +
49L LEU* 2.8 28.0 + - - +
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Residues in contact with LEU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ILE* 3.1 16.1 + - + +
43L GLN* 3.1 24.8 + - + +
44L PRO 3.4 0.4 - - - -
45L HIS* 1.3 77.4 - - - +
47L ASP* 1.3 60.2 + - - +
49L LEU* 3.1 14.0 + - + +
50L ASN* 2.8 30.5 + - - +
76L ALA* 4.8 3.8 - - + -
79L LEU* 3.8 24.0 - - + -
80L ILE* 3.3 25.6 - - + -
83L LEU* 3.9 27.4 - - + -
97L TYR* 4.2 15.7 - - + +
100L ILE* 3.6 16.0 - - + +
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Residues in contact with ASP 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K SER* 3.4 21.6 - - - +
93K THR* 4.7 10.0 + - - +
96K THR* 3.4 40.8 + - - +
97K TYR* 4.7 8.5 + - - -
44L PRO 4.8 4.4 + - - +
45L HIS 3.4 0.4 - - - -
46L LEU* 1.3 76.0 - - - +
48L GLN* 1.3 64.0 + - - +
50L ASN* 3.3 8.2 + - - +
51L LEU* 3.0 19.2 + - - +
96L THR* 4.9 0.7 - - - +
97L TYR* 3.9 20.3 + - - -
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Residues in contact with GLN 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K LYS* 4.4 4.5 + - + -
89K ASP* 3.4 35.7 + - + +
92K SER* 3.4 17.9 + - - +
32L GLN* 3.2 24.8 + - - +
33L TRP* 4.4 3.5 - - + -
44L PRO 5.4 0.2 + - - -
45L HIS* 3.1 41.6 + - + +
47L ASP* 1.3 80.0 - - - +
49L LEU* 1.3 56.4 + - - +
51L LEU* 3.2 4.3 + - + +
52L VAL* 2.8 42.5 + - + +
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Residues in contact with LEU 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L TRP* 3.8 25.3 - - + -
42L ILE* 5.5 3.1 - - + -
45L HIS 2.8 17.5 + - - +
46L LEU* 3.1 14.3 + - + +
48L GLN* 1.3 73.4 - - - +
50L ASN* 1.3 58.1 + - - +
52L VAL* 3.2 5.4 + - + +
53L LEU* 2.9 44.8 + - + +
59L ILE* 3.5 33.2 - - + -
72L VAL* 3.8 20.6 - - + -
76L ALA* 4.4 9.6 - - + -
100L ILE* 3.7 20.0 - - + -
103L TRP* 4.3 11.4 - - + -
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Residues in contact with ASN 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K THR* 5.6 2.4 + - - +
46L LEU 2.8 16.1 + - - +
47L ASP* 3.5 11.2 - - - +
49L LEU* 1.3 74.4 - - - +
51L LEU* 1.3 56.8 + - - +
53L LEU* 3.4 1.7 + - - -
54L ARG 3.0 22.2 + - - -
96L THR 3.3 22.9 - - - +
97L TYR* 3.2 12.7 - - + +
98L ARG 4.3 0.7 + - - -
99L HIS* 3.0 56.6 - - - +
100L ILE* 3.1 21.9 - - + +
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Residues in contact with LEU 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K ASP* 4.1 5.4 - - - +
91K LYS* 3.9 28.9 - - + +
92K SER* 3.8 33.0 - - - +
95K THR* 4.6 11.4 - - + +
47L ASP 3.0 13.6 + - - +
48L GLN* 3.5 8.7 - - + +
50L ASN* 1.3 75.0 + - - +
52L VAL* 1.3 67.1 + - - +
54L ARG* 3.2 57.3 + - - +
55L ASP* 3.7 8.0 + - - +
99L HIS* 5.3 0.4 - - - -
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Residues in contact with VAL 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L GLN* 5.3 2.9 - - - +
33L TRP* 4.0 23.6 - - + +
48L GLN* 2.8 30.6 + - + +
49L LEU* 3.4 7.4 - - + +
51L LEU* 1.3 73.9 - - - +
53L LEU* 1.3 61.6 + - + +
55L ASP 3.2 0.3 + - - -
56L ASN* 3.0 48.9 + - + +
59L ILE* 3.6 35.7 - - + +
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Residues in contact with LEU 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J ARG* 4.1 1.7 - - - -
49L LEU* 2.9 39.8 + - + +
50L ASN 3.9 4.5 - - - +
52L VAL* 1.3 75.3 - - + +
54L ARG* 1.3 65.6 + - - +
55L ASP 3.2 0.2 - - - -
56L ASN 3.1 19.1 - - - +
57L THR 4.0 4.5 - - - +
58L PHE 4.2 6.3 - - - -
59L ILE* 4.1 15.5 - - + -
99L HIS* 3.6 17.1 - - + +
100L ILE* 3.9 9.2 - - - -
102L ARG* 3.0 23.6 + - - +
103L TRP* 3.5 58.1 - - + -
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Residues in contact with ARG 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J ARG* 3.3 60.1 - - + +
99J HIS* 4.5 11.3 + - + -
102J ARG* 3.7 17.2 - - - +
2006J SO4 3.3 14.6 + - - -
91K LYS* 4.4 8.7 - - - +
95K THR* 4.2 8.6 - - - +
98K ARG* 4.1 6.1 - - - +
50L ASN 3.0 6.8 + - - +
51L LEU* 3.2 36.1 + - - +
53L LEU* 1.3 79.5 - - - +
55L ASP* 1.3 92.1 + - - +
99L HIS* 3.5 43.3 - - + +
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Residues in contact with ASP 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J ARG* 4.1 12.7 - - - +
102J ARG* 3.8 23.0 - - - +
105J ASP* 4.7 9.4 - - - +
91K LYS* 5.5 1.0 + - - -
51L LEU* 4.2 6.6 - - - +
52L VAL 3.2 3.3 + - - +
53L LEU 3.2 0.2 - - - -
54L ARG* 1.3 125.1 + - - +
56L ASN* 1.3 74.0 + - - +
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Residues in contact with ASN 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J ARG* 4.0 4.0 - - - -
105J ASP* 5.1 5.2 - - - +
29L GLN* 5.7 1.0 - - - +
52L VAL* 3.0 36.5 + - + +
53L LEU* 3.1 11.1 - - - +
54L ARG 3.6 0.4 - - - -
55L ASP* 1.3 92.8 - - - +
57L THR* 1.3 66.0 + - - +
58L PHE 3.3 17.7 + - - +
59L ILE 5.1 0.2 - - - -
61L SER* 2.6 30.9 + - - +
102L ARG* 3.1 14.0 + - - -
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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