Contacts of the helix formed by residues 45 - 56 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32O GLN* 4.4 3.1 + - + -
33O TRP* 3.8 18.5 - - + -
36O VAL* 3.6 30.2 - - + +
41O GLN* 3.0 37.7 + - + +
42O ILE* 2.9 11.1 + - - +
44O PRO* 1.3 76.5 - - + +
46O LEU* 1.3 60.2 + - - +
47O ASP 3.4 2.2 - - - -
48O GLN* 2.9 30.5 + - - +
49O LEU* 2.9 27.9 + - - +
88P LYS* 3.5 38.4 - - + +
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Residues in contact with LEU 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O ILE* 3.1 13.4 + - + +
43O GLN* 3.1 26.0 + - + +
44O PRO 3.5 0.2 - - - -
45O HIS* 1.3 77.0 - - - +
47O ASP* 1.3 57.7 + - - +
49O LEU* 3.0 16.8 + - + +
50O ASN* 2.9 27.0 + - - +
76O ALA* 4.4 6.1 - - + -
79O LEU* 4.1 20.0 - - + -
80O ILE* 3.8 20.4 - - + -
83O LEU* 3.7 30.1 - - + -
97O TYR* 4.1 17.5 - - + +
100O ILE* 3.4 24.7 - - + +
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Residues in contact with ASP 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O GLN 5.1 0.2 + - - -
44O PRO 4.9 4.8 + - - +
45O HIS* 3.4 1.2 - - - +
46O LEU* 1.3 75.0 - - - +
48O GLN* 1.3 62.2 + - - +
50O ASN* 3.3 7.8 + - - +
51O LEU* 2.9 24.1 + - - +
96O THR* 4.8 1.4 - - - +
97O TYR* 3.9 19.9 + - - -
92P SER* 3.8 15.8 - - - +
93P THR* 4.8 7.9 + - - +
96P THR* 3.5 40.6 + - - +
97P TYR* 4.7 9.9 + - - -
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Residues in contact with GLN 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O GLN* 3.5 30.1 + - - +
33O TRP* 4.2 9.0 - - + -
44O PRO 5.5 0.4 + - - -
45O HIS* 2.9 42.5 + - - +
47O ASP* 1.3 78.6 - - - +
49O LEU* 1.3 61.7 + - - +
51O LEU* 3.2 2.1 + - - +
52O VAL* 3.0 34.9 + - + +
88P LYS* 4.3 5.8 + - + +
89P ASP* 3.9 32.2 + - + +
92P SER* 3.3 16.6 - - - +
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Residues in contact with LEU 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O TRP* 3.8 23.5 - - + -
42O ILE* 5.5 2.2 - - + -
45O HIS 2.9 14.0 + - - +
46O LEU* 3.0 20.8 + - + +
48O GLN* 1.3 75.8 - - - +
50O ASN* 1.3 58.1 + - - +
52O VAL* 3.3 6.1 + - + +
53O LEU* 3.0 48.4 + - + +
59O ILE* 3.7 28.0 - - + -
72O VAL* 3.8 22.9 - - + -
76O ALA* 4.3 10.1 - - + -
100O ILE* 4.0 17.9 - - + -
103O TRP* 4.3 6.3 - - + -
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Residues in contact with ASN 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O LEU 2.9 14.7 + - - +
47O ASP* 3.5 8.3 - - - +
49O LEU* 1.3 78.0 - - - +
51O LEU* 1.3 61.0 + - - +
53O LEU 3.4 0.3 + - - -
54O ARG 3.0 18.4 + - - -
96O THR 3.1 24.1 - - - +
97O TYR* 3.2 12.9 - - + +
98O ARG 4.3 0.5 + - - -
99O HIS* 3.0 56.7 + - - +
100O ILE* 3.1 23.7 - - + +
96P THR* 5.5 2.9 + - - +
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Residues in contact with LEU 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O ASP 2.9 16.7 + - - +
48O GLN 3.2 4.0 + - - +
50O ASN* 1.3 73.9 + - - +
52O VAL* 1.3 70.1 + - + +
54O ARG* 3.2 54.0 + - - +
55O ASP* 3.9 6.5 + - - +
99O HIS* 5.2 0.7 - - - -
89P ASP* 4.3 2.9 - - - +
91P LYS* 3.6 41.5 - - + +
92P SER* 3.5 26.9 - - - +
95P THR* 4.5 12.1 - - + +
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Residues in contact with VAL 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O GLN* 3.6 21.1 - - - +
32O GLN* 6.1 0.4 - - - +
33O TRP* 4.5 9.0 - - + -
48O GLN* 3.0 23.6 + - + +
49O LEU* 3.5 9.0 - - + +
51O LEU* 1.3 79.4 - - + +
53O LEU* 1.3 67.0 + - + +
54O ARG 3.1 1.0 + - - -
55O ASP 3.2 1.0 + - - -
56O ASN* 2.9 40.2 + - + +
59O ILE* 3.4 37.5 - - + +
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Residues in contact with LEU 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M ARG* 4.1 2.1 + - - -
49O LEU* 3.0 45.2 + - + +
50O ASN 3.4 0.2 + - - -
52O VAL* 1.3 76.0 - - + +
54O ARG* 1.3 63.9 + - - +
55O ASP 3.2 0.4 - - - -
56O ASN 3.2 19.4 - - - +
57O THR 3.9 5.6 - - - +
58O PHE 4.2 0.9 - - - +
59O ILE* 4.1 16.4 - - + +
99O HIS* 3.7 18.9 - - + +
100O ILE* 4.1 9.9 - - - -
102O ARG* 3.0 26.6 + - - +
103O TRP* 3.5 54.1 - - + +
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Residues in contact with ARG 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98M ARG* 3.4 42.4 - - + +
99M HIS* 4.7 12.6 + - + -
102M ARG* 3.8 17.2 + - - +
2008M SO4 3.3 36.0 + - - -
50O ASN 3.0 6.0 + - - +
51O LEU* 3.3 33.8 - - - +
52O VAL 3.1 0.4 + - - -
53O LEU* 1.3 79.8 - - - +
55O ASP* 1.3 90.3 + - - +
99O HIS* 3.5 43.2 + - + +
91P LYS* 4.1 9.1 - - - +
95P THR* 4.1 6.7 - - - +
98P ARG* 3.6 8.5 - - - +
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Residues in contact with ASP 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98M ARG* 4.0 14.0 - - - +
102M ARG* 3.8 20.1 - - - +
105M ASP* 4.6 9.0 - - - +
51O LEU* 4.3 6.7 - - - +
52O VAL 3.2 2.8 + - - +
54O ARG* 1.3 122.4 + - - +
56O ASN* 1.3 74.7 + - - +
91P LYS* 5.4 1.4 + - - -
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Residues in contact with ASN 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M ARG* 3.9 5.2 - - - -
105M ASP* 5.0 5.8 - - - +
52O VAL* 2.9 36.0 + - + +
53O LEU* 3.2 11.3 - - - +
54O ARG 3.5 0.4 - - - -
55O ASP* 1.3 93.0 - - - +
57O THR* 1.3 64.6 + - - +
58O PHE 3.4 17.2 + - - +
61O SER* 2.9 29.3 + - - +
102O ARG* 3.1 13.3 + - - -
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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