Contacts of the helix formed by residues 41 - 56 (chain Q) 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 GLN 41 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q VAL* 2.9 12.7 + - + +
39Q SER* 3.3 34.4 + - - +
40Q GLY* 1.3 76.6 - - - +
42Q ILE* 1.3 63.6 + - - +
43Q GLN 3.2 2.2 - - - -
44Q PRO* 3.2 17.2 - - + +
45Q HIS* 2.7 40.3 + - + +
88R LYS* 3.3 32.5 + - - +
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Residues in contact with ILE 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q TRP* 4.7 15.7 - - + -
36Q VAL* 3.6 12.7 + - + +
37Q LEU* 4.8 11.0 - - + -
40Q GLY* 3.4 6.0 - - - +
41Q GLN* 1.3 77.2 - - - +
43Q GLN* 1.3 67.9 + - + +
45Q HIS* 2.9 12.5 + - + -
46Q LEU* 3.1 23.9 + - + +
49Q LEU* 4.7 4.3 - - + -
72Q VAL* 4.2 25.1 - - + +
75Q VAL* 3.2 36.8 - - + -
76Q ALA* 4.7 7.0 - - + -
79Q LEU* 3.8 20.6 - - + -
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Residues in contact with GLN 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Q GLY 5.0 1.2 + - - +
41Q GLN* 4.4 0.2 - - - +
42Q ILE* 1.3 82.7 - - + +
44Q PRO* 1.3 70.7 - - + +
45Q HIS 3.1 1.2 + - - -
46Q LEU* 3.3 23.8 + - + +
79Q LEU* 3.8 34.6 - - + +
83Q LEU* 4.0 21.2 - - + +
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Residues in contact with PRO 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Q GLY 5.2 0.9 - - - +
41Q GLN* 3.2 31.6 - - + +
43Q GLN* 1.3 93.7 - - + +
45Q HIS* 1.3 60.5 + - + -
46Q LEU 3.5 0.4 + - - -
47Q ASP* 4.7 6.2 + - - +
48Q GLN 5.4 0.7 + - - -
88R LYS* 3.7 34.4 + - + +
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Residues in contact with HIS 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G LYS* 5.3 6.1 - - + -
33Q TRP* 3.8 16.7 - - + -
36Q VAL* 3.6 32.9 - - + +
41Q GLN* 2.7 36.2 + - + +
42Q ILE* 2.9 11.3 + - - +
44Q PRO* 1.3 81.3 - - + +
46Q LEU* 1.3 58.1 + - - +
47Q ASP 3.3 2.5 - - - -
48Q GLN* 3.2 28.8 + - - +
49Q LEU* 2.9 27.4 + - - +
88R LYS* 3.6 38.9 - - + +
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Residues in contact with LEU 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q ILE* 3.1 24.1 + - + +
43Q GLN* 3.3 20.0 + - + +
45Q HIS* 1.3 74.2 - - - +
47Q ASP* 1.3 68.2 + - - +
49Q LEU* 4.3 7.6 - - + -
50Q ASN* 2.9 21.0 + - - +
76Q ALA* 5.0 4.3 - - + -
79Q LEU* 3.8 22.9 - - + -
80Q ILE* 4.1 14.8 - - + -
83Q LEU* 3.5 32.5 - - + -
97Q TYR* 4.0 21.3 - - + +
100Q ILE* 3.5 25.1 - - + +
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Residues in contact with ASP 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q GLN 5.0 0.4 + - - -
44Q PRO 4.7 4.5 + - - +
45Q HIS* 3.3 1.2 - - - +
46Q LEU* 1.3 76.4 - - - +
48Q GLN* 1.3 62.7 + - - +
50Q ASN* 3.4 7.0 + - - +
51Q LEU* 3.0 18.7 + - - +
96Q THR* 4.8 0.9 - - - +
97Q TYR* 3.8 22.3 + - - -
92R SER* 3.6 20.3 - - - +
93R THR* 4.8 7.7 + - - +
96R THR* 3.5 39.5 + - - +
97R TYR* 4.6 11.3 + - - -
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Residues in contact with GLN 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G LYS* 3.4 36.2 - - - +
32Q GLN* 5.7 2.2 + - - -
33Q TRP* 4.0 21.5 - - + +
36Q VAL* 5.6 0.2 - - - +
44Q PRO 5.4 0.6 + - - -
45Q HIS* 3.2 34.6 + - - +
47Q ASP* 1.3 75.8 - - - +
49Q LEU* 1.3 65.8 + - - +
51Q LEU* 3.1 2.5 + - + +
52Q VAL* 2.9 41.7 + - + +
88R LYS* 5.0 1.9 - - + +
89R ASP* 4.1 15.5 - - + +
92R SER* 3.2 19.0 + - - +
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Residues in contact with LEU 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q TRP* 3.7 24.6 - - + -
42Q ILE* 4.7 3.8 - - + -
45Q HIS 2.9 17.3 + - - +
46Q LEU* 3.2 15.5 + - + +
48Q GLN* 1.3 76.0 - - - +
50Q ASN* 1.3 63.4 + - - +
52Q VAL* 3.4 3.0 + - + +
53Q LEU* 3.0 43.8 + - + +
59Q ILE* 3.5 33.7 - - + -
72Q VAL* 3.9 20.2 - - + -
76Q ALA* 4.6 3.4 - - + -
100Q ILE* 3.8 20.9 - - + -
103Q TRP* 4.2 12.3 - - + -
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Residues in contact with ASN 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Q LEU 2.9 16.0 + - - +
47Q ASP* 3.6 7.6 - - - +
49Q LEU* 1.3 78.8 - - - +
51Q LEU* 1.3 56.9 + - - +
54Q ARG 2.9 22.5 + - - -
95Q THR 5.5 0.2 - - - +
96Q THR 3.2 23.5 - - - +
97Q TYR* 3.3 11.1 - - + +
98Q ARG* 4.2 0.9 + - - +
99Q HIS* 2.8 60.5 + - - +
100Q ILE* 3.0 23.9 - - + +
96R THR* 5.6 2.4 + - - +
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Residues in contact with LEU 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q ASP 3.0 9.3 + - - +
48Q GLN* 3.1 2.9 + - + +
50Q ASN* 1.3 73.4 - - - +
52Q VAL* 1.3 69.1 + - + +
54Q ARG* 3.2 61.0 + - - +
55Q ASP* 3.8 6.7 + - - +
99Q HIS* 5.3 0.4 - - - -
89R ASP* 4.1 3.8 - - - +
91R LYS* 3.7 37.5 - - + +
92R SER* 3.3 35.9 - - - +
95R THR* 4.6 12.3 - - + +
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Residues in contact with VAL 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q GLN* 6.0 0.7 - - - +
33Q TRP* 4.5 11.2 - - + +
48Q GLN* 2.9 38.5 + - + +
49Q LEU* 3.7 6.7 - - + +
51Q LEU* 1.3 78.6 - - + +
53Q LEU* 1.3 61.2 + - + +
55Q ASP 3.2 0.7 + - - -
56Q ASN* 3.0 46.6 + - + +
59Q ILE* 3.4 40.8 - - + +
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Residues in contact with LEU 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q LEU* 3.0 47.3 + - + +
52Q VAL* 1.3 76.3 - - + +
54Q ARG* 1.3 58.1 + - - +
56Q ASN 3.1 17.5 + - - +
57Q THR 3.9 7.0 - - - +
58Q PHE 4.1 0.9 - - - -
59Q ILE* 4.0 21.5 - - + +
99Q HIS* 3.7 14.4 - - + +
100Q ILE* 4.0 10.3 - - - -
102Q ARG* 2.6 39.8 + - - +
103Q TRP* 3.7 50.0 - - + -
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Residues in contact with ARG 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50Q ASN 2.9 7.9 + - - +
51Q LEU* 3.2 36.6 - - - +
53Q LEU* 1.3 79.8 - - - +
55Q ASP* 1.3 87.3 + - - +
99Q HIS* 3.5 41.9 - - + +
102Q ARG* 4.2 1.7 + - - -
91R LYS* 5.0 3.8 - - - +
95R THR* 4.2 12.9 - - - +
98R ARG* 4.4 0.8 - - - +
98S ARG* 3.5 54.9 - - + +
99S HIS* 4.6 7.6 + - + -
102S ARG* 3.7 17.5 + - - +
2010S SO4 3.3 26.7 + - - -
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Residues in contact with ASP 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Q LEU* 4.3 5.7 - - - +
52Q VAL 3.2 3.1 + - - +
54Q ARG* 1.3 121.1 + - - +
56Q ASN* 1.3 75.6 + - - +
98S ARG* 3.9 13.2 + - - +
102S ARG* 3.7 22.0 - - - +
105S ASP* 4.4 9.9 - - - +
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Residues in contact with ASN 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q VAL* 3.0 35.2 + - + +
53Q LEU* 3.1 12.3 - - - +
54Q ARG 3.6 0.4 - - - -
55Q ASP* 1.3 93.2 - - - +
57Q THR* 1.3 63.1 + - - +
58Q PHE 3.5 16.3 + - - +
59Q ILE 5.4 0.2 - - - -
61Q SER* 3.0 30.0 + - - +
102Q ARG* 3.0 18.1 + - - -
102S ARG* 3.9 2.2 - - - -
105S ASP* 4.9 5.7 - - - +
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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
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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