Contacts of the helix formed by residues 23 - 39 (chain T) 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 23 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T SER 4.8 2.2 - - - +
22T PHE* 1.3 76.1 - - - +
24T LYS* 1.3 65.4 + - + +
25T GLU* 3.2 32.2 - - - +
26T GLN* 2.8 26.8 + - - +
27T SER* 2.8 29.8 + - - -
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Residues in contact with LYS 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M ALA 3.2 14.4 + - - +
86M SER* 3.1 27.4 + - - +
87M SER 3.0 27.7 + - - +
88M LYS* 5.2 6.0 - - + +
90M VAL* 6.2 3.8 - - + -
23T THR* 1.3 76.7 - - + +
25T GLU* 1.3 80.2 + - - +
27T SER* 3.6 5.9 - - - -
28T ALA* 2.7 37.3 + - - +
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Residues in contact with GLU 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M ALA 4.9 1.2 - - - +
23T THR* 3.2 25.6 - - - +
24T LYS* 1.3 111.8 - - - +
26T GLN* 1.3 60.8 + - + +
28T ALA* 3.5 6.3 + - - +
29T GLN* 2.9 46.2 + - - +
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Residues in contact with GLN 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T SER 4.0 2.8 - - - +
22T PHE* 3.3 18.1 - - + -
23T THR* 2.8 41.7 + - - +
25T GLU* 1.3 76.5 - - + +
27T SER* 1.3 57.8 - - - +
29T GLN* 2.9 8.4 + - - +
30T ALA* 2.8 31.9 + - - +
60T VAL* 3.0 45.0 + - + +
61T SER* 3.5 22.0 + - - -
62T THR* 4.0 9.7 - - - +
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Residues in contact with SER 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T PHE* 3.6 24.1 - - - +
23T THR 2.8 22.1 + - - -
24T LYS* 3.6 7.0 - - - -
26T GLN* 1.3 72.5 - - - +
28T ALA* 1.3 58.1 + - - +
30T ALA* 3.2 4.2 + - - +
31T ALA* 2.9 29.4 + - - +
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Residues in contact with ALA 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T LYS 2.7 22.0 + - - +
25T GLU* 3.8 7.2 - - - +
27T SER* 1.3 73.9 - - - +
29T GLN* 1.3 58.6 + - + +
31T ALA* 3.3 8.6 + - - +
32T GLN* 2.9 27.4 + - - +
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Residues in contact with GLN 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T GLU* 2.9 35.2 + - - +
26T GLN* 2.9 10.1 + - - +
28T ALA* 1.3 74.6 - - + +
30T ALA* 1.3 64.6 + - - +
32T GLN* 2.9 37.4 - - + +
33T TRP* 3.1 19.4 + - + -
52T VAL* 5.6 4.7 - - - +
59T ILE 4.2 14.6 - - - +
60T VAL* 4.6 11.0 - - + +
61T SER* 5.1 5.0 + - - -
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Residues in contact with ALA 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T PHE* 4.0 20.9 - - + -
26T GLN 2.8 15.8 + - - +
27T SER* 3.6 8.1 - - - +
29T GLN* 1.3 73.7 - - - +
31T ALA* 1.3 64.0 + - - +
33T TRP* 3.3 2.3 + - - +
34T GLU* 3.0 22.7 + - - +
60T VAL* 4.5 7.0 - - + +
68T THR* 3.5 26.4 + - - +
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Residues in contact with ALA 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T SER 2.9 16.7 + - - +
28T ALA* 3.6 9.6 - - - +
29T GLN 3.2 0.2 - - - -
30T ALA* 1.3 77.6 - - - +
32T GLN* 1.3 60.5 + - - +
34T GLU* 3.2 9.3 - - - +
35T SER* 3.0 22.2 + - - -
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Residues in contact with GLN 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T ALA 2.9 11.0 + - - +
29T GLN* 2.9 40.8 - - - +
31T ALA* 1.3 73.2 - - - +
33T TRP* 1.3 85.2 + - - +
35T SER* 2.7 21.5 + - - -
36T VAL* 2.9 27.5 + - + +
45T HIS* 5.5 2.2 + - - -
48T GLN* 4.2 23.9 + - - +
52T VAL* 5.8 1.7 - - - +
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Residues in contact with TRP 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T GLN* 3.1 34.2 + - + +
30T ALA 3.9 0.7 - - - +
32T GLN* 1.3 91.2 + - - +
34T GLU* 1.3 66.1 + - - +
36T VAL* 3.3 9.8 + - + +
37T LEU* 3.0 29.8 + - + +
42T ILE* 4.2 24.2 - - + -
45T HIS* 3.9 26.9 - + + -
48T GLN* 4.0 18.2 - - - -
49T LEU* 3.8 44.2 - - + -
52T VAL* 4.5 14.3 - - + +
59T ILE* 3.4 29.7 + - + +
60T VAL* 5.2 0.7 - - + -
68T THR* 3.9 21.5 - - + -
72T VAL* 4.2 12.1 - - + -
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Residues in contact with GLU 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T ALA 3.0 14.9 + - - +
31T ALA* 3.2 14.4 - - - +
32T GLN 3.1 0.2 - - - -
33T TRP* 1.3 77.0 - - - +
35T SER* 1.3 58.7 + - - +
37T LEU* 3.1 14.0 + - - +
38T LYS* 2.9 36.8 + - + +
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Residues in contact with SER 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31T ALA 3.0 12.7 + - - -
32T GLN* 2.7 24.4 + - - +
34T GLU* 1.3 75.4 - - - +
36T VAL* 1.3 56.6 + - - +
38T LYS* 3.3 10.5 + - - +
39T SER* 2.9 29.7 + - - -
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Residues in contact with VAL 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32T GLN* 2.9 27.8 + - + +
33T TRP* 3.4 17.9 - - + +
35T SER* 1.3 76.3 - - - +
37T LEU* 1.3 58.5 + - - +
39T SER* 2.9 18.9 + - - -
41T GLN* 2.9 42.9 + - - +
42T ILE* 3.3 28.3 - - + -
45T HIS* 3.7 35.0 - - + +
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Residues in contact with LEU 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T TRP* 3.0 22.4 + - + +
34T GLU* 3.4 11.0 - - - +
36T VAL* 1.3 77.4 - - - +
38T LYS* 1.3 63.2 + - + +
40T GLY* 3.0 14.1 + - - -
42T ILE* 3.8 29.2 - - + -
68T THR* 6.0 0.9 - - + -
71T HIS* 3.6 49.8 - - + +
72T VAL* 4.0 12.3 - - + -
75T VAL* 3.9 15.3 - - + -
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Residues in contact with LYS 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T GLU* 2.9 26.6 + - + +
35T SER* 3.3 9.4 + - - +
37T LEU* 1.3 74.4 - - + +
39T SER* 1.3 59.7 + - - +
40T GLY 3.5 0.5 + - - -
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Residues in contact with SER 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T SER 2.9 19.0 + - - -
36T VAL* 2.9 12.8 + - - -
38T LYS* 1.3 75.7 - - - +
40T GLY* 1.3 60.3 + - - +
41T GLN* 3.5 15.1 + - - +
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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