Contacts of the helix formed by residues 23 - 39 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M SER 3.5 13.9 - - - +
22M PHE* 1.3 77.3 - - - +
24M LYS* 1.3 60.4 + - - +
25M GLU* 3.6 10.2 + - - +
26M GLN* 2.9 38.1 + - - +
27M SER* 2.9 27.7 + - - -
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Residues in contact with LYS 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M THR* 1.3 74.4 - - - +
25M GLU* 1.3 56.5 - - - +
27M SER* 3.4 8.5 + - - -
28M ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M THR* 3.7 9.8 - - - +
24M LYS* 1.3 77.1 - - - +
26M GLN* 1.3 61.7 + - + +
28M ALA* 3.3 5.9 + - - +
29M GLN* 2.9 52.7 + - - +
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Residues in contact with GLN 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M SER* 3.8 3.4 + - - -
22M PHE* 3.4 25.3 - - + +
23M THR* 2.9 49.3 + - - +
25M GLU* 1.3 75.9 - - + +
27M SER* 1.3 60.6 - - - +
29M GLN* 3.3 4.7 + - - +
30M ALA* 2.9 25.5 + - - +
60M VAL* 2.7 47.0 - - + +
61M SER* 3.2 23.2 - - - +
62M THR* 3.6 8.5 - - - +
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Residues in contact with SER 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M TYR* 5.2 5.9 - - - -
22M PHE* 3.5 18.4 - - - -
23M THR 2.9 13.6 + - - -
24M LYS* 3.5 12.6 - - - -
25M GLU 3.3 0.2 - - - -
26M GLN* 1.3 77.5 - - - +
28M ALA* 1.3 56.4 + - - +
30M ALA* 3.1 5.4 + - - +
31M ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K SER 5.9 1.3 - - - +
22K PHE* 4.3 13.2 - - + +
27K SER* 5.5 3.6 - - - +
24M LYS 2.9 17.8 + - - +
25M GLU* 3.7 7.6 - - - +
26M GLN 3.3 0.2 - - - -
27M SER* 1.3 74.3 - - - +
29M GLN* 1.3 58.2 + - + +
31M ALA* 3.4 7.9 + - - +
32M GLN* 3.0 46.9 + - - +
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Residues in contact with GLN 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLU* 2.9 45.3 + - - +
26M GLN* 3.7 7.9 - - - +
28M ALA* 1.3 75.1 - - + +
30M ALA* 1.3 64.5 + - - +
32M GLN* 3.2 17.5 + - - +
33M TRP* 3.1 38.0 + - + +
52M VAL* 5.8 2.6 - - - +
59M ILE 4.4 11.8 - - - +
60M VAL* 4.4 9.6 - - + +
61M SER* 4.7 8.3 + - - -
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Residues in contact with ALA 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M TYR* 5.6 6.7 - - + +
22M PHE* 4.5 10.3 - - + -
26M GLN 2.9 14.0 + - - +
27M SER* 3.1 11.6 + - - +
29M GLN* 1.3 74.2 - - - +
31M ALA* 1.3 57.5 + - - +
33M TRP* 3.3 3.5 + - - +
34M GLU* 2.9 29.3 + - - +
60M VAL* 4.3 11.1 - - + +
68M THR* 3.7 26.3 + - - +
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Residues in contact with ALA 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M SER 3.0 15.8 + - - +
28M ALA* 3.5 9.0 - - - +
30M ALA* 1.3 78.2 - - - +
32M GLN* 1.3 61.4 + - + +
34M GLU* 3.4 7.3 + - - +
35M SER* 3.1 23.4 + - - -
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Residues in contact with GLN 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K PHE 3.2 25.1 + - - +
23K THR* 3.4 4.7 + - - -
24K LYS* 3.2 36.0 - - + +
27K SER* 4.3 4.2 + - - -
28M ALA* 3.0 28.8 + - - +
29M GLN* 3.2 20.0 + - - +
31M ALA* 1.3 78.1 - - + +
33M TRP* 1.3 63.1 + - + +
35M SER* 3.2 11.2 + - - -
36M VAL* 3.1 27.7 + - + +
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Residues in contact with TRP 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M GLN* 3.1 33.0 + - + +
30M ALA 3.8 2.5 - - - +
32M GLN* 1.3 76.8 - - + +
34M GLU* 1.3 63.8 + - - +
36M VAL* 3.3 21.7 + - + +
37M LEU* 3.0 29.9 + - + +
42M ILE* 5.4 4.7 - - + -
45M HIS* 4.0 22.9 - - + -
48M GLN* 4.0 22.7 - - + -
49M LEU* 3.7 48.9 - - + -
52M VAL* 4.6 10.6 - - + +
59M ILE* 3.5 28.9 + - + +
60M VAL* 5.3 1.1 - - + -
68M THR* 3.8 24.2 - - + -
72M VAL* 4.5 20.0 - - + -
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Residues in contact with GLU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M ALA 2.9 17.6 + - - +
31M ALA* 3.4 7.8 + - - +
32M GLN 3.4 0.2 - - - -
33M TRP* 1.3 75.5 - - - +
35M SER* 1.3 57.7 + - - +
37M LEU* 3.1 13.3 + - + +
38M LYS* 2.9 32.9 + - + +
68M THR* 5.4 0.8 - - - +
71M HIS* 5.3 11.7 - - - +
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Residues in contact with SER 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M ALA 3.1 14.0 + - - -
32M GLN* 3.2 15.1 + - - -
33M TRP 3.2 0.4 - - - -
34M GLU* 1.3 72.8 - - - +
36M VAL* 1.3 68.0 + - - +
38M LYS* 3.2 37.9 + - - +
39M SER* 3.1 21.0 + - - -
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Residues in contact with VAL 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M GLN* 3.1 19.5 + - + +
33M TRP* 3.3 24.4 + - + +
35M SER* 1.3 79.3 + - - +
37M LEU* 1.3 61.2 + - + +
39M SER* 3.4 4.1 + - - -
40M GLY 3.3 2.3 + - - -
41M GLN* 3.0 57.4 + - + +
42M ILE* 3.8 9.0 - - + +
45M HIS* 3.5 37.2 - - + +
48M GLN* 5.6 0.7 - - - +
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Residues in contact with LEU 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G GLN* 3.7 5.7 - - - +
79G LEU* 5.1 1.0 - - - +
33M TRP* 3.0 18.8 + - + +
34M GLU* 3.1 16.8 + - + +
36M VAL* 1.3 79.1 - - + +
38M LYS* 1.3 63.5 + - - +
40M GLY* 3.0 15.0 + - - -
42M ILE* 4.9 11.7 - - + +
68M THR* 4.9 1.8 - - + +
71M HIS* 3.2 54.1 - - + +
72M VAL* 3.9 22.4 - - + +
75M VAL* 4.0 21.1 - - + -
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Residues in contact with LYS 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G GLN* 3.9 3.7 + - - +
78G PRO* 5.7 3.4 - - + +
79G LEU* 3.7 28.4 - - + +
82G ASP* 3.1 40.5 + - + +
83G LEU* 6.1 0.5 - - - +
34M GLU* 2.9 27.5 + - + +
35M SER* 3.2 31.9 + - - +
37M LEU* 1.3 77.3 - - - +
39M SER* 1.3 76.0 + - - +
40M GLY 3.3 1.0 + - - -
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Residues in contact with SER 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G GLN* 4.1 6.5 + - - -
82G ASP* 3.1 13.9 + - - -
83G LEU* 5.8 4.0 - - - +
86G SER* 5.3 4.2 - - - -
35M SER 3.1 12.6 + - - -
36M VAL* 3.7 5.8 - - - -
38M LYS* 1.3 102.8 + - - +
40M GLY* 1.3 62.0 + - - +
41M GLN* 3.3 26.8 + - - +
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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