Contacts of the helix formed by residues 23 - 39 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21P SER 4.9 2.5 - - - +
22P PHE* 1.3 75.2 - - - +
24P LYS* 1.3 60.3 + - - +
25P GLU* 3.6 8.9 + - - +
26P GLN* 3.0 42.9 + - - +
27P SER* 2.9 28.2 + - - -
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Residues in contact with LYS 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P THR* 1.3 72.3 - - - +
25P GLU* 1.3 56.8 + - - +
27P SER* 4.0 4.1 - - - -
28P ALA* 3.0 29.6 + - - +
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Residues in contact with GLU 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P THR* 3.1 7.7 + - - +
24P LYS* 1.3 77.8 - - - +
26P GLN* 1.3 62.1 + - + +
28P ALA* 3.9 4.9 - - - +
29P GLN* 3.0 41.7 + - - +
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Residues in contact with GLN 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P SER 3.8 3.6 - - - +
22P PHE* 3.2 26.2 - - + -
23P THR* 3.0 40.6 + - - +
25P GLU* 1.3 73.8 - - - +
27P SER* 1.3 60.4 + - - +
29P GLN* 3.2 4.8 + - - +
30P ALA* 2.9 27.7 + - - +
60P VAL* 2.8 42.1 + - + +
61P SER* 3.2 21.9 + - - -
62P THR* 4.0 10.9 - - - +
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Residues in contact with SER 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P PHE* 3.1 33.3 + - - +
23P THR 2.9 15.4 + - - -
24P LYS* 4.0 5.2 - - - -
26P GLN* 1.3 76.5 - - - +
28P ALA* 1.3 62.2 + - - +
30P ALA* 3.7 2.5 + - - +
31P ALA* 3.2 21.8 + - - +
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Residues in contact with ALA 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P LYS 3.0 21.1 + - - +
25P GLU* 4.0 7.4 - - - +
26P GLN 3.2 0.2 - - - -
27P SER* 1.3 76.0 - - - +
29P GLN* 1.3 60.0 + - + +
31P ALA* 3.2 9.9 + - - +
32P GLN* 2.8 43.7 + - - +
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Residues in contact with GLN 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P GLU* 3.0 29.0 + - - +
26P GLN* 3.2 6.9 + - - +
28P ALA* 1.3 76.0 - - + +
30P ALA* 1.3 60.5 + - - +
32P GLN* 3.4 23.2 + - - +
33P TRP* 3.0 46.4 + - + +
52P VAL* 6.0 1.0 - - - +
59P ILE 4.6 9.9 - - - +
60P VAL* 5.1 8.6 - - + -
61P SER* 5.2 4.5 + - - -
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Residues in contact with ALA 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P PHE* 3.8 23.1 - - + -
26P GLN 2.9 15.8 + - - +
27P SER 3.8 4.7 - - - +
29P GLN* 1.3 74.5 - - - +
31P ALA* 1.3 64.7 + - - +
33P TRP* 3.3 3.8 + - - +
34P GLU* 3.0 23.6 + - - +
60P VAL* 4.4 4.8 - - + +
68P THR* 3.4 29.9 + - - +
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Residues in contact with ALA 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P SER 3.2 12.8 + - - +
28P ALA* 3.2 11.6 + - - +
30P ALA* 1.3 79.1 - - - +
32P GLN* 1.3 61.4 + - + +
34P GLU* 3.3 16.9 + - - +
35P SER* 3.0 22.2 + - - -
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Residues in contact with GLN 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P ALA* 2.8 35.9 + - - +
29P GLN* 3.5 27.6 + - - +
30P ALA 3.2 0.4 - - - -
31P ALA* 1.3 74.2 - - + +
33P TRP* 1.3 57.9 + - + +
35P SER* 2.4 27.5 + - - -
36P VAL* 3.0 16.5 + - + +
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Residues in contact with TRP 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P GLN* 3.0 36.6 + - + +
30P ALA 3.8 0.2 - - - +
32P GLN* 1.3 77.4 - - + +
34P GLU* 1.3 56.8 + - - +
36P VAL* 3.3 23.2 + - + +
37P LEU* 2.9 33.7 + - - +
42P ILE* 4.5 6.7 - - + -
45P HIS* 4.2 22.0 - + + -
48P GLN* 4.5 15.5 - - + -
49P LEU* 3.7 48.0 - - + -
52P VAL* 4.2 17.8 - - + +
59P ILE* 3.3 29.4 + - + +
60P VAL* 5.0 1.3 - - + -
68P THR* 3.6 24.5 - - + -
72P VAL* 4.4 17.3 - - + -
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Residues in contact with GLU 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P ALA 3.0 13.4 + - - +
31P ALA* 3.5 17.3 - - - +
33P TRP* 1.3 76.7 - - - +
35P SER* 1.3 58.9 + - - +
37P LEU* 3.4 13.3 + - + +
38P LYS* 2.8 53.4 + - + +
68P THR* 5.5 0.2 - - - +
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Residues in contact with SER 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P ALA 3.0 12.4 + - - -
32P GLN* 2.4 28.6 + - - -
34P GLU* 1.3 74.7 - - - +
36P VAL* 1.3 60.3 + - - +
38P LYS* 3.6 8.3 - - - +
39P SER* 2.7 43.0 + - - -
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Residues in contact with VAL 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P GLN* 3.0 16.1 + - + +
33P TRP* 3.3 20.9 - - + +
35P SER* 1.3 83.5 + - - +
37P LEU* 1.3 58.6 + - - +
39P SER* 3.0 10.6 + - - -
41P GLN* 2.9 49.2 + - - +
42P ILE* 3.5 26.9 + - + -
45P HIS* 3.9 33.7 - - + +
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Residues in contact with LEU 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P TRP* 2.9 24.1 + - + +
34P GLU* 3.6 10.8 - - + +
36P VAL* 1.3 74.6 - - - +
38P LYS* 1.3 64.8 + - + +
40P GLY* 3.0 13.9 + - - -
42P ILE* 3.6 22.2 - - + -
68P THR* 5.3 1.3 - - + +
71P HIS* 3.7 29.2 - - + +
72P VAL* 3.9 13.7 - - + -
75P VAL* 3.1 37.7 - - + -
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Residues in contact with LYS 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P GLU* 2.8 46.6 + - + +
35P SER* 3.2 8.0 + - - +
37P LEU* 1.3 72.5 - - - +
39P SER* 1.3 59.8 + - - +
40P GLY 3.5 0.7 + - - -
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Residues in contact with SER 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P SER* 2.7 26.5 + - - -
36P VAL* 3.0 12.6 + - - -
38P LYS* 1.3 70.8 - - - +
40P GLY* 1.3 60.3 + - - +
41P GLN* 3.3 35.5 + - - +
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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