Contacts of the helix formed by residues 27 - 44 (chain D) in PDB entry 5HP1
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 27 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C ILE* 4.1 27.8 - - + -
384C GLY 3.5 12.8 - - - +
385C LYS* 5.3 2.2 - - - -
386C THR* 6.0 0.2 - - - +
26D LEU* 1.3 76.5 - - - +
28D GLU* 1.3 65.4 + - - +
29D GLU* 3.5 14.1 + - - +
30D LYS* 3.1 32.4 + - + +
31D ILE* 3.0 21.5 + - - +
404D GLU* 4.0 19.1 - - - +
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Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C TYR* 5.3 3.3 + - - -
383C TRP 4.5 5.7 - - - +
384C GLY* 2.8 21.9 + - - +
385C LYS* 5.2 8.5 - - + +
27D THR* 1.3 72.5 - - - +
29D GLU* 1.3 64.8 + - - +
31D ILE* 3.4 2.6 + - - +
32D LYS* 3.0 54.8 + - + +
135D ILE* 3.7 32.6 - - + +
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D THR* 3.5 16.2 + - - +
28D GLU* 1.3 81.4 - - - +
30D LYS* 1.3 60.8 + - + +
32D LYS* 3.5 8.8 + - - +
33D ALA* 3.1 28.4 + - - +
64D LYS* 5.2 1.7 + - - -
71D TRP* 3.6 39.7 + - + +
404D GLU* 4.2 15.9 - - - +
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Residues in contact with LYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 4.2 22.9 - - + -
27D THR* 3.1 30.3 + - + +
29D GLU* 1.3 82.7 - - + +
31D ILE* 1.3 61.2 + - - +
33D ALA* 3.3 6.0 + - - +
34D LEU* 3.0 34.6 + - - +
61D PHE* 4.2 4.0 - - + -
62D ALA* 2.5 47.2 + - + +
63D ILE* 4.7 1.2 - - - +
71D TRP* 4.3 15.7 - - + -
403D THR* 3.6 29.8 + - - -
404D GLU* 3.3 26.9 + - - +
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 3.6 36.8 - - + +
27D THR 3.0 14.9 + - - +
28D GLU* 3.9 4.9 - - - +
30D LYS* 1.3 75.2 - - - +
32D LYS* 1.3 64.9 + - + +
34D LEU* 3.3 5.4 + - - +
35D VAL* 2.9 36.5 + - + +
132D ILE* 4.6 2.5 - - + -
133D PRO* 3.7 31.6 - - + +
134D SER* 4.0 5.2 - - - -
135D ILE* 3.8 35.2 - - + +
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Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLU* 3.0 51.9 + - + +
29D GLU* 3.8 7.6 - - - +
31D ILE* 1.3 78.8 - - + +
33D ALA* 1.3 63.1 + - - +
35D VAL* 3.5 4.9 + - - +
36D GLU* 3.2 25.1 + - - +
135D ILE* 5.7 2.2 - - - +
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Residues in contact with ALA 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU 3.1 16.3 + - - +
30D LYS 3.7 4.7 - - - +
31D ILE 3.3 0.2 - - - -
32D LYS* 1.3 78.1 - - - +
34D LEU* 1.3 57.2 + - - +
36D GLU* 4.0 5.3 - - - +
37D ILE* 3.0 36.1 + - + +
62D ALA* 4.3 6.1 - - + -
71D TRP* 3.3 48.0 - - + -
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 3.6 31.6 - - + -
30D LYS 3.0 17.0 + - - +
31D ILE* 3.9 4.3 - - - +
33D ALA* 1.3 74.4 - - - +
35D VAL* 1.3 58.6 + - - +
37D ILE* 4.4 2.5 - - + -
38D CYS* 2.7 42.5 + - - +
60D VAL* 4.0 17.9 - - + -
61D PHE* 3.6 31.2 - - - +
62D ALA* 4.3 7.4 - - + -
73D LYS* 3.7 33.9 - - + -
132D ILE* 4.3 18.6 - - + -
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 2.9 30.0 + - + +
32D LYS* 4.0 4.7 - - - +
34D LEU* 1.3 76.4 - - - +
36D GLU* 1.3 58.9 + - - +
38D CYS* 3.8 0.9 - - - +
39D THR* 2.9 42.0 + - - +
132D ILE* 4.1 27.1 - - + -
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LYS 3.2 14.4 + - - +
33D ALA* 4.0 6.0 - - - +
35D VAL* 1.3 81.7 - - - +
37D ILE* 1.3 68.9 + - + +
39D THR* 3.2 8.0 + - - +
40D GLU* 3.1 22.8 + - + +
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Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA* 3.0 28.2 + - + +
34D LEU* 3.8 5.6 - - + +
36D GLU* 1.3 81.5 - - + +
38D CYS* 1.3 60.4 + - - +
40D GLU* 3.3 7.0 + - - +
41D MET* 2.9 46.5 + - + +
62D ALA* 5.6 0.4 - - + -
71D TRP* 3.8 34.1 - - + +
72D ARG 4.4 0.7 - - - +
73D LYS* 4.2 33.9 - - + +
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Residues in contact with CYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 2.7 30.2 + - - +
35D VAL* 4.0 2.0 - - - +
37D ILE* 1.3 71.5 - - - +
39D THR* 1.3 60.1 + - - +
41D MET* 3.7 3.3 - - - +
42D GLU* 2.9 31.2 + - - +
47D ILE* 3.8 15.2 - - + +
73D LYS* 4.3 18.6 - - - -
130D PHE* 3.9 24.9 - - - -
132D ILE* 3.5 27.8 - - + -
144D TYR* 4.4 11.1 - - + +
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Residues in contact with THR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D VAL* 2.9 30.5 + - - +
36D GLU* 3.2 8.4 + - - +
38D CYS* 1.3 75.7 - - - +
40D GLU* 1.3 64.2 + - - +
42D GLU* 3.2 11.4 + - - +
43D LYS* 3.0 53.6 + - + +
144D TYR* 5.4 2.7 + - - -
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLU* 3.1 10.8 + - + +
37D ILE* 3.7 8.5 - - - +
39D THR* 1.3 82.0 - - - +
41D MET* 1.3 62.8 + - + +
43D LYS* 3.5 18.9 + - - +
44D GLU* 3.2 53.0 + - - +
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Residues in contact with MET 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ILE* 2.9 38.0 + - + +
38D CYS* 3.8 7.0 - - - +
39D THR 3.2 0.4 - - - -
40D GLU* 1.3 77.9 - - + +
42D GLU* 1.3 61.7 + - - +
44D GLU* 3.2 8.9 + - - +
45D GLY 3.2 3.1 + - - -
46D LYS* 3.0 55.7 + - + +
47D ILE* 3.7 17.6 + - + -
73D LYS* 4.2 15.5 - - - -
116D PHE* 4.0 21.8 - - + -
146D TYR* 3.8 32.1 - - + +
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Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D CYS 2.9 17.8 + - - +
39D THR* 3.7 8.1 - - - +
41D MET* 1.3 76.0 - - - +
43D LYS* 1.3 64.2 + - - +
45D GLY* 3.1 13.3 + - - -
47D ILE* 3.6 23.4 - - + +
48D SER* 4.7 4.2 - - - -
49D LYS* 3.1 51.9 + - - +
144D TYR* 4.0 13.7 + - + -
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Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D THR* 3.0 41.1 + - + +
40D GLU* 3.7 22.9 - - - +
42D GLU* 1.3 77.2 - - + +
44D GLU* 1.3 61.1 + - + +
45D GLY 3.4 0.7 + - - -
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLU* 3.2 43.1 + - - +
41D MET* 3.2 7.9 + - - +
42D GLU 3.1 0.8 - - - -
43D LYS* 1.3 79.0 - - + +
45D GLY* 1.3 56.6 + - - +
46D LYS* 3.2 48.6 + - + +
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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
------------------------------------------------------------
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