Contacts of the helix formed by residues 29 - 41 (chain D) in PDB entry 5JGH
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 SER 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D LYS 4.4 0.2 - - - -
28D ALA* 1.3 74.2 - - - +
30D LYS* 1.3 67.5 + - - +
31D ARG* 3.4 4.7 - - - -
32D THR* 4.0 1.8 - - - -
33D GLN* 3.0 26.8 + - - +
8E T 3.7 12.8 + - - -
9E T 3.6 30.1 - - - -
17F A 3.2 20.8 + - - -
18F A 3.1 19.6 + - - -
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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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29D SER* 1.3 78.5 - - - +
31D ARG* 1.3 63.5 + - + +
33D GLN* 3.8 10.2 - - - +
34D LEU* 3.2 20.4 + - - +
8E T 4.5 1.5 + - - +
9E T 3.0 35.5 + - - +
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Residues in contact with ARG 31 (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 SER* 3.4 3.6 - - - -
30D LYS* 1.3 78.3 - - + +
32D THR* 1.3 61.2 + - - +
34D LEU* 3.2 14.3 + - + +
35D ARG* 2.9 33.2 + - + +
116D PRO 6.1 0.2 - - - -
118D LYS* 2.8 31.9 - - - +
176D TYR* 3.7 20.9 + - - -
8E T 4.4 8.9 + - - -
19F T 5.8 4.3 - - - +
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Residues in contact with THR 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 ALA* 3.6 11.9 - - + -
29D SER* 3.5 3.6 + - - +
30D LYS 3.4 0.2 - - - -
31D ARG* 1.3 75.8 - - - +
33D GLN* 1.3 55.3 + - - +
35D ARG* 3.3 7.4 + - + +
36D ASN* 2.6 62.9 + - - +
18F A 2.6 39.2 + - - +
19F T 4.5 9.5 + - - +
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Residues in contact with GLN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 4.8 14.0 - - - +
28D ALA* 3.4 30.8 + - + +
29D SER 3.0 20.5 + - - +
30D LYS* 3.8 8.7 - - - +
32D THR* 1.3 75.6 - - - +
34D LEU* 1.3 51.6 + - - +
36D ASN* 3.5 6.1 - - - +
37D GLU* 2.6 61.5 + - - +
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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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30D LYS 3.2 11.6 + - - +
31D ARG* 3.2 18.7 + - + +
32D THR 3.2 0.6 - - - -
33D GLN* 1.3 78.5 - - - +
35D ARG* 1.3 51.8 + - + +
37D GLU* 3.2 14.3 + - + +
38D LEU* 2.5 63.5 + - + +
115D PRO* 4.9 10.1 - - + -
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Residues in contact with ARG 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 ARG* 2.9 22.1 + - + +
32D THR* 3.7 8.7 - - + +
34D LEU* 1.3 71.0 - - - +
36D ASN* 1.3 56.6 + - - +
38D LEU* 2.8 8.1 + - - -
39D ILE* 2.4 61.5 + - + +
111D ASP* 6.2 2.0 - - - +
114D LEU* 3.3 26.8 - - + +
115D PRO* 3.1 42.5 + - + +
116D PRO* 4.4 1.2 - - - +
117D LYS* 3.4 49.7 - - - +
19F T 5.8 2.0 - - - -
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Residues in contact with ASN 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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28D ALA* 4.1 11.7 - - - +
32D THR* 2.6 46.4 + - - +
33D GLN* 3.6 5.3 - - - +
35D ARG* 1.3 70.6 - - - +
37D GLU* 1.3 58.3 + - + +
39D ILE* 3.7 12.7 - - - +
40D LYS* 2.8 30.5 + - - +
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Residues in contact with GLU 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 GLN* 2.6 47.3 + - - +
34D LEU* 3.5 14.4 + - + +
36D ASN* 1.3 73.3 - - + +
38D LEU* 1.3 60.0 + - - +
40D LYS* 3.3 23.4 + - + +
41D GLN* 3.5 16.1 + - - +
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Residues in contact with LEU 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* 2.5 51.6 + - + +
35D ARG* 2.8 7.8 + - - +
37D GLU* 1.3 68.2 - - - +
39D ILE* 1.3 65.9 + - + +
41D GLN* 3.2 16.4 + - + +
42D GLY 3.3 0.3 + - - -
110D PHE* 3.2 26.7 - - + -
114D LEU* 5.3 6.1 - - + -
115D PRO* 4.0 28.9 - - + -
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Residues in contact with ILE 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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20B T 4.5 8.1 - - - +
35D ARG* 2.4 62.4 + - + +
36D ASN* 3.7 12.1 - - - +
38D LEU 1.3 66.5 - - - -
40D LYS* 1.3 59.3 + - - +
42D GLY* 2.8 21.7 + - - -
43D PRO 5.4 0.2 - - - +
107D LYS* 4.2 22.3 + - - +
110D PHE* 3.9 8.5 - - + -
111D ASP* 5.7 2.9 - - - +
114D LEU* 3.9 19.5 - - + -
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Residues in contact with LYS 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 ASN 2.8 17.6 + - - +
37D GLU* 3.4 12.8 - - + +
38D LEU 3.1 0.2 - - - -
39D ILE* 1.3 77.5 - - - +
41D GLN* 1.3 73.1 + - - +
42D GLY 3.4 5.7 + - - +
44D LYS* 4.9 10.4 - - - +
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Residues in contact with GLN 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 GLU 3.5 14.3 + - - +
38D LEU* 3.2 10.5 + - + +
40D LYS* 1.3 89.0 - - - +
42D GLY* 1.3 67.0 + - - +
110D PHE* 4.5 3.9 - - + -
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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