Contacts of the helix formed by residues 31 - 40 (chain D) in PDB entry 5J7F
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 LYS 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ARG 3.5 1.8 + - - -
30D PRO* 1.3 74.9 - - - +
32D PRO* 1.3 80.1 - - + +
33D LEU* 4.5 15.1 - - + +
34D LEU* 3.2 7.8 + - - +
35D LEU* 2.8 18.5 + - - +
85D LEU* 4.1 20.5 - - - +
105D ARG 5.0 2.4 + - - +
106D ASN* 3.0 56.9 + - + +
107D LEU 4.4 1.1 - - - +
108D VAL* 3.5 22.2 - - + -
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Residues in contact with PRO 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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30D PRO 4.7 0.2 - - - +
31D LYS* 1.3 89.3 - - + +
33D LEU* 1.3 59.8 + - + +
35D LEU* 3.1 10.8 + - + +
36D LYS* 2.8 30.4 + - - +
108D VAL* 4.6 8.3 - - + -
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Residues in contact with LEU 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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31D LYS* 3.4 16.0 - - + +
32D PRO* 1.3 79.2 - - + +
34D LEU* 1.3 63.3 + - - +
36D LYS* 3.3 30.2 + - - +
37D LEU* 3.1 21.7 + - - +
81D LEU* 3.9 21.4 - - + +
84D ASP* 6.0 1.3 - - + -
85D LEU* 3.7 27.1 - - + -
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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 PRO* 3.8 20.0 - - + -
31D LYS* 3.2 13.4 + - + +
33D LEU* 1.3 75.4 - - - +
35D LEU* 1.3 65.1 + - - +
37D LEU* 3.3 5.6 + - + +
38D LEU* 3.1 28.3 + - + +
53D VAL* 4.8 4.7 - - + -
57D LEU* 4.0 29.8 - - + -
85D LEU* 3.8 26.4 - - + +
86D PHE* 5.6 5.2 - - + -
103D ILE* 4.6 20.0 - - + -
106D ASN* 3.6 34.8 - - + +
107D LEU* 4.7 1.3 - - + -
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Residues in contact with LEU 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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30D PRO* 3.9 19.2 - - + +
31D LYS 2.8 13.0 + - - +
32D PRO* 3.4 13.2 - - + +
34D LEU* 1.3 79.7 - - - +
36D LYS* 1.3 57.4 + - - +
38D LEU* 3.1 8.6 + - + +
39D LYS* 2.8 50.1 + - + +
45D LYS 3.4 21.8 - - - +
46D ASP* 4.1 27.1 - - - +
48D TYR* 4.2 15.3 - - + +
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Residues in contact with LYS 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 PRO 2.8 12.3 + - - +
33D LEU* 3.5 33.5 + - - +
34D LEU 3.2 0.2 - - - -
35D LEU* 1.3 72.0 - - - +
37D LEU* 1.3 68.1 + - - +
39D LYS* 3.0 11.3 + - + +
40D SER* 3.0 24.8 + - - -
81D LEU* 4.7 13.7 - - - +
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Residues in contact with LEU 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 LEU 3.1 9.6 + - - +
34D LEU* 3.4 9.2 - - + +
36D LYS* 1.3 79.3 - - - +
38D LEU* 1.3 67.8 + - + +
40D SER* 2.7 25.9 + - - -
41D VAL* 3.8 5.4 + - - +
56D TYR 5.2 0.4 - - - +
57D LEU* 3.4 28.7 - - + -
60D TYR* 4.0 36.0 - - + -
81D LEU* 3.5 26.7 - - + -
82D LEU* 4.1 24.7 - - + +
85D LEU* 3.8 13.7 - - + -
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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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30D PRO* 4.1 17.5 - - + -
34D LEU* 3.1 21.4 + - + +
35D LEU* 3.1 9.4 + - + +
37D LEU* 1.3 89.6 - - + +
39D LYS* 1.3 60.1 + - - +
41D VAL* 3.2 16.1 + - - +
43D ALA* 3.2 30.8 + - + +
48D TYR* 3.8 33.2 - - + -
53D VAL* 4.1 24.0 - - + +
56D TYR* 3.6 25.6 - - + -
57D LEU* 4.2 9.4 - - + -
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Residues in contact with LYS 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 LEU* 2.8 44.6 + - + +
36D LYS* 3.0 11.6 + - + +
38D LEU* 1.3 68.0 - - - +
40D SER* 1.3 62.9 + - - +
41D VAL 3.0 7.7 + - - -
42D GLY* 3.0 12.6 + - - -
43D ALA* 3.2 24.9 - - + +
44D GLN* 2.9 27.8 + - - -
45D LYS 3.2 14.5 + - - -
46D ASP* 4.3 7.9 + - - -
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Residues in contact with SER 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 LYS* 3.0 12.6 + - - -
37D LEU* 2.7 21.8 + - - -
39D LYS* 1.3 76.9 - - - +
41D VAL* 1.3 59.4 + - - +
42D GLY 3.5 0.4 - - - -
60D TYR* 3.9 19.6 - - - -
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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
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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