Contacts of the helix formed by residues 31 - 40 (chain K) in PDB entry 4QOC
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29K ARG 3.6 0.2 + - - -
30K PRO* 1.3 78.2 - - - +
32K PRO* 1.3 77.8 - - + +
33K LEU* 3.4 3.4 - - + +
34K LEU 3.3 3.8 + - - +
35K LEU* 3.0 17.0 + - - +
104K TYR 4.8 1.2 + - - -
105K ARG* 2.9 29.4 + - - +
106K ASN* 2.9 23.9 + - + +
107K LEU* 4.0 19.4 + - - +
108K VAL* 4.3 16.8 - - + -
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Residues in contact with PRO 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K PRO 4.6 0.7 - - - +
31K LYS* 1.3 89.6 - - + +
33K LEU* 1.3 66.9 + - + +
35K LEU* 3.4 8.8 + - + +
36K LYS* 3.0 28.8 + - - +
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Residues in contact with LEU 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K LYS* 3.4 2.4 - - + +
32K PRO* 1.3 85.8 - - + +
34K LEU* 1.3 66.7 + - - +
36K LYS* 3.3 16.9 + - + +
37K LEU* 3.0 20.8 + - - +
81K LEU* 4.7 19.6 - - + +
85K LEU* 4.6 17.2 - - + +
106K ASN* 5.6 2.9 - - - +
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Residues in contact with LEU 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K PRO* 3.7 20.4 - - + -
31K LYS* 3.3 8.2 + - - +
33K LEU* 1.3 78.9 - - - +
35K LEU* 1.3 53.5 + - - +
37K LEU* 2.9 7.7 + - + +
38K LEU* 2.8 52.3 + - + +
53K VAL* 4.5 12.8 - - + -
57K LEU* 4.2 25.1 - - + -
85K LEU* 4.2 18.7 - - + +
86K PHE* 6.0 1.6 - - + -
103K ILE* 5.2 3.8 - - + +
106K ASN* 3.4 43.6 - - + +
107K LEU* 4.6 6.5 - - + -
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Residues in contact with LEU 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K PRO* 3.9 17.0 - - + +
31K LYS 3.0 17.7 + - - +
32K PRO* 3.6 9.2 - - + +
34K LEU* 1.3 76.9 - - - +
36K LYS* 1.3 57.9 + - - +
38K LEU* 3.1 5.7 + - + +
39K LYS* 2.9 45.3 + - + +
45K LYS 3.4 23.8 - - - +
46K ASP* 3.4 28.0 - - + +
48K TYR* 3.8 20.0 - - + +
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Residues in contact with LYS 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K PRO 3.0 17.7 + - - +
33K LEU* 3.5 16.8 - - + +
35K LEU* 1.3 76.6 - - - +
37K LEU* 1.3 61.6 + - - +
39K LYS* 3.5 7.1 + - - +
40K SER* 3.1 25.9 + - - -
81K LEU* 5.9 7.5 - - + +
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Residues in contact with LEU 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K LEU 3.0 12.7 + - - +
34K LEU* 2.9 12.4 + - + +
36K LYS* 1.3 75.6 - - - +
38K LEU* 1.3 78.1 + - + +
40K SER* 2.6 23.8 + - - -
41K VAL* 3.6 6.1 + - - +
56K TYR 5.0 0.7 - - - +
57K LEU* 4.0 21.3 - - + -
60K TYR* 3.7 59.2 - - + +
81K LEU* 4.5 15.6 - - + +
82K LEU* 4.7 4.0 - - + -
85K LEU* 3.7 22.9 - - + -
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Residues in contact with LEU 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K PRO* 3.7 31.0 - - + -
34K LEU* 2.8 37.8 + - + +
35K LEU* 3.1 7.4 + - - +
37K LEU* 1.3 78.3 - - + +
39K LYS* 1.3 61.6 - - - +
41K VAL* 3.0 23.1 + - - +
43K ALA* 3.1 24.7 + - + +
48K TYR* 4.1 17.5 - - + +
53K VAL* 4.2 19.1 - - + +
56K TYR* 3.3 27.8 - - + -
57K LEU* 4.1 10.1 - - + +
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Residues in contact with LYS 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K LEU* 2.9 33.1 + - + +
36K LYS* 4.1 5.8 - - - +
38K LEU* 1.3 70.4 - - - +
40K SER* 1.3 57.8 + - - +
41K VAL 3.0 10.4 + - - -
42K GLY* 3.1 11.3 + - - -
43K ALA* 3.3 26.5 + - + +
44K GLN* 4.6 6.2 + - - +
45K LYS 3.6 26.7 - - - +
46K ASP* 3.2 19.5 + - - -
48K TYR* 4.4 1.6 - - - +
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Residues in contact with SER 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K LYS* 3.1 19.1 + - - -
37K LEU* 2.6 22.2 + - - -
39K LYS* 1.3 77.0 - - - +
41K VAL* 1.3 64.6 + - - +
42K GLY 3.6 0.7 - - - -
60K TYR* 4.3 10.6 - - - -
64K LYS* 4.6 12.0 + - - -
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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