Contacts of the helix formed by residues 31 - 40 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I ARG 3.6 1.8 + - - +
30I PRO* 1.3 74.9 - - - +
32I PRO* 1.3 80.0 - - + +
33I LEU 3.5 1.8 - - - +
34I LEU 3.0 5.4 + - - +
35I LEU* 2.9 18.8 + - - -
105I ARG 4.3 11.2 + - - +
106I ASN* 3.0 32.7 + - + +
107I LEU* 4.0 13.0 + - - +
108I VAL* 3.9 26.3 - - + +
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Residues in contact with PRO 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I PRO 4.0 0.2 - - - -
31I LYS* 1.3 91.0 - - + +
33I LEU* 1.3 58.6 + - - +
35I LEU* 3.2 7.7 + - + +
36I LYS* 2.9 29.2 + - - +
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Residues in contact with LEU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I LYS* 3.5 1.4 - - - +
32I PRO* 1.3 79.2 - - - +
34I LEU* 1.3 62.2 + - - +
36I LYS* 3.4 15.3 + - + -
37I LEU* 3.2 38.3 + - + +
81I LEU* 4.0 20.2 - - + +
84I ASP* 4.3 9.9 - - + -
85I LEU* 3.6 44.9 - - + +
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Residues in contact with LEU 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I PRO* 3.7 23.6 - - + -
31I LYS* 3.0 9.5 + - - +
33I LEU* 1.3 78.1 - - - +
35I LEU* 1.3 64.0 + - - +
37I LEU* 3.3 3.8 + - + +
38I LEU* 3.1 29.9 + - + +
53I VAL* 4.4 6.5 - - + -
57I LEU* 4.3 28.3 - - + -
85I LEU* 3.6 30.3 - - + +
103I ILE* 4.3 22.4 - - + -
106I ASN* 3.6 30.5 - - + +
107I LEU* 4.5 3.8 - - + -
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Residues in contact with LEU 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I PRO* 3.5 36.9 - - + +
31I LYS 2.9 11.6 + - - +
32I PRO* 3.5 10.5 - - + +
34I LEU* 1.3 75.5 - - - +
36I LYS* 1.3 66.8 + - - +
38I LEU* 3.0 5.6 + - + +
39I LYS* 2.8 60.3 + - + +
45I LYS 3.8 18.8 - - - +
46I ASP* 4.5 9.6 - - + +
48I TYR* 3.9 8.3 - - + +
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Residues in contact with LYS 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I PRO 2.9 15.4 + - - +
33I LEU* 3.7 20.2 - - + +
34I LEU 3.3 0.2 - - - -
35I LEU* 1.3 76.8 - - - +
37I LEU* 1.3 65.9 + - + +
39I LYS* 3.2 7.7 + - - +
40I SER* 3.0 23.2 + - - -
81I LEU* 4.5 18.4 - - + -
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Residues in contact with LEU 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I LEU* 3.2 17.7 + - + +
34I LEU* 3.6 6.5 - - - +
35I LEU 3.2 0.6 - - - -
36I LYS* 1.3 81.8 - - + +
38I LEU* 1.3 59.8 + - - +
40I SER* 2.7 24.6 + - - -
41I VAL* 3.7 7.6 - - - +
57I LEU* 4.9 8.7 - - + -
60I TYR* 3.7 36.9 - - + +
81I LEU* 3.8 35.2 - - + -
82I LEU* 4.1 26.9 - - + +
85I LEU* 3.9 26.9 - - + -
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Residues in contact with LEU 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I PRO* 3.9 28.9 - - + -
34I LEU* 3.1 24.8 + - + +
35I LEU* 3.0 9.7 + - - +
37I LEU* 1.3 73.5 - - - +
39I LYS* 1.3 62.6 + - + +
41I VAL* 3.0 18.7 - - - +
43I ALA* 3.0 31.8 + - + +
48I TYR* 4.4 15.3 - - + +
53I VAL* 4.0 27.8 - - + +
56I TYR* 3.3 30.3 - - + -
57I LEU* 4.0 14.8 - - + +
60I TYR* 6.3 0.2 - - + -
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Residues in contact with LYS 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ASP* 3.7 26.6 + - - +
35I LEU* 2.8 54.7 + - + +
36I LYS* 3.6 7.0 - - - +
38I LEU* 1.3 72.7 - - + +
40I SER* 1.3 58.6 + - - +
41I VAL 3.0 5.2 - - - -
42I GLY* 2.8 21.3 + - - -
43I ALA* 3.3 22.3 - - + +
44I GLN 4.3 0.2 - - - -
45I LYS 3.4 26.9 - - - +
48I TYR* 3.8 7.4 - - - +
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Residues in contact with SER 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I LYS* 3.0 13.9 + - - -
37I LEU* 2.7 19.7 + - - -
39I LYS* 1.3 75.7 - - - +
41I VAL* 1.3 57.1 + - - +
42I GLY 3.4 0.9 - - - -
60I TYR* 3.3 25.4 - - - -
64I LYS* 5.9 1.9 - - - -
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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