Contacts of the helix formed by residues 31 - 39 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ARG* 4.9 12.9 + - - +
66A LEU 5.6 1.2 + - - -
68A ASP* 6.3 0.6 - - - +
71A GLN* 4.9 12.5 - - + +
76A TYR* 3.8 54.3 - - + +
29G ARG 4.5 0.2 - - - -
30G PRO* 1.3 74.3 - - - +
32G PRO* 1.3 78.2 - - + +
33G LEU* 3.3 3.4 + - + +
34G LEU 3.3 2.8 + - - +
35G LEU* 3.0 19.2 + - - +
105G ARG 3.1 26.3 + - - +
106G ASN* 2.9 25.1 + - + +
107G LEU* 3.7 23.4 + - - +
108G VAL* 4.2 3.8 - - + -
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Residues in contact with PRO 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLN* 5.5 4.9 - - + +
72A GLN* 3.0 38.6 - - + +
74A ILE* 6.3 1.8 - - + -
76A TYR* 3.6 16.8 - - - +
30G PRO 4.8 0.2 - - - +
31G LYS* 1.3 87.6 - - + +
33G LEU* 1.3 57.2 + - - +
35G LEU* 3.2 10.3 + - + +
36G LYS* 2.9 28.8 + - - +
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Residues in contact with LEU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 4.4 21.5 - - + +
71A GLN* 6.1 3.9 - - + +
72A GLN* 3.7 19.9 + - - +
31G LYS* 3.5 2.7 - - + +
32G PRO* 1.3 78.9 - - - +
34G LEU* 1.3 62.0 + - - +
36G LYS* 3.2 22.6 + - + +
37G LEU* 3.1 16.6 + - - +
81G LEU* 4.2 17.7 - - + +
84G ASP* 5.1 7.2 - - + -
85G LEU* 2.6 44.1 - - + +
106G ASN* 5.1 1.6 - - - +
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G PRO* 3.8 20.4 - - + -
31G LYS* 3.3 8.0 + - - +
33G LEU* 1.3 75.6 - - - +
35G LEU* 1.3 60.6 + - - +
37G LEU* 3.1 5.3 + - + -
38G LEU* 2.8 48.7 + - + +
53G VAL* 4.7 11.9 - - + -
57G LEU* 4.0 28.0 - - + -
85G LEU* 3.1 19.1 - - + +
86G PHE* 5.9 3.6 - - + -
103G ILE* 4.8 5.8 - - + +
106G ASN* 3.6 40.7 - - + +
107G LEU* 4.7 6.7 - - + -
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Residues in contact with LEU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G PRO* 4.1 18.8 - - + +
31G LYS 3.0 13.9 + - - +
32G PRO* 3.4 12.8 - - + +
34G LEU* 1.3 76.6 - - - +
36G LYS* 1.3 64.1 + - - +
38G LEU* 4.3 5.8 - - + -
39G LYS* 2.9 24.8 + - - +
44G GLN* 2.6 47.1 - - + +
45G LYS 4.2 11.9 - - - +
48G TYR* 3.7 23.1 - - + +
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Residues in contact with LYS 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G PRO 2.9 13.6 + - - +
33G LEU* 3.3 25.3 - - + +
34G LEU 3.2 0.2 - - - -
35G LEU* 1.3 78.4 - - - +
37G LEU* 1.3 63.4 + - - +
39G LYS* 3.7 26.0 + - - +
40G SER* 3.5 16.6 + - - -
81G LEU* 4.5 18.6 - - + +
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Residues in contact with LEU 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G LEU 3.1 8.5 + - - +
34G LEU* 3.1 10.8 + - + +
36G LYS* 1.3 79.5 - - - +
38G LEU* 1.3 71.8 + - + +
40G SER* 2.6 27.9 + - - -
41G VAL* 4.0 1.2 + - - +
56G TYR 4.7 1.6 - - - +
57G LEU* 4.0 18.6 - - + -
60G TYR* 3.5 57.8 - - + -
81G LEU* 4.0 24.1 - - + +
82G LEU* 4.0 23.1 - - + -
85G LEU* 4.6 7.6 - - + -
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Residues in contact with LEU 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G PRO* 3.6 33.4 - - + -
34G LEU* 2.8 39.9 + - + +
35G LEU* 3.2 9.2 + - + +
37G LEU* 1.3 83.6 - - + +
39G LYS* 1.3 57.3 + - - +
41G VAL* 2.8 30.9 + - - +
42G GLY* 2.9 7.4 + - - -
48G TYR* 4.2 25.4 - - + +
53G VAL* 4.2 19.5 - - + +
56G TYR* 3.5 29.6 - - + +
57G LEU* 4.5 3.8 - - + -
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Residues in contact with LYS 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G LEU 2.9 11.4 + - - +
36G LYS* 3.8 30.5 - - - +
38G LEU* 1.3 72.0 - - - +
40G SER* 1.3 60.1 + - - +
41G VAL 2.8 6.5 + - - -
42G GLY 3.3 18.0 + - - +
44G GLN* 2.5 53.2 - - + +
48G TYR* 5.4 0.4 + - - -
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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