Contacts of the helix formed by residues 33 - 45 (chain V) in PDB entry 4GGF
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 ASN 33 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26V LEU* 3.6 31.6 + - - +
32V LEU* 1.3 75.9 - - - +
34V GLN* 1.3 60.5 + - - +
35V GLY* 3.2 5.4 + - - -
36V GLU* 2.9 39.5 + - - +
37V PHE* 3.0 26.9 + - - +
63V MET* 3.8 2.5 - - - -
72V LYS 4.0 7.6 - - - +
73V GLN* 3.5 17.0 + - - +
202V SO4 2.7 31.7 + - - +
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Residues in contact with GLN 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V ASN* 1.3 76.5 - - - +
35V GLY* 1.3 58.6 + - - +
37V PHE* 3.5 1.7 + - - +
38V LYS* 2.9 61.8 + - + +
60V GLU* 3.5 38.5 + - - +
63V MET* 3.7 33.3 - - + +
64V GLU* 5.6 2.1 - - - +
72V LYS 4.5 2.0 + - - +
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Residues in contact with GLY 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V LEU* 5.6 5.4 - - - -
33V ASN* 3.2 7.0 + - - -
34V GLN* 1.3 79.0 - - - +
36V GLU* 1.3 61.2 + - - +
38V LYS* 3.4 9.7 + - - +
39V GLU* 3.1 23.4 + - - +
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Residues in contact with GLU 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V TYR* 3.0 28.9 - - - +
23V SER 3.0 5.5 - - - +
25V LYS* 4.3 7.4 - - + -
26V LEU* 2.8 38.3 + - + +
31V THR 3.1 4.5 - - - +
32V LEU* 3.2 10.5 - - + -
33V ASN* 2.9 35.7 + - - +
35V GLY* 1.3 72.4 - - - +
37V PHE* 1.3 67.1 + - - +
39V GLU* 3.2 9.6 + - - +
40V LEU* 3.0 23.4 + - - +
204V CA 2.5 31.0 - - - -
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Residues in contact with PHE 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V LEU* 4.2 21.4 - - + +
33V ASN 3.0 17.2 + - - +
34V GLN 3.7 4.0 - - - +
36V GLU* 1.3 79.0 - - - +
38V LYS* 1.3 63.9 + - + +
40V LEU* 3.2 5.2 + - + +
41V VAL* 2.9 48.0 + - + +
59V ILE* 3.9 19.3 - - + -
62V ILE* 3.9 20.9 - - + -
63V MET* 3.8 44.9 - - + -
66V LEU* 4.0 5.4 - - + -
74V LEU* 3.6 21.3 - - + -
79V PHE* 4.4 8.5 - + - -
82V LEU* 3.8 18.4 - - + -
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Residues in contact with LYS 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34V GLN* 2.9 43.4 + - + +
35V GLY* 3.7 8.1 - - - +
37V PHE* 1.3 77.4 - - + +
39V GLU* 1.3 58.0 + - - +
41V VAL* 3.5 1.5 + - - +
42V ARG* 2.9 31.8 + - - +
53V ASN* 4.8 0.5 - - - +
56V GLU* 2.8 37.3 + - + +
59V ILE* 3.9 24.9 - - + -
60V GLU* 2.7 43.9 + - - +
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Residues in contact with GLU 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V TYR* 3.5 18.9 - - + -
25V LYS* 3.2 33.8 + - - +
35V GLY 3.1 16.4 + - - +
36V GLU* 3.7 7.1 - - - +
37V PHE 3.2 0.2 - - - -
38V LYS* 1.3 73.7 - - - +
40V LEU* 1.3 65.2 + - - +
42V ARG* 3.3 14.4 + - - +
43V LYS* 2.6 61.3 + - - +
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Residues in contact with LEU 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U LEU* 4.2 12.1 - - + -
18V THR* 4.0 17.3 - - + +
19V PHE* 4.3 8.1 - - - -
22V TYR* 3.8 38.9 - - + -
32V LEU* 4.3 9.9 - - + -
36V GLU 3.0 13.4 + - - +
37V PHE* 3.5 8.5 - - + +
39V GLU* 1.3 75.3 - - - +
41V VAL* 1.3 61.6 + - + +
44V ASP* 2.8 31.8 + - + +
45V LEU* 3.6 21.7 + - + -
79V PHE* 3.9 34.8 - - + -
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Residues in contact with VAL 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V PHE* 2.9 54.7 + - + +
38V LYS* 3.9 4.9 - - - +
40V LEU* 1.3 79.3 - - + +
42V ARG* 1.3 60.1 + - - +
45V LEU* 3.2 36.4 - - + -
49V LEU* 3.7 17.7 - - + -
53V ASN* 2.9 37.4 + - - +
59V ILE* 3.7 22.7 - - + -
82V LEU* 4.7 0.2 - - + -
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Residues in contact with ARG 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38V LYS 2.9 18.7 + - - +
39V GLU* 3.7 20.4 - - - +
41V VAL* 1.3 78.4 - - - +
43V LYS* 1.3 96.1 + - + +
46V GLN* 3.3 21.7 + - - +
53V ASN* 3.3 18.8 + - + +
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Residues in contact with LYS 43 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3U THR* 3.5 3.8 - - - +
22V TYR* 3.8 20.6 - - - +
39V GLU* 2.6 43.2 + - + +
42V ARG* 1.3 118.2 - - - +
44V ASP* 1.3 67.2 + - - +
45V LEU 3.4 0.2 - - - -
46V GLN* 3.0 33.9 + - - +
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Residues in contact with ASP 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U THR* 2.6 35.1 + - - +
4U GLU* 5.7 0.3 + - - +
5U LEU* 3.9 16.4 + - + +
6U GLU* 3.4 6.4 - - - +
18V THR* 3.6 21.0 - - + +
21V GLN* 4.6 2.8 - - - +
22V TYR* 2.7 43.5 + - - -
40V LEU* 2.8 16.0 + - + +
43V LYS* 1.3 78.1 - - - +
45V LEU* 1.3 59.3 + - - +
46V GLN 3.5 1.1 - - - -
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Residues in contact with LEU 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U LEU* 3.7 18.2 - - + -
6U GLU* 3.2 18.4 - - + -
9U LEU* 4.7 3.6 - - + -
40V LEU* 3.6 16.5 + - + -
41V VAL* 3.2 19.1 + - + +
44V ASP* 1.3 84.9 - - - +
46V GLN* 1.3 64.1 + - - +
47V ASN 3.1 3.6 - - - -
48V PHE* 4.2 7.2 - - + -
49V LEU* 2.9 40.5 + - + +
53V ASN* 3.5 6.9 + - - -
82V LEU* 4.2 7.2 - - + -
83V MET* 4.0 14.8 - - + -
86V LEU* 3.7 32.1 - - + -
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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