Contacts of the helix formed by residues 50 - 59 (chain S) 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 GLY 50 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38S LEU* 5.0 0.2 - - - -
47S ARG 2.8 15.9 + - - -
48S LYS 3.1 2.7 - - - -
49S LYS* 1.3 79.5 - - - +
51S ALA* 1.3 60.6 + - - -
52S ASP 3.4 2.5 - - - -
53S VAL* 3.3 4.4 + - - -
54S TRP* 3.0 31.0 + - - -
102S GOL 3.6 13.5 - - - -
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Residues in contact with ALA 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ARG* 5.6 2.0 - - + +
34S LEU* 4.0 3.1 - - - +
35S LYS* 4.0 24.0 - - + +
38S LEU* 3.7 24.7 - - + +
47S ARG 4.6 1.0 + - - -
50S GLY* 1.3 68.8 - - - -
52S ASP* 1.3 64.0 + - - +
54S TRP* 3.4 1.7 + - - +
55S PHE* 2.8 30.2 + - - +
102S GOL 3.1 29.1 + - - +
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Residues in contact with ASP 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ARG* 3.0 46.3 + - - +
51S ALA* 1.3 75.6 - - - +
53S VAL* 1.3 68.2 + - + +
55S PHE* 3.7 2.1 - - - +
56S LYS* 3.0 24.6 + - - +
102S GOL 2.9 29.5 + - - +
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Residues in contact with VAL 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S LYS* 3.4 47.3 - - + +
50S GLY* 3.3 2.9 + - - +
51S ALA 3.2 0.4 - - - -
52S ASP* 1.3 80.5 - - + +
54S TRP* 1.3 62.7 + - - +
56S LYS* 3.4 5.1 + - - +
57S GLU* 3.1 32.5 + - + +
102S GOL 5.3 1.1 - - - +
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Residues in contact with TRP 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S LEU* 4.2 6.1 - - + -
38S LEU* 3.9 26.9 - - + -
46S ILE* 2.9 56.1 + - + +
47S ARG* 5.0 0.9 - - - -
49S LYS* 3.3 42.2 - - + +
50S GLY 3.0 23.9 + - - +
51S ALA 3.7 4.5 - - - +
53S VAL* 1.3 78.0 - - - +
55S PHE* 1.3 62.9 + - - +
57S GLU* 3.1 11.9 + - - +
58S LEU* 2.9 50.6 + - + +
74S LEU* 3.7 25.4 - - + -
77S LYS* 4.1 31.2 - - + -
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Residues in contact with PHE 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S VAL 3.9 3.4 - - - -
30S TYR 3.8 4.7 - - - -
31S ARG* 3.5 61.2 - - + +
34S LEU* 3.6 15.0 - - + +
51S ALA 2.8 21.6 + - - +
52S ASP* 3.7 4.5 - - - +
54S TRP* 1.3 74.8 - - - +
56S LYS* 1.3 58.5 + - - +
58S LEU* 3.2 1.5 + - - -
59S ASP* 2.9 49.9 + - + +
64S GLY* 3.4 31.4 - - - -
65S ALA* 3.7 2.5 - - - -
66S VAL* 3.8 25.4 - - + -
103S GOL 3.8 18.2 - - - -
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Residues in contact with LYS 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ARG* 5.8 2.2 - - - +
52S ASP 3.0 16.3 + - - +
53S VAL* 3.8 5.6 - - - +
54S TRP 3.3 0.2 - - - -
55S PHE* 1.3 81.7 - - + +
57S GLU* 1.3 62.6 + - + +
59S ASP* 3.8 13.3 + - - +
62S THR* 6.0 0.7 - - + +
77U LYS* 5.5 4.5 + - - -
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Residues in contact with GLU 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S LYS* 2.9 43.3 + - - +
53S VAL* 3.1 21.2 + - + +
54S TRP* 3.1 18.4 + - + +
56S LYS* 1.3 79.0 - - + +
58S LEU* 1.3 62.5 + - + +
60S ILE* 3.4 21.5 - - - +
73S ILE* 5.0 2.9 - - + +
77S LYS* 4.0 12.9 + - - +
77U LYS* 5.2 2.3 + - - +
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Residues in contact with LEU 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S LEU* 4.2 26.9 - - + -
54S TRP* 2.9 39.2 + - + +
55S PHE 4.1 0.2 - - - +
57S GLU* 1.3 77.6 - - + +
59S ASP* 1.3 60.1 + - - +
60S ILE* 2.9 13.7 + - - +
66S VAL* 3.9 21.1 - - + -
70S GLU* 3.2 44.7 - - - +
71S PHE* 5.4 0.7 - - + -
73S ILE* 3.8 16.6 - - + -
74S LEU* 3.7 37.7 - - + +
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Residues in contact with ASP 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S PHE* 2.9 34.0 + - + +
56S LYS* 3.8 10.3 + - - +
57S GLU 3.4 0.4 - - - -
58S LEU* 1.3 73.2 - - - +
60S ILE* 1.3 63.1 + - - +
61S ASN* 3.1 4.2 - - - +
62S THR* 3.1 19.9 + - + +
63S ASP* 3.0 12.1 + - - +
64S GLY* 2.8 27.0 + - - -
65S ALA 3.5 12.3 - - - +
66S VAL* 4.8 0.4 - - + -
70S GLU* 3.6 3.4 - - - -
101S CA 2.3 31.3 - - - -
77U LYS* 5.3 1.0 - - - -
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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