Contacts of the helix formed by residues 53 - 64 (chain H) in PDB entry 5G04
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 53 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533F VAL* 5.5 2.4 - - - +
534F GLU* 5.4 7.6 - - - +
565F ASN 4.3 15.8 + - - -
566F SER* 4.5 10.3 - - - -
48H TYR* 3.0 24.0 + - + +
51H SER* 3.1 18.5 - - - +
52H GLY* 1.3 76.6 - - - +
54H ALA* 1.3 64.4 + - - +
55H TYR* 3.3 37.5 + - + +
56H LYS* 3.3 33.1 + - + +
57H ALA 3.4 8.1 + - - -
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Residues in contact with ALA 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H TYR* 4.3 21.3 - - + +
52H GLY* 3.0 9.9 + - - +
53H LYS* 1.3 73.3 - - - +
55H TYR* 1.3 61.7 + - + +
57H ALA 3.2 2.3 + - - +
58H TYR* 3.0 24.3 + - - +
78H CYS* 3.5 10.7 - - - -
81H ASP* 3.6 24.9 - - - +
82H LEU* 3.8 17.0 - - + -
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Residues in contact with TYR 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531F TYR* 4.1 4.3 - - + -
533F VAL* 3.7 12.1 - - - +
562F MET* 3.5 44.2 - - + +
563F ASP* 3.6 32.9 + - + -
566F SER* 4.9 0.2 + - - -
52H GLY 5.1 1.1 - - - -
53H LYS* 3.6 34.3 + - + +
54H ALA* 1.3 78.2 - - - +
56H LYS* 1.3 103.5 + - + +
58H TYR* 3.1 6.4 + - + +
59H ARG* 2.8 38.7 + - + +
82H LEU* 3.9 18.5 - - + +
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Residues in contact with LYS 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531F TYR* 3.3 34.1 + - + +
532F ARG* 3.8 18.8 - - - +
533F VAL* 3.4 21.9 - - - +
534F GLU* 4.7 7.8 + - - -
48H TYR* 3.4 45.3 - - + -
53H LYS* 3.3 24.1 + - + +
54H ALA 3.2 0.2 - - - -
55H TYR* 1.3 117.6 + - + +
57H ALA* 1.3 57.9 + - - +
59H ARG* 3.3 2.6 + - - +
60H LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H ALA* 3.2 33.0 - - + +
48H TYR* 3.8 4.4 - - + +
49H TYR* 3.8 15.7 - - + +
53H LYS 3.4 2.3 + - - +
54H ALA 3.2 8.1 + - - +
56H LYS* 1.3 80.6 - - - +
58H TYR* 1.3 56.9 + - - +
60H LEU* 3.8 5.4 - - - +
61H LEU* 2.9 35.2 + - - +
74H LEU* 4.3 2.0 - - + -
78H CYS* 3.8 15.0 - - - -
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Residues in contact with TYR 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ALA 3.0 13.3 + - - +
55H TYR* 3.1 8.5 + - + +
57H ALA* 1.3 74.5 - - - +
59H ARG* 1.3 74.1 + - + +
61H LEU 3.7 0.2 - - - -
62H LYS* 2.7 60.7 + - + +
75H LEU* 3.9 9.3 - - + +
78H CYS* 3.8 12.0 - - + -
79H CYS* 3.6 18.4 - - - -
82H LEU* 3.4 26.7 - - + -
84H LYS* 3.3 26.0 + - + -
87H GLU* 2.6 45.5 + - - -
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Residues in contact with ARG 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526F ARG* 5.1 1.8 - - - +
530F ASN* 3.2 54.8 + - - +
531F TYR* 4.1 24.8 - - + +
558F ASP* 5.4 4.4 + - - -
562F MET* 3.4 38.1 + - - +
55H TYR* 2.8 21.3 + - + +
56H LYS 3.9 2.9 - - - +
58H TYR* 1.3 91.1 - - + +
60H LEU* 1.3 64.5 + - - +
62H LYS* 4.0 2.8 - - - +
63H GLY* 3.1 21.3 + - - -
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Residues in contact with LEU 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531F TYR* 3.7 29.5 - - + +
32H TYR* 4.3 10.5 - - + -
41H LEU* 3.7 21.8 - - + +
44H LEU* 3.5 34.8 - - + -
45H ALA* 3.7 16.4 - - + +
48H TYR* 3.7 17.0 - - + -
56H LYS 2.9 15.9 + - - +
57H ALA 3.8 3.6 - - - +
59H ARG* 1.3 77.1 - - - +
61H LEU* 1.3 63.7 + - + +
63H GLY* 3.5 0.3 + - - -
64H HIS* 3.2 44.4 + - + +
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Residues in contact with LEU 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LEU* 3.7 30.3 - - + +
45H ALA* 3.3 35.7 - - + -
57H ALA 2.9 16.1 + - - +
60H LEU* 1.3 75.0 - - - +
62H LYS* 1.3 62.1 + - - +
64H HIS* 2.6 26.8 - - - +
66H CYS* 4.1 10.8 - - - -
71H CYS* 4.3 14.6 - - - +
74H LEU* 3.8 24.5 - - + -
75H LEU* 3.7 42.2 - - + +
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Residues in contact with LYS 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H TYR* 2.7 50.6 + - + +
59H ARG* 4.2 2.9 - - - +
60H LEU 3.4 0.2 - - - -
61H LEU* 1.3 74.5 - - - +
63H GLY* 1.3 62.6 + - - +
64H HIS 3.6 2.8 + - - +
75H LEU* 4.1 11.2 - - + +
87H GLU* 3.4 31.8 + - - +
248K LYS* 4.0 24.0 - - - +
439K VAL* 4.9 12.6 + - - +
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Residues in contact with GLY 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ARG 3.1 17.1 + - - -
60H LEU 3.9 1.8 - - - -
62H LYS* 1.3 78.0 - - - +
64H HIS* 1.3 67.5 + - - +
65H SER 4.0 1.2 + - - -
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Residues in contact with HIS 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531F TYR* 5.9 1.6 - + - -
32H TYR* 3.0 32.2 + + - -
36H HIS* 4.5 14.3 + + - -
41H LEU* 3.8 21.6 - - + +
60H LEU* 3.2 40.1 + - + +
61H LEU* 2.6 24.3 - - - +
62H LYS 4.1 2.5 - - - +
63H GLY* 1.3 82.9 - - - +
65H SER* 1.3 64.5 + - - +
66H CYS* 3.6 4.7 + - - +
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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