Contacts of the helix formed by residues 53 - 64 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48F TYR* 3.0 24.7 + - + +
51F SER* 3.1 16.7 - - - +
52F GLY* 1.3 76.8 - - - +
54F ALA* 1.3 63.9 + - - +
55F TYR* 3.3 42.3 + - + +
56F LYS* 3.3 31.2 + - + +
57F ALA 3.4 8.3 + - - -
533H VAL* 4.5 2.8 - - - +
534H GLU* 5.0 9.6 - - - +
565H ASN 4.5 5.5 + - - -
566H SER* 3.9 23.0 - - - -
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Residues in contact with ALA 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F TYR* 4.2 22.9 - - + +
52F GLY* 3.0 9.8 + - - +
53F LYS* 1.3 71.5 - - - +
55F TYR* 1.3 61.1 + - + +
57F ALA 3.2 2.5 + - - +
58F TYR* 3.0 24.6 + - - +
78F CYS* 3.5 9.9 - - - -
81F ASP* 3.6 24.9 - - - +
82F LEU* 3.9 16.4 - - + -
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Residues in contact with TYR 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLY 5.1 1.1 - - - -
53F LYS* 3.3 35.0 + - + -
54F ALA* 1.3 76.9 - - - +
56F LYS* 1.3 103.1 + - + +
58F TYR* 3.1 5.7 + - + +
59F ARG* 2.8 42.8 + - - +
82F LEU* 3.9 19.3 - - + +
531H TYR* 3.8 3.8 - - + -
533H VAL* 3.3 15.1 - - - +
562H MET* 3.3 47.3 - - + +
563H ASP* 3.4 36.5 + - + -
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Residues in contact with LYS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F TYR* 3.4 40.6 - - + -
53F LYS* 3.3 24.3 + - + +
54F ALA 3.2 0.4 - - - -
55F TYR* 1.3 118.4 + - + +
57F ALA* 1.3 57.5 + - - +
59F ARG* 3.3 2.3 + - - +
60F LEU* 2.9 30.7 + - - +
531H TYR* 3.3 34.8 + - + +
532H ARG* 3.6 21.1 - - - +
533H VAL* 3.3 21.8 - - - +
534H GLU* 4.4 8.3 + - - -
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F ALA* 3.2 32.3 - - + +
48F TYR* 3.8 4.7 - - + +
49F TYR* 3.8 16.4 - - + +
53F LYS 3.4 2.1 + - - +
54F ALA 3.2 8.8 + - - +
56F LYS* 1.3 79.0 - - - +
58F TYR* 1.3 56.2 + - - +
60F LEU* 3.8 5.4 - - - +
61F LEU* 2.9 35.0 + - - +
74F LEU* 4.3 1.8 - - + -
78F CYS* 3.8 15.3 - - - -
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Residues in contact with TYR 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ALA 3.0 12.8 + - - +
55F TYR* 3.4 8.1 - - - +
57F ALA* 1.3 74.9 - - - +
59F ARG* 1.3 75.9 - - + +
61F LEU* 3.4 0.3 + - - -
62F LYS* 2.7 59.2 + - + +
75F LEU* 3.9 9.5 - - + +
78F CYS* 3.8 14.1 - - + -
79F CYS* 3.6 19.5 - - - -
82F LEU* 3.4 27.4 - - + -
84F LYS* 3.3 26.1 + - + -
87F GLU* 2.6 46.6 + - - -
295Y GLU* 5.5 1.4 + - - -
299Y MET* 5.8 3.1 - - + +
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F TYR* 2.8 26.0 + - - +
58F TYR* 1.3 94.0 - - + +
60F LEU* 1.3 64.0 + - - +
62F LYS* 4.7 2.0 - - - -
63F GLY* 3.1 21.1 + - - -
84F LYS* 5.9 2.6 - - - +
530H ASN* 3.6 38.7 + - - +
531H TYR* 3.6 25.1 - - + +
558H ASP* 5.2 4.0 + - - -
562H MET* 3.2 51.1 + - - +
299Y MET* 3.9 19.6 - - + +
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F TYR* 4.4 4.9 - - + -
41F LEU* 3.7 21.4 - - + +
44F LEU* 3.5 37.7 - - + -
45F ALA* 3.7 17.5 - - + +
48F TYR* 3.6 17.3 - - + -
56F LYS 2.9 17.0 + - - +
57F ALA 3.8 3.8 - - - +
59F ARG* 1.3 75.7 - - - +
61F LEU* 1.3 64.0 + - - +
63F GLY* 3.5 0.6 + - - -
64F HIS* 3.2 41.7 + - + +
531H TYR* 3.2 34.7 - - + +
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 4.1 20.4 - - + -
45F ALA* 3.4 28.9 - - + -
57F ALA 2.9 17.1 + - - +
60F LEU* 1.3 74.7 - - - +
62F LYS* 1.3 61.4 + - - +
64F HIS 2.7 26.0 - - - +
66F CYS* 3.9 15.3 - - - -
71F CYS* 3.7 42.2 - - + +
74F LEU* 4.1 23.3 - - + -
75F LEU* 3.7 31.4 - - + +
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Residues in contact with LYS 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F TYR* 2.7 48.0 + - + +
59F ARG* 4.7 0.2 - - - -
61F LEU* 1.3 75.0 - - - +
63F GLY* 1.3 63.0 + - - +
75F LEU* 4.0 13.2 - - + +
87F GLU* 3.2 33.7 + - - +
91F ILE* 6.2 0.2 - - + -
292Y LEU* 3.4 37.3 - - + +
295Y GLU* 3.0 35.1 + - + -
296Y GLN* 3.3 26.0 - - - +
299Y MET* 4.1 23.8 - - + -
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Residues in contact with GLY 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ARG 3.1 16.0 + - - -
60F LEU 3.9 2.0 - - - -
61F LEU 3.3 0.4 - - - -
62F LYS* 1.3 76.9 - - - +
64F HIS* 1.3 64.6 + - - +
296Y GLN* 3.2 21.1 + - - +
299Y MET* 3.6 25.2 - - - -
300Y LEU* 3.3 16.9 - - - +
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Residues in contact with HIS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TYR* 3.0 32.6 + + - +
36F HIS* 4.6 12.1 + + - -
41F LEU* 3.7 26.0 - - + +
60F LEU* 3.2 37.1 + - + +
61F LEU* 2.7 23.7 - - - +
63F GLY* 1.3 81.1 - - - +
65F SER* 1.3 64.3 + - - +
66F CYS* 3.6 4.9 + - - -
531H TYR* 5.5 3.6 - + - -
269Y ASP* 3.2 23.6 - - - +
296Y GLN* 3.6 4.1 - - - +
300Y LEU* 5.3 4.3 - - + +
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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