Contacts of the helix formed by residues 69 - 77 (chain W) in PDB entry 5K0Y
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 THR 69 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U ILE* 4.9 1.8 - - + -
171U GLU* 3.0 34.9 + - + -
67W LEU* 4.1 16.4 - - + +
68W ILE* 1.3 78.9 - - - +
70W PRO* 1.3 76.0 - - - +
71W ALA 4.3 0.7 - - - -
72W VAL* 3.3 16.3 + - - +
73W VAL* 3.4 21.8 + - - +
88W LEU* 4.0 5.2 - - - -
106W GLN* 4.3 9.4 - - - +
107W VAL 3.8 13.9 - - - +
108W ILE* 4.2 16.2 - - + -
109W TYR* 4.9 0.7 - - - -
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Residues in contact with PRO 70 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1593A G 4.2 10.5 - - + +
69W THR* 1.3 89.6 - - - +
71W ALA* 1.4 56.5 + - - +
73W VAL 3.4 0.5 + - - -
74W SER* 3.0 25.9 + - - -
81W GLY* 3.6 22.2 - - - +
84W ALA* 3.2 17.0 - - + +
85W ARG* 3.9 31.0 - - + +
88W LEU* 4.2 8.3 - - + -
106W GLN* 3.9 17.9 - - + +
107W VAL* 3.5 23.8 - - + +
109W TYR* 4.8 0.2 - - + -
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Residues in contact with ALA 71 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1593A G 5.9 0.2 - - - -
166U ILE* 3.8 25.2 - - + +
167U LYS* 3.7 22.2 - - + +
171U GLU* 3.4 28.7 - - - +
69W THR* 3.4 1.4 + - - -
70W PRO* 1.4 76.4 - - - +
72W VAL* 1.4 56.7 + - - +
74W SER* 3.4 2.9 + - - -
75W GLU* 3.0 36.9 + - - +
106W GLN* 4.2 5.2 + - - +
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Residues in contact with VAL 72 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167U LYS* 4.9 4.7 - - + -
171U GLU* 3.6 11.0 - - - +
65W TYR* 4.2 11.0 - - + -
67W LEU* 3.8 21.3 - - + +
69W THR* 3.3 26.8 + - - +
70W PRO 3.4 0.4 - - - -
71W ALA* 1.4 74.1 - - - +
73W VAL* 1.4 57.9 + - - +
75W GLU* 3.2 14.5 + - - +
76W ARG* 2.9 62.8 + - + +
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Residues in contact with VAL 73 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58W LEU* 4.0 19.5 - - + -
65W TYR* 3.9 24.2 - - + -
68W ILE* 3.8 21.5 - - + -
69W THR 3.4 14.8 + - - +
70W PRO 3.4 7.8 + - - +
72W VAL* 1.4 73.1 - - + +
74W SER* 1.4 56.7 + - - +
76W ARG 3.4 0.7 + - - +
77W LEU* 3.0 52.6 + - + +
79W ILE* 4.0 9.0 - - + -
84W ALA* 4.2 10.3 - - + +
87W ALA* 5.8 0.9 - - + -
88W LEU* 4.1 11.0 - - + -
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Residues in contact with SER 74 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166U ILE* 3.3 17.2 - - - +
46W ASN* 3.9 8.9 + - - -
70W PRO 3.0 14.1 + - - -
71W ALA* 3.4 11.4 - - - -
73W VAL* 1.4 74.6 - - - +
75W GLU* 1.4 56.7 + - - +
77W LEU 3.0 25.1 - - - +
79W ILE* 2.9 32.9 + - - +
80W ARG 2.9 13.3 + - - -
81W GLY* 3.9 14.4 - - - -
84W ALA* 4.0 0.4 - - - +
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Residues in contact with GLU 75 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165U ASN* 3.2 28.6 + - - +
166U ILE* 4.4 15.7 - - + -
167U LYS* 3.4 32.2 - - - +
46W ASN* 5.3 3.8 + - - +
71W ALA 3.0 22.9 + - - +
72W VAL* 3.5 10.0 - - - +
74W SER* 1.4 76.3 - - - +
76W ARG* 1.4 59.0 + - + +
77W LEU 3.0 12.1 - - - +
78W LYS* 5.6 0.2 - - - +
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Residues in contact with ARG 76 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103U LEU* 5.8 6.1 - - - +
57W LYS* 3.7 17.5 + - - -
61W GLU* 4.0 13.0 + - - +
64W ASN* 3.8 25.7 + - - +
65W TYR* 3.4 58.0 - - - +
67W LEU 5.3 2.0 + - - -
72W VAL* 2.9 34.7 + - + +
73W VAL 4.0 3.4 - - - +
75W GLU* 1.4 77.2 - - + +
77W LEU* 1.4 58.7 + - + +
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Residues in contact with LEU 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46W ASN* 4.9 0.3 + - - -
54W THR* 3.5 33.7 - - + +
57W LYS* 3.7 44.4 - - + +
58W LEU* 4.2 14.1 - - + +
61W GLU* 4.1 8.5 - - - +
65W TYR* 4.7 3.8 - - - +
73W VAL* 3.0 38.2 + - + +
74W SER 3.0 10.7 - - - +
75W GLU 3.0 10.0 - - - +
76W ARG* 1.4 76.8 - - - +
78W LYS* 1.4 73.3 + - - +
79W ILE* 3.8 17.0 - - + +
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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
------------------------------------------------------------
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