Contacts of the strand formed by residues 69 - 74 (chain C) in PDB entry 4PAR
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 ILE 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C TYR* 3.7 1.8 - - - -
64C PHE* 2.9 45.2 + - + +
67C LEU* 3.3 26.9 - - + +
68C GLY* 1.3 78.8 - - - +
70C HIS* 1.3 68.8 + - - +
71C ILE* 5.0 2.2 - - + -
119C LYS* 3.7 23.8 - - - +
121C PHE* 3.8 31.4 - - + -
149C GLU* 4.8 2.7 - - + +
150C ILE* 4.5 25.4 - - + +
153C ALA* 3.7 29.6 - - + -
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Residues in contact with HIS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLN* 4.5 0.4 - - + -
50C VAL* 4.0 19.7 - - + -
60C THR* 2.9 34.5 + - + +
62C LEU 3.3 4.3 - - - +
63C TYR* 3.2 45.0 - + - +
69C ILE* 1.3 74.3 - - - +
71C ILE* 1.3 69.0 + - - +
113C ILE* 4.5 1.8 - - + -
115C ILE* 4.0 6.1 - - + +
118C HIS* 3.4 34.4 + + + -
119C LYS 2.9 9.5 + - - -
120C ILE* 3.7 24.4 - - + -
121C PHE* 2.9 27.6 + - - -
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.9 4.5 - - + -
30C VAL* 6.1 1.8 - - + -
33C ILE* 3.7 29.4 - - + -
60C THR* 4.4 0.7 - - - -
61C ASP* 3.4 8.5 + - + +
62C LEU* 2.9 44.3 + - + +
64C PHE* 4.0 17.7 - - + -
69C ILE* 5.0 2.0 - - + -
70C HIS* 1.3 81.4 - - - +
72C GLU* 1.3 65.7 + - - +
73C VAL* 5.5 1.6 - - + -
121C PHE* 3.4 13.7 - - + +
123C VAL* 4.4 10.1 - - + -
146C ILE* 3.6 40.2 - - + -
150C ILE* 4.0 16.8 - - + -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LYS* 3.9 13.9 - - - +
59C LEU 4.4 4.7 - - - +
60C THR* 5.1 6.1 - - + -
61C ASP* 3.9 8.3 - - - +
71C ILE* 1.3 78.0 - - - +
73C VAL* 1.3 68.5 + - - +
74C ASP* 3.7 1.0 + - - -
95C PRO* 3.3 18.6 - - + +
96C LEU* 2.8 33.4 + - - +
97C TYR* 2.8 22.9 + - - +
120C ILE* 4.5 8.0 - - + +
121C PHE 2.9 10.2 + - - +
122C ARG* 3.2 30.1 + - + +
123C VAL* 2.9 23.0 + - - +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LYS* 3.6 25.3 + - + -
25C TYR* 4.7 2.7 - - + -
26C GLU* 4.3 18.2 - - - +
29C VAL* 4.0 37.2 - - + -
30C VAL* 5.4 1.3 - - + -
61C ASP* 3.1 17.7 + - + +
71C ILE* 5.5 2.0 - - + -
72C GLU* 1.3 77.4 - - - +
74C ASP* 1.3 59.0 + - - +
75C GLU* 3.9 15.7 - - - +
97C TYR* 3.2 23.9 + - - -
123C VAL* 3.6 11.4 - - + +
125C VAL* 4.8 4.3 - - + -
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Residues in contact with ASP 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLU* 3.7 2.6 + - - +
73C VAL* 1.3 69.6 - - - +
75C GLU* 1.3 62.8 + - - +
76C GLY* 3.6 4.6 + - - -
87C TYR* 2.6 33.1 + - - -
96C LEU* 3.6 18.9 - - + +
97C TYR* 3.7 3.6 - - - -
122C ARG* 4.8 10.8 - - + -
123C VAL 2.8 12.4 + - - +
124C ASN* 2.8 29.9 - - - +
125C VAL* 3.2 27.5 + - - +
126C PHE 4.6 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