Contacts of the strand formed by residues 57 - 64 (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 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C PHE* 4.2 20.6 - - + -
50C VAL 3.9 6.5 - - - +
51C ARG* 4.5 12.8 - - - +
55C LYS 5.0 1.3 - - - +
56C LYS* 1.3 74.4 - - - +
58C ALA* 1.3 68.8 + - - +
98C SER* 3.4 2.9 - - - -
99C ILE* 2.7 54.4 + - + +
104C SER* 3.1 46.3 + - - +
107C MET* 4.2 10.5 - - + -
108C ARG* 4.8 1.3 - - + +
112C ILE* 3.8 30.5 - - + -
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Residues in contact with ALA 58 (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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49C PHE* 3.5 3.6 - - - -
50C VAL* 2.8 35.0 + - + -
52C LEU* 3.6 25.6 - - + -
56C LYS 3.8 0.6 + - - -
57C ILE* 1.3 79.4 - - - +
59C LEU* 1.3 64.7 + - - +
95C PRO* 3.5 21.5 - - + -
97C TYR 3.3 18.4 - - - +
98C SER* 3.9 1.8 - - - +
99C ILE* 5.5 0.2 - - - -
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASN* 3.9 28.5 - - - +
23C LYS* 4.7 2.7 + - - +
47C GLN* 4.5 6.3 - - - +
48C GLN 3.3 10.8 - - - +
49C PHE* 3.9 26.2 - - + -
50C VAL* 4.5 0.9 - - - -
58C ALA* 1.3 78.1 - - - +
60C THR* 1.3 67.2 + - - +
61C ASP* 4.0 17.3 - - - +
72C GLU* 4.4 5.4 - - - +
85C MET* 4.0 35.9 - - + -
95C PRO* 3.8 14.2 - - - +
97C TYR* 3.6 9.5 + - - +
98C SER* 5.9 0.9 - - - -
99C ILE* 4.9 11.9 - - + -
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Residues in contact with THR 60 (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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47C GLN* 3.0 6.9 + - - -
48C GLN* 2.9 41.5 + - - +
50C VAL* 4.3 8.5 - - + -
59C LEU* 1.3 79.9 - - - +
61C ASP* 1.3 64.2 + - - +
62C LEU 4.3 4.2 + - - -
63C TYR* 4.3 0.2 - - - +
70C HIS* 2.9 47.3 + - + +
71C ILE 4.5 4.7 - - - -
72C GLU* 5.1 7.6 - - + -
95C PRO* 4.2 12.8 - - + -
115C ILE* 5.9 0.2 - - + -
120C ILE* 4.2 17.0 - - + -
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Residues in contact with ASP 61 (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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22C ASN* 5.2 0.9 + - - +
23C LYS* 2.7 38.5 + - - -
26C GLU* 3.9 33.1 - - + +
30C VAL* 3.9 11.6 - - + +
46C THR* 3.3 26.9 - - - +
47C GLN* 3.4 4.9 + - - +
59C LEU* 4.0 8.5 - - - +
60C THR* 1.3 77.0 - - - +
62C LEU* 1.3 61.9 + - - +
71C ILE* 3.4 10.9 + - + +
72C GLU* 4.5 1.7 - - - +
73C VAL* 3.1 28.9 + - + +
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Residues in contact with LEU 62 (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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30C VAL* 4.0 25.1 - - + -
33C ILE* 4.1 24.2 - - + -
34C ILE* 4.3 6.3 - - + -
44C PHE* 3.7 30.3 - - + -
45C VAL 3.4 14.6 - - - +
46C THR* 3.8 12.6 - - + -
60C THR* 3.5 2.1 + - - -
61C ASP* 1.3 79.3 - - - +
63C TYR* 1.3 62.3 + - - +
64C PHE* 4.0 28.0 - - + -
69C ILE 4.0 0.2 - - - +
70C HIS* 3.3 6.9 + - - +
71C ILE* 2.9 47.8 + - + +
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Residues in contact with TYR 63 (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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44C PHE* 3.2 4.8 - - - -
45C VAL* 2.6 45.6 + - + +
48C GLN* 3.5 33.0 - - + -
62C LEU* 1.3 75.8 - - - +
64C PHE* 1.3 78.0 + - - +
65C PRO* 3.2 38.4 + - + +
68C GLY* 4.2 4.7 - - - -
69C ILE 3.7 4.9 - - - -
70C HIS* 3.2 36.1 - + - +
113C ILE* 3.4 23.6 - - + +
118C HIS* 3.4 21.6 + + - -
188C ASN* 4.2 8.3 + - - -
286C ARG* 4.9 7.6 - - - -
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Residues in contact with PHE 64 (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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33C ILE* 4.7 2.2 - - + -
34C ILE* 4.2 10.5 - - + -
37C LEU* 3.8 28.3 - - + -
39C ASP 5.8 0.2 - - - -
42C LEU* 4.2 22.4 - - + -
43C LYS 3.4 15.5 - - - +
44C PHE* 3.7 15.5 - - + -
62C LEU* 4.0 21.3 - - + -
63C TYR* 1.3 73.1 - - - +
65C PRO* 1.3 58.0 - - - +
66C GLN* 3.4 1.3 - - + +
67C LEU* 3.3 20.5 + - + -
68C GLY* 2.8 29.8 + - - -
69C ILE* 2.9 29.5 + - + +
71C ILE* 4.0 16.6 - - + -
150C ILE* 3.6 26.5 - - + -
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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