Contacts of the strand formed by residues 45 - 51 (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 VAL 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C TYR* 3.8 10.8 - - - +
16C GLN* 3.8 5.4 - - - +
43C LYS* 4.6 7.6 - - - -
44C PHE* 1.3 80.5 - - - +
46C THR* 1.3 74.8 + - - +
47C GLN 4.2 0.2 + - - -
48C GLN* 3.4 30.7 - - + +
62C LEU* 3.4 3.0 - - - +
63C TYR* 2.6 52.6 + - + +
65C PRO* 4.3 15.0 - - + -
278C ASN* 3.6 25.4 - - + +
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Residues in contact with THR 46 (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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16C GLN* 2.7 42.1 + - - +
17C LEU* 4.6 0.9 - - + -
19C ARG* 2.7 41.1 + - - -
26C GLU* 5.1 2.5 - - - +
30C VAL* 4.0 15.9 - - + -
44C PHE* 4.5 7.2 - - + -
45C VAL* 1.3 77.8 - - - +
47C GLN* 1.3 73.6 + - - +
48C GLN 3.2 3.0 + - - -
61C ASP 3.3 14.6 - - - +
62C LEU* 3.8 13.5 - - + -
278C ASN* 5.8 0.3 - - - +
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Residues in contact with GLN 47 (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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19C ARG* 3.5 31.5 + - - +
20C THR* 2.9 29.8 + - - +
21C LYS* 4.4 0.4 - - - +
22C ASN* 3.2 33.0 + - - +
26C GLU* 3.5 24.9 + - - +
46C THR* 1.3 77.6 - - - +
48C GLN* 1.3 64.7 + - - +
49C PHE* 3.4 16.1 + - + -
59C LEU* 4.6 8.1 - - + -
60C THR 3.0 17.3 + - - -
61C ASP* 3.4 5.3 + - - +
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Residues in contact with GLN 48 (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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45C VAL* 3.4 26.3 - - + +
46C THR 3.2 2.4 - - - -
47C GLN* 1.3 76.3 - - - +
49C PHE* 1.3 94.7 + - - +
50C VAL* 3.6 6.2 + - + +
59C LEU* 3.3 2.4 - - - -
60C THR* 2.9 39.6 + - - +
63C TYR* 3.5 37.1 - - + -
111C ASP* 3.4 23.8 + - - +
113C ILE* 3.9 24.8 - - + +
278C ASN* 5.0 5.5 + - - +
286C ARG* 5.6 1.7 + - - -
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Residues in contact with PHE 49 (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* 3.4 11.5 + - + -
48C GLN* 1.3 96.0 + - - +
50C VAL* 1.3 60.5 + - - +
57C ILE* 4.2 11.7 - - + -
58C ALA 3.5 4.3 - - - +
59C LEU* 3.9 33.2 - - + -
99C ILE* 4.3 8.1 - - + -
107C MET* 3.8 24.9 - - + -
110C GLU* 3.5 43.1 - - + -
111C ASP 3.3 14.6 + - - +
112C ILE* 4.1 12.6 - - + -
113C ILE* 3.3 13.0 + - - +
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Residues in contact with VAL 50 (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* 3.7 11.0 - - + +
49C PHE* 1.3 79.3 - - - +
51C ARG* 1.3 60.4 - - - +
52C LEU* 3.6 4.4 + - + -
57C ILE* 3.9 4.3 - - - -
58C ALA* 2.8 59.7 + - + +
59C LEU* 4.2 0.7 - - - +
60C THR* 4.3 5.8 - - + -
70C HIS* 4.0 18.2 - - + -
95C PRO* 3.9 18.8 - - + -
112C ILE* 3.7 5.4 - - - +
113C ILE* 3.6 8.1 - - + -
115C ILE* 3.5 30.7 - - + -
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Residues in contact with ARG 51 (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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50C VAL* 1.3 71.0 - - - +
52C LEU* 1.3 76.8 + - - +
53C SER 4.0 0.2 + - - -
55C LYS* 3.9 24.9 + - - +
56C LYS 4.5 2.4 + - - -
57C ILE* 4.5 8.1 - - - +
108C ARG* 6.2 0.4 - - - +
112C ILE* 3.6 43.1 + - + +
113C ILE 2.8 22.4 + - - +
114C SER* 4.7 0.2 - - - -
115C ILE* 3.8 20.3 - - - +
238C ILE* 3.9 30.1 + - - +
239C SER 4.9 0.9 - - - +
240C PRO* 3.6 37.3 - - + +
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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