Contacts of the strand formed by residues 58 - 63 (chain F) in PDB entry 6CP3
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 58 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F THR* 4.8 4.3 - - - +
22F ASP* 4.7 9.0 - - + -
23F VAL 3.5 15.9 - - - +
24F HIS* 3.3 13.9 + - + +
30F LEU* 3.9 4.1 - - - +
53F HIS* 3.7 2.9 - - - +
54F LEU* 2.8 44.3 + - + +
55F GLY 2.9 13.1 + - - +
56F GLU* 3.2 16.6 + - - +
57F ASN* 1.3 79.1 + - - +
59F VAL* 1.3 72.9 + - - +
13Y PHE* 5.7 6.9 - - + -
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Residues in contact with VAL 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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22F ASP* 3.4 4.5 - - - +
23F VAL* 2.9 50.3 + - + +
25F PHE* 3.7 22.2 - - + -
30F LEU* 4.0 10.5 - - + +
31F PRO 4.4 4.3 - - - +
37F LEU* 4.5 0.7 - - + -
50F VAL* 4.0 22.4 - - + -
52F GLN 3.7 4.0 - - - +
53F HIS* 3.3 34.3 - - + +
54F LEU* 5.2 0.2 - - - -
58F THR* 1.3 81.2 - - - +
60F ARG* 1.3 60.3 + - - +
61F THR* 3.9 12.6 - - + -
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Residues in contact with ARG 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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17F ILE* 4.7 11.5 - - - +
20F ILE* 4.0 16.6 - - + +
22F ASP* 3.2 39.7 + - - +
51F ALA* 3.1 9.2 + - - +
52F GLN* 2.9 61.2 + - + +
54F LEU* 3.4 32.7 - - + +
59F VAL* 1.3 74.1 - - - +
61F THR* 1.3 60.3 + - - +
271F LEU 4.1 13.5 + - - -
272F LEU* 3.7 24.2 - - + +
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Residues in contact with THR 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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20F ILE* 3.4 8.8 - - - +
21F VAL* 2.8 59.2 + - - +
23F VAL* 4.8 3.3 - - + +
37F LEU* 4.2 9.9 - - + -
48F LEU* 3.9 8.7 - - - +
49F GLU 3.2 16.6 - - - -
50F VAL* 3.6 29.4 - - + -
51F ALA* 4.0 0.9 - - - +
59F VAL* 3.9 15.7 - - + -
60F ARG* 1.3 78.1 - - - +
62F ILE* 1.3 64.7 + - - +
272F LEU* 5.4 0.2 - - - -
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Residues in contact with ILE 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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19F ALA 3.8 4.3 - - - +
20F ILE* 3.7 14.1 - - + -
48F LEU* 3.5 3.9 - - - +
49F GLU* 2.9 35.1 + - + +
51F ALA* 4.0 22.0 - - + -
61F THR* 1.3 76.4 - - - +
63F ALA* 1.3 64.2 + - - +
64F MET* 3.9 9.7 + - + +
227F GLY* 3.8 23.8 - - - -
230F ALA* 6.0 3.6 - - + -
231F ARG* 3.8 25.6 - - - +
268F VAL* 4.0 28.0 - - + -
272F LEU* 4.1 13.7 - - + -
274F ARG* 6.1 1.1 - - - +
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Residues in contact with ALA 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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19F ALA* 3.1 25.5 + - - +
21F VAL* 4.5 3.4 - - + -
48F LEU* 3.7 16.2 - - + -
62F ILE* 1.3 74.6 - - - +
64F MET* 1.3 58.0 + - - +
65F ASP* 3.1 24.2 + - - +
67F THR* 3.7 21.1 - - + -
225F PRO* 4.7 3.1 - - - +
227F GLY* 3.3 20.2 + - - -
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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