Contacts of the strand formed by residues 64 - 69 (chain C) in PDB entry 1YCY
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 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLY 5.8 0.5 + - - -
21C VAL* 3.8 14.1 - - + -
22C SER 3.5 7.9 - - - +
23C VAL* 4.7 1.3 - - + -
41C ILE* 4.0 16.2 - - + -
59C ILE* 3.9 26.9 - - + -
60C GLY 3.8 13.7 - - - +
61C LEU* 2.9 42.8 + - + +
62C GLU 3.3 3.4 - - - +
63C ASP* 1.3 77.7 - - - +
65C ASN* 1.3 65.2 + - - +
66C TRP* 3.8 9.6 - - - +
67C ILE* 3.7 28.3 - - + -
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Residues in contact with ASN 65 (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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23A VAL* 5.4 7.2 - - + +
24A GLY* 5.4 9.3 - - - +
59A ILE* 3.8 16.8 - - - +
60A GLY 4.1 8.5 + - - -
63A ASP* 4.6 22.1 - - - +
22C SER* 2.8 33.2 + - - +
24C GLY* 3.4 31.7 + - - +
63C ASP 4.8 1.0 + - - -
64C ILE* 1.3 75.0 - - - +
66C TRP* 1.3 74.2 + - + +
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Residues in contact with TRP 66 (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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23A VAL* 4.8 12.3 - - + +
29A PHE* 3.9 32.1 - + - -
57A MSE 4.0 29.2 - - + -
58A LEU 3.2 17.3 - - - +
59A ILE* 4.5 1.6 - - + -
20C ALA* 4.1 9.0 - - + -
21C VAL* 3.5 4.8 - - - +
22C SER* 2.9 54.8 + - - +
64C ILE* 4.0 2.5 - - - -
65C ASN* 1.3 89.8 - - + +
67C ILE* 1.3 67.9 - - - +
68C MSE 3.3 47.6 - - + -
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Residues in contact with ILE 67 (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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57A MSE 3.4 4.0 - - - +
58A LEU* 2.9 39.5 + - + +
7C LEU* 5.2 3.4 - - + -
11C LEU* 4.4 22.7 - - + -
14C TRP* 3.9 19.7 - - + -
19C VAL* 4.2 19.3 - - + -
20C ALA 3.2 10.1 - - - +
21C VAL* 4.4 10.1 - - + -
33C LEU* 6.2 1.8 - - + -
41C ILE* 4.7 14.4 - - + -
61C LEU* 4.5 17.7 - - + -
64C ILE* 3.7 20.4 - - + -
66C TRP* 1.3 79.2 - - - +
68C MSE 1.3 68.0 + - - +
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Residues in contact with MSE 68 (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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29A PHE* 5.6 4.0 - - + -
46A VAL* 5.4 2.9 - - - -
53A ARG* 3.7 36.6 - - + +
54A GLY* 4.4 1.1 - - - -
56A GLN 3.3 17.7 - - - +
57A MSE 4.7 12.1 - - + +
14C TRP* 3.9 3.4 - - - -
19C VAL* 3.2 5.7 - - - -
20C ALA* 2.7 58.4 + - + +
66C TRP* 3.3 33.9 - - + -
67C ILE* 1.3 81.2 - - - +
69C LEU* 1.3 68.3 + - - +
70C LEU* 3.5 13.2 + - + +
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Residues in contact with LEU 69 (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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54A GLY* 3.8 3.8 - - - -
55A LYS* 3.3 30.1 + - + -
56A GLN* 3.4 24.9 + - + +
13C GLU 5.4 1.1 - - - +
14C TRP* 3.4 57.1 - - + +
17C HIS* 3.6 34.3 - - + -
18C LYS 3.7 6.3 - - - +
19C VAL* 4.4 5.2 - - + -
68C MSE 1.3 71.9 - - - +
70C LEU* 1.3 76.0 + - - +
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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