Contacts of the strand formed by residues 67 - 71 (chain C) in PDB entry 1YKN
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 PHE 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 4.0 26.2 - - + -
18C HIS* 4.7 2.0 - + - +
21C LEU* 3.6 50.7 - - + -
22C ALA* 4.6 11.9 - - + -
36C TRP* 5.1 0.2 - + - -
66C SER* 1.3 75.8 - - - +
68C LEU* 1.3 63.5 + - - +
69C GLU* 3.7 22.9 - - + -
94C ARG* 3.4 42.4 - - + -
95C THR 3.7 10.8 - - - -
96C ALA* 4.4 1.3 - - + +
129C SER 3.9 0.5 - - - +
130C LEU* 3.8 0.3 - - - -
131C PHE* 3.0 59.3 + + + +
475D ILE* 4.7 2.5 - - + -
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Residues in contact with LEU 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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55C VAL* 4.6 1.8 - - + -
66C SER* 3.7 21.8 - - - +
67C PHE* 1.3 81.9 - - - +
69C GLU* 1.4 64.5 + - - +
70C VAL* 4.9 4.5 - - + -
94C ARG* 3.3 6.6 - - - +
95C THR* 2.8 48.1 + - + +
96C ALA* 4.8 0.9 - - - -
97C THR* 4.9 0.4 - - + -
104C TRP* 3.6 54.7 - - + +
128C ILE* 4.5 17.9 - - + -
129C SER 3.3 8.5 - - - +
130C LEU* 4.0 15.9 - - + -
187C ILE* 4.9 7.9 - - + -
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE* 3.7 15.8 - - + -
68C LEU* 1.4 74.6 - - - +
70C VAL* 1.4 64.8 + - - +
92C PHE* 3.8 21.0 - - + -
93C GLY 3.5 5.4 - - - -
94C ARG* 2.8 48.3 + - - -
127C ASN 3.8 0.2 - - - +
128C ILE* 3.5 4.2 - - - +
129C SER* 2.8 40.0 + - - +
131C PHE* 4.0 7.5 - - + -
473D LYS* 2.9 39.3 + - - +
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Residues in contact with VAL 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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39C LEU* 4.0 17.7 - - + -
68C LEU* 4.9 9.0 - - + -
69C GLU* 1.4 83.1 - - - +
71C TRP* 1.3 62.8 + - - +
92C PHE* 3.2 12.7 - - - -
93C GLY* 3.1 34.3 + - - +
95C THR* 5.4 0.7 - - + -
104C TRP* 6.2 2.5 - - + -
106C LEU* 3.9 35.2 - - + -
126C ILE* 4.0 13.7 - - + -
127C ASN 3.1 7.4 - - - +
128C ILE* 4.1 19.5 - - + -
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Residues in contact with TRP 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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70C VAL* 1.3 77.5 - - - +
72C GLN* 1.3 60.2 + - - +
79C TYR* 3.3 32.5 - + + -
80C GLN 3.8 18.4 - - - -
81C ASP* 3.9 7.6 - - + -
91C SER* 3.3 37.0 - - - -
92C PHE* 3.7 15.5 - + + -
127C ASN* 2.8 50.3 + - + +
344D SER 3.4 21.6 + - - -
347D THR* 3.1 32.2 + - - -
348D GLY* 3.3 28.5 - - - -
349D PRO* 3.5 21.8 - - + -
470D ILE* 3.6 28.3 - - + -
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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