Contacts of the strand formed by residues 92 - 96 (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 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.6 29.4 - - + -
36C TRP 4.9 0.2 - - - +
39C LEU* 3.9 13.0 - - - +
69C GLU* 3.8 40.4 - - + -
70C VAL 3.2 19.7 - - - -
71C TRP* 3.7 17.0 - + + -
83C TYR* 3.4 28.6 + + + -
90C ASN* 3.2 4.3 - - - +
91C SER* 1.3 80.9 - - - +
93C GLY* 1.4 64.3 + - - +
94C ARG* 4.0 11.7 - - - -
349D PRO* 3.6 28.7 - - + -
351D PHE* 3.7 24.9 - + - -
470D ILE* 5.3 6.5 - - + -
473D LYS* 5.7 0.4 - - - -
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Residues in contact with GLY 93 (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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35C ILE* 4.7 2.2 - - - -
36C TRP 3.5 12.6 - - - -
39C LEU* 3.9 11.9 - - - -
69C GLU* 3.5 5.2 - - - +
70C VAL* 3.1 34.5 + - - +
92C PHE* 1.4 86.5 - - - +
94C ARG* 1.3 65.3 + - - +
106C LEU* 5.0 0.2 - - - -
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Residues in contact with ARG 94 (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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21C LEU* 3.6 22.2 + - - +
35C ILE* 3.8 47.4 + - + +
36C TRP* 3.0 35.1 + - + +
37C ASN* 3.2 6.7 + - - +
67C PHE* 3.4 22.4 - - + -
68C LEU 3.3 10.1 - - - +
69C GLU* 2.8 43.3 + - - -
70C VAL* 5.9 0.2 - - - -
92C PHE* 4.0 11.9 - - + -
93C GLY* 1.3 74.9 - - - -
95C THR* 1.3 63.5 + - - +
106C LEU* 4.6 2.5 - - - -
351D PHE* 5.5 1.2 - - - -
396D LEU* 4.9 3.6 - - - +
398D GLU* 2.8 42.6 + - - -
473D LYS* 3.8 9.1 - - - +
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Residues in contact with THR 95 (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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36C TRP* 3.8 14.7 - - - -
37C ASN* 4.0 5.9 + - - +
67C PHE* 3.6 5.2 - - - -
68C LEU* 2.8 49.6 + - + +
70C VAL* 5.4 0.7 - - + -
94C ARG* 1.3 76.9 - - - +
96C ALA* 1.3 72.9 + - - +
104C TRP* 3.5 29.1 - - + +
105C THR 2.9 25.3 + - - -
106C LEU* 3.8 20.0 - - + -
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Residues in contact with ALA 96 (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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18C HIS* 3.6 23.6 - - + +
22C ALA* 4.6 0.9 - - + -
36C TRP* 3.7 22.7 - - + -
66C SER 3.5 15.7 - - - +
67C PHE* 4.4 3.4 - - + +
68C LEU* 4.7 1.6 - - - +
95C THR* 1.3 83.9 + - - +
97C THR* 1.3 61.5 + - - +
98C THR* 4.3 6.8 + - + +
101C ALA* 4.8 2.8 - - - +
103C GLU 4.0 2.1 - - - +
104C TRP* 3.5 21.2 - - - -
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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