Contacts of the strand formed by residues 67 - 71 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K VAL* 3.9 31.0 - - + -
18K HIS* 4.6 3.4 - + + -
21K LEU* 3.8 44.2 - - + -
22K ALA* 4.7 11.7 - - + -
36K TRP* 5.0 0.7 - + - -
65K ASP 3.8 0.4 + - - -
66K SER* 1.3 73.7 - - - +
68K LEU* 1.4 61.7 + - - +
69K GLU* 3.4 39.3 - - + -
94K ARG* 3.5 27.1 - - + -
95K THR 3.8 7.6 - - - -
96K ALA* 4.5 0.9 - - - +
130K LEU* 3.8 1.6 - - - +
131K PHE* 2.8 59.5 + + + +
475L ILE* 4.6 2.9 - - + -
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Residues in contact with LEU 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K VAL* 5.0 1.8 - - + -
66K SER* 3.6 22.2 - - - +
67K PHE* 1.4 78.5 - - - +
69K GLU* 1.4 64.0 + - - +
70K VAL* 5.0 3.4 - - + -
94K ARG* 3.3 7.4 - - - +
95K THR* 2.9 49.9 + - + +
96K ALA* 4.7 0.2 - - - -
104K TRP* 3.8 50.3 - - + +
128K ILE* 4.0 25.1 - - + -
129K SER 3.2 6.7 - - - +
130K LEU* 4.3 12.1 - - + -
187K ILE* 4.4 11.4 - - + -
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Residues in contact with GLU 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K PHE* 3.4 23.9 - - + -
68K LEU* 1.4 72.7 - - - +
70K VAL* 1.3 62.5 + - - +
92K PHE* 3.8 21.4 - - + -
93K GLY 3.6 4.5 - - - -
94K ARG* 2.8 41.2 + - - -
127K ASN 3.9 0.3 - - - +
128K ILE* 3.5 4.3 - - - +
129K SER* 2.9 40.7 + - - +
131K PHE* 4.0 5.3 - - + -
473L LYS* 2.8 40.2 + - - +
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Residues in contact with VAL 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K LEU* 4.3 10.5 - - + -
68K LEU* 5.0 8.3 - - + +
69K GLU* 1.3 80.1 - - - +
71K TRP* 1.3 61.7 + - - +
72K GLN* 5.4 1.1 - - - +
91K SER 4.3 0.4 - - - -
92K PHE* 3.4 10.9 - - - -
93K GLY* 3.1 41.8 + - - +
95K THR* 5.2 2.2 - - + -
104K TRP* 6.1 2.0 - - + -
106K LEU* 3.8 35.4 - - + -
126K ILE* 4.0 11.7 - - + -
127K ASN 3.1 6.7 - - - +
128K ILE* 4.0 23.3 - - + -
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Residues in contact with TRP 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K VAL* 1.3 75.5 - - - +
72K GLN* 1.4 56.9 - - - +
79K TYR* 3.2 36.9 - + + -
80K GLN 3.9 15.7 - - - -
81K ASP* 3.9 8.3 - - + -
91K SER* 3.3 41.5 - - - -
92K PHE* 3.7 12.8 - - + -
126K ILE* 4.8 0.4 - - - -
127K ASN* 2.9 51.9 + - + -
344L SER 3.5 20.5 + - - -
347L THR* 3.0 34.2 + - - -
348L GLY* 3.3 27.8 - - - -
349L PRO* 3.4 22.0 - - + -
470L ILE* 3.8 24.9 - - + -
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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