Contacts of the strand formed by residues 161 - 165 (chain K) in PDB entry 1ZUM
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 VAL 161 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63K VAL* 4.4 6.7 - - + +
66K ALA* 4.0 7.4 - - + -
67K ARG* 3.6 46.9 - - + +
70K PHE* 5.1 0.4 - - + -
160K GLY* 1.3 70.2 - - - -
162K CYS* 1.3 61.4 + - - +
188K VAL* 3.7 16.8 - - + +
190K VAL* 3.9 27.4 - - + -
237K ASP 3.8 17.0 - - - +
238K VAL* 3.7 14.7 - - + +
239K ASP* 2.8 33.4 + - - +
240K LYS 3.2 6.2 + - - -
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Residues in contact with CYS 162 (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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159K VAL* 4.7 3.1 - - - -
160K GLY 3.8 5.2 - - - -
161K VAL* 1.3 77.2 - - - +
163K GLY* 1.3 62.6 + - - +
164K GLN* 3.6 7.6 + - + +
187K ASN* 3.7 31.9 - - - -
188K VAL 2.8 13.6 + - - +
189K VAL* 3.5 11.6 - - + -
190K VAL 3.1 22.8 + - - +
238K VAL* 4.5 0.2 - - - -
240K LYS* 3.3 20.9 - - + +
485K TYR* 3.7 31.4 - - + -
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Residues in contact with GLY 163 (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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162K CYS* 1.3 72.1 - - - +
164K GLN* 1.3 63.0 + - - +
165K ILE 4.2 0.4 - - - -
190K VAL* 3.4 10.8 - - - -
232K ILE* 3.6 24.7 - - - -
238K VAL* 3.6 8.2 - - - +
240K LYS* 2.6 15.6 + - - +
241K VAL* 3.3 4.0 - - - -
242K ALA* 2.9 27.1 + - - +
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Residues in contact with GLN 164 (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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162K CYS* 3.9 8.7 - - + +
163K GLY* 1.3 78.8 - - - +
165K ILE* 1.3 57.7 + - - +
166K ILE* 4.8 0.7 - - + -
178K LYS* 2.9 45.9 + - + +
179K LEU* 3.9 0.9 - - - +
182K ALA* 3.5 12.5 - - - +
189K VAL* 3.2 27.1 - - + +
190K VAL 3.0 10.6 + - - +
191K MET* 3.2 28.4 - - + +
192K LYS* 2.7 32.6 + - - +
232K ILE* 4.6 1.2 - - - +
242K ALA* 3.7 5.8 - - + -
485K TYR* 3.1 24.7 + - - +
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Residues in contact with ILE 165 (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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164K GLN* 1.3 76.3 - - - +
166K ILE* 1.3 67.9 - - - +
178K LYS* 4.7 0.7 - - - -
192K LYS* 3.5 34.5 - - + +
225K GLY* 6.5 0.4 - - - -
229K GLY* 3.9 26.7 - - - +
232K ILE* 4.8 6.5 - - + -
233K ALA* 5.1 3.6 - - + -
241K VAL* 4.5 16.6 - - + -
242K ALA 3.0 11.7 + - - +
243K PHE* 3.9 40.2 - - + -
244K THR* 3.4 24.8 + - - +
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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