Contacts of the strand formed by residues 399 - 401 (chain K) in PDB entry 1UW9
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 CYS 399 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K LEU* 3.3 16.4 - - + -
170K LEU 4.0 3.4 - - - -
171K GLY* 3.7 22.0 - - - -
199K PHE* 4.1 8.1 - - - -
239K TYR* 3.5 23.3 - - - +
325K HIS* 4.8 4.9 - - + -
375K MET* 4.1 7.5 - - + +
376K PRO 2.9 7.1 + - - -
377K VAL* 3.2 20.7 - - + +
378K ALA 2.8 25.5 + - - -
398K ALA* 1.3 73.0 - - - +
400K LEU* 1.3 63.0 + - - +
401K GLN* 4.0 8.3 - - - -
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Residues in contact with LEU 400 (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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168K GLY* 5.4 3.6 - - - -
169K LEU 2.8 14.7 + - - +
170K LEU* 3.3 13.8 - - + +
171K GLY 2.8 22.0 + - - +
378K ALA* 3.4 25.6 - - + +
382K ILE* 4.8 0.2 - - + -
387K MET* 3.7 28.5 - - - -
390K LEU* 4.1 26.2 - - + +
391K VAL* 4.6 5.4 - - + -
394K PHE* 4.4 7.0 - - + -
395K GLY 5.8 0.9 - - - +
398K ALA* 4.3 17.5 - - + +
399K CYS* 1.3 75.9 - - - +
401K GLN* 1.3 61.2 + - - +
402K PHE* 3.7 15.7 - - + -
424K LEU* 4.1 17.3 - - + -
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Residues in contact with GLN 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K GLY* 3.3 19.3 - - - -
172K CYS* 3.9 5.7 - - - +
173K THR* 4.3 2.3 + - - +
201K KCX 3.3 20.9 - - - +
239K TYR* 2.8 45.9 + - - -
292K HIS* 4.0 0.2 - - - -
327K HIS* 3.7 4.7 - - - -
377K VAL* 3.4 26.4 - - + +
378K ALA 2.8 9.9 + - - -
379K SER* 3.3 31.8 + - - +
380K GLY 4.2 2.4 + - - -
382K ILE* 3.3 22.5 - - - +
399K CYS* 4.0 2.9 - - - -
400K LEU* 1.3 74.4 - - - +
402K PHE* 1.3 65.8 + - - +
403K GLY 4.0 2.0 + - - +
1478R CAP 4.3 1.5 + - - +
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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