Contacts of the helix formed by residues 337 - 344 (chain A) in PDB entry 4NYK
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 THR 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A PHE 5.8 4.5 - - - +
154A ASN* 6.4 1.3 - - - +
335A TYR 4.6 4.0 - - - +
336A CYS* 1.3 76.6 - - - +
338A PRO* 1.3 70.8 - - + +
339A GLU* 3.6 8.1 + - - +
340A GLN* 2.8 50.5 + - - +
341A TYR* 2.8 11.2 + - - -
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Residues in contact with PRO 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A HIS* 3.3 30.7 - - + +
112A ALA* 4.1 10.3 - - + -
115A LEU* 3.8 14.6 - - + +
153A PHE* 3.5 38.4 - - + +
154A ASN* 5.9 0.4 - - - -
155A MET* 3.9 14.1 - - + +
336A CYS 3.9 0.2 - - - -
337A THR* 1.3 85.8 - - - +
339A GLU* 1.3 57.4 + - - +
341A TYR* 3.3 12.3 + - + +
342A LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A THR* 3.1 8.8 + - - +
338A PRO* 1.3 79.9 - - - +
340A GLN* 1.3 59.0 + - + +
342A LYS* 3.4 5.5 + - - +
343A GLU* 2.9 34.6 + - - +
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Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A CYS 3.5 21.9 + - - +
323A ASN* 3.8 8.9 + - - +
324A CYS* 3.4 26.9 - - + +
334A PRO* 6.2 0.5 - - - +
335A TYR 3.9 3.1 - - - +
336A CYS* 3.5 0.9 - - - -
337A THR* 2.8 45.7 + - - +
339A GLU* 1.3 77.2 - - + +
341A TYR* 1.3 54.2 + - - +
343A GLU* 5.0 0.9 - - - -
344A CYS* 2.8 19.4 + - + +
345A ALA* 2.7 32.4 + - - -
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Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 3.8 14.4 - - + -
155A MET* 3.6 33.9 - - + -
159A TYR* 4.3 9.2 - + - -
191A ARG* 6.3 1.3 - - + -
239A GLU* 3.9 18.4 - - - -
326A MET* 3.5 37.0 - - + +
327A VAL* 2.9 35.8 + - + +
328A HIS* 4.8 3.1 + + - -
336A CYS* 3.4 32.3 - - + -
337A THR 2.8 12.0 + - - -
338A PRO* 3.3 11.2 - - + +
340A GLN* 1.3 77.7 - - - +
342A LYS* 1.3 62.2 + - - +
345A ALA* 3.6 6.2 + - - -
346A ASP* 2.9 33.8 + - - +
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 6.1 2.2 - - + -
115A LEU* 3.7 22.2 - - + +
338A PRO 2.9 16.3 + - - +
339A GLU* 3.9 6.3 - - - +
341A TYR* 1.3 78.0 - - - +
343A GLU* 1.3 66.5 + - - +
346A ASP* 4.8 3.0 - - - +
347A PRO* 4.2 8.8 - - - +
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A GLU* 2.9 17.6 + - - +
340A GLN* 5.0 0.9 - - - -
342A LYS* 1.3 85.5 - - - +
344A CYS* 1.3 62.4 + - + +
347A PRO* 3.8 12.8 - - - +
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Residues in contact with CYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ASN 3.6 7.0 - - - -
322A CYS* 2.0 63.3 - - + +
340A GLN* 2.8 17.5 + - + +
342A LYS 3.7 0.4 - - - -
343A GLU* 1.3 82.6 - - + +
345A ALA* 1.3 64.0 + - - +
346A ASP 3.5 1.3 - - - -
347A PRO* 3.5 3.9 - - - +
348A ALA* 3.1 26.0 + - - +
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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