Contacts of the helix formed by residues 338 - 345 (chain A) in PDB entry 5IY8
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 SER 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 4.7 4.7 - - - -
316A THR 2.4 26.8 + - - -
317A MET 3.2 15.7 + - - -
318A VAL 3.7 7.9 - - - -
320A ASN* 3.3 12.3 - - - +
336A LEU* 3.3 14.6 + - - +
337A LYS* 1.3 76.9 - - - +
339A LEU* 1.3 67.4 + - - +
340A LYS 3.3 0.7 - - - -
341A GLN* 3.1 21.0 + - - -
342A ARG* 3.0 20.6 + - - +
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Residues in contact with LEU 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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256A PRO* 5.7 4.5 - - + -
260A VAL* 5.3 6.1 - - + -
276A LEU* 4.0 22.6 - - + +
317A MET* 3.5 25.3 + - + +
318A VAL* 3.9 11.2 - - + +
338A SER* 1.3 74.5 - - - +
340A LYS* 1.3 64.0 + - - +
342A ARG* 3.3 12.9 + - - +
343A LEU* 3.2 28.1 + - - +
1161B GLU* 4.3 29.8 - - + +
1164B SER* 4.4 20.6 - - - +
1165B MET* 3.7 33.4 - - + -
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Residues in contact with LYS 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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318A VAL* 3.0 19.5 + - + +
319A ASP* 3.4 40.3 + - + +
321A GLU* 5.3 9.1 + - - +
338A SER 3.3 0.2 - - - -
339A LEU* 1.3 74.6 - - - +
341A GLN* 1.3 69.9 + - - +
343A LEU* 3.1 4.5 + - - +
344A LYS* 2.9 53.8 + - + +
1434A GLU 6.1 0.2 - - - -
1435A THR* 5.2 0.4 - - - -
1436A VAL* 3.5 37.6 - - + +
1437A ASP* 5.9 2.2 - - - +
1165B MET* 4.2 1.5 - - + +
42Y C 5.7 3.0 + - - -
43Y G 4.4 13.8 + - - -
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Residues in contact with GLN 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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319A ASP* 3.2 23.6 + - - -
320A ASN* 3.3 11.7 + - - +
321A GLU* 3.3 43.7 + - + +
336A LEU 4.9 4.7 - - - +
337A LYS* 3.8 32.3 + - + +
338A SER* 3.1 35.0 + - - +
340A LYS* 1.3 79.9 + - - +
342A ARG* 1.3 64.3 + - - +
344A LYS* 3.2 19.8 + - - +
345A GLY 4.3 2.9 + - - -
347A GLU* 4.9 5.7 - - - +
348A GLY* 4.9 1.0 - - - -
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Residues in contact with ARG 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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260A VAL* 3.9 27.1 + - - +
274A ASP* 2.9 36.6 + - - -
275A ASP* 3.7 13.1 + - - -
276A LEU* 3.9 11.9 - - - +
337A LYS* 3.1 30.4 + - + +
338A SER 3.0 13.8 + - - +
339A LEU* 3.6 22.2 - - + +
340A LYS 3.2 0.4 - - - -
341A GLN* 1.3 76.5 - - - +
343A LEU* 1.3 63.1 + - + +
347A GLU 4.7 0.2 - - - +
348A GLY* 3.0 25.8 - - - -
349A ARG* 3.1 27.9 + - + +
1070B LEU* 5.2 3.0 - - - +
1161B GLU* 4.6 9.4 + - - +
67M VAL* 4.1 14.0 - - - +
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Residues in contact with LEU 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 LEU* 3.2 17.4 + - - +
340A LYS 3.1 8.3 + - - +
342A ARG* 1.3 82.6 - - + +
344A LYS* 1.3 65.8 + - - +
345A GLY 3.8 1.4 - - - +
348A GLY* 3.6 11.0 - - - -
349A ARG* 4.1 8.7 - - + +
350A VAL* 3.8 29.8 + - + +
1435A THR* 4.3 3.1 - - - -
1436A VAL* 4.2 17.0 - - + +
1439A LEU* 5.2 4.3 - - + -
1158B LEU* 4.1 13.9 - - + -
1161B GLU* 3.5 31.6 - - + +
1162B LEU* 4.0 27.1 - - + -
1165B MET* 4.0 17.7 - - + -
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Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLU* 5.0 10.1 + - - +
340A LYS* 2.9 43.1 + - + +
341A GLN* 3.2 12.9 + - - +
343A LEU* 1.3 76.7 - - - +
345A GLY* 1.3 65.9 + - - +
351A ARG* 4.7 7.4 + - - +
1433A GLU* 4.6 7.2 - - - +
1434A GLU 5.2 0.4 - - - -
1435A THR* 3.2 39.8 - - + +
43Y G 3.2 45.9 + - - -
44Y A 3.9 19.3 + - - +
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Residues in contact with GLY 345 (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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341A GLN 4.3 4.2 + - - -
343A LEU 3.7 1.6 + - - +
344A LYS* 1.3 86.8 - - - +
346A LYS* 1.3 61.5 + - - +
347A GLU* 3.2 14.5 + - - -
348A GLY* 2.9 20.8 + - - +
351A ARG* 3.9 14.4 - - - +
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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