Contacts of the helix formed by residues 369 - 377 (chain A) in PDB entry 4Y49
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 LYS 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A LEU* 4.5 16.6 - - + +
366A ARG* 5.3 3.6 - - + +
367A LYS 2.2 18.8 + - - +
368A SER* 1.3 71.2 - - - +
370A VAL* 1.3 60.9 + - - +
372A PRO* 4.5 1.5 - - - +
373A LEU* 4.1 16.1 + - - +
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Residues in contact with VAL 370 (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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336A LEU* 5.0 11.2 - - + -
362A LEU* 4.1 15.9 - - + +
363A TYR* 5.7 4.3 - - + -
366A ARG 3.7 17.7 - - - +
367A LYS* 3.0 4.2 + - - -
369A LYS* 1.3 74.7 - - + +
371A SER* 1.3 52.5 + - - +
372A PRO 2.7 9.1 - - - -
373A LEU* 3.1 4.9 + - - +
374A LEU* 2.5 41.8 + - + +
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Residues in contact with SER 371 (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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363A TYR* 3.2 39.4 - - - -
367A LYS* 3.8 32.3 - - - +
368A SER* 4.7 5.2 - - - -
370A VAL* 1.3 73.4 - - - +
372A PRO* 1.3 55.9 - - - +
374A LEU* 4.0 3.1 - - - -
375A GLU* 4.0 12.7 - - - +
404A HIS* 3.4 14.2 + - - -
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Residues in contact with PRO 372 (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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368A SER 3.7 18.8 - - - +
369A LYS 4.6 2.9 - - - +
370A VAL 2.7 6.7 - - - -
371A SER* 1.3 74.6 - - - +
373A LEU* 1.3 65.3 + - - +
374A LEU 3.1 0.7 - - - -
375A GLU* 3.2 5.3 + - + +
376A LYS* 3.0 25.6 + - - +
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Residues in contact with LEU 373 (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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333A LYS* 6.2 4.5 - - + -
336A LEU* 3.9 27.8 - - + -
337A SER* 4.8 14.3 - - - -
340A LEU* 5.8 1.3 - - + -
369A LYS 4.1 7.0 + - - +
370A VAL 3.1 6.3 + - - +
372A PRO* 1.3 78.1 - - - +
374A LEU* 1.3 56.8 + - - +
376A LYS* 3.2 4.5 + - - +
377A ILE* 3.0 31.1 + - - +
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Residues in contact with LEU 374 (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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340A LEU* 6.1 5.6 - - + -
363A TYR* 3.1 32.8 + - + +
370A VAL* 2.5 30.6 + - + +
371A SER* 4.0 0.7 - - - -
373A LEU* 1.3 72.9 - - - +
375A GLU* 1.3 60.4 + - - +
376A LYS 3.1 1.0 + - - -
377A ILE* 3.3 13.6 + - - +
378A VAL* 3.8 12.6 + - - +
404A HIS* 5.2 0.3 - - - -
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Residues in contact with GLU 375 (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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371A SER 4.0 13.1 - - - +
372A PRO* 3.2 9.7 + - + +
374A LEU* 1.3 77.6 - - - +
376A LYS* 1.3 57.2 + - - +
377A ILE 3.6 0.2 - - - -
378A VAL* 4.5 2.8 - - - +
379A LEU* 4.2 19.9 + - - +
404A HIS* 3.5 34.1 + - + +
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Residues in contact with LYS 376 (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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372A PRO 3.0 15.8 + - - +
373A LEU* 3.6 5.2 - - - +
375A GLU* 1.3 77.1 - - - +
377A ILE* 1.3 54.3 + - - +
378A VAL 3.4 5.2 - - - -
379A LEU* 5.9 0.7 - - - -
380A ASP* 3.0 32.1 - - - +
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Residues in contact with ILE 377 (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 SER* 5.7 6.5 - - - +
340A LEU* 5.9 3.8 - - + -
341A ARG* 4.9 20.6 - - + +
344A VAL* 6.0 0.5 - - - +
345A LEU* 3.8 22.2 - - - +
373A LEU 3.0 16.9 + - - +
374A LEU* 3.3 7.9 + - - +
376A LYS* 1.3 76.4 - - - +
378A VAL* 1.3 59.5 + - - +
380A ASP* 4.6 4.9 - - - -
381A TYR* 4.5 3.9 - - - +
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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