Contacts of the helix formed by residues 437 - 449 (chain A) in PDB entry 1YHY
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 PHE 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A ILE* 3.4 31.2 - - + -
299A SER* 3.3 24.5 - - - -
300A LYS* 3.8 9.0 - - - -
302A PRO* 3.4 39.9 - - + -
324A THR 3.2 28.5 + - - -
325A GLY 4.0 15.0 - - - +
326A ILE* 3.9 8.7 - - + -
327A PRO* 5.6 0.4 - - + -
435A LEU* 4.2 16.6 - - + -
436A ASP* 1.3 79.5 + - - +
438A GLY* 1.3 58.2 + - - +
439A VAL* 3.2 2.9 - - - -
440A TRP* 3.2 14.1 + - + +
441A ARG* 2.8 38.1 + - + +
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Residues in contact with GLY 438 (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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436A ASP* 3.0 15.1 + - - -
437A PHE* 1.3 78.2 - - - +
439A VAL* 1.3 62.5 + - - +
441A ARG* 3.1 18.9 + - - +
442A ASN* 2.9 33.8 + - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASP* 5.3 2.1 + - - +
437A PHE* 3.2 0.8 - - - -
438A GLY* 1.3 76.4 - - - +
440A TRP* 1.3 65.3 + - - +
442A ASN* 3.2 5.1 + - - +
443A GLU* 3.0 24.7 + - + +
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Residues in contact with TRP 440 (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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300A LYS 3.3 18.8 + - - +
301A LYS* 3.4 41.4 - - + -
302A PRO* 3.0 32.5 + - + -
303A VAL* 3.9 7.7 - - + +
327A PRO* 4.2 8.5 - - + -
359A TYR* 4.7 1.1 - + - -
360A ALA* 3.5 26.0 - - - -
363A HIS* 3.8 21.1 - - + -
364A SER* 4.2 0.2 - - - -
437A PHE* 3.2 11.4 + - + +
439A VAL* 1.3 78.1 - - - +
441A ARG* 1.3 66.5 + - - +
443A GLU* 2.8 58.1 + - + +
444A LEU* 3.0 49.9 + - + +
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Residues in contact with ARG 441 (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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324A THR 5.6 0.2 + - - -
325A GLY* 3.6 29.0 + - - +
327A PRO* 4.6 15.0 - - + -
344A LEU* 3.6 30.9 - - + +
435A LEU 5.6 0.4 + - - -
436A ASP* 3.7 7.1 + - - +
437A PHE* 2.8 27.9 + - - +
438A GLY* 3.1 31.1 - - - +
440A TRP* 1.3 77.1 - - - +
442A ASN* 1.3 58.6 + - - +
444A LEU* 3.3 10.4 + - - +
445A ASN* 2.9 40.3 + - - +
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Residues in contact with ASN 442 (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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438A GLY* 2.9 27.2 + - - +
439A VAL* 3.8 5.2 - - - +
441A ARG* 1.3 74.6 - - - +
443A GLU* 1.3 62.4 + - - +
444A LEU 2.9 5.9 + - - -
445A ASN* 3.9 17.1 + - - +
446A VAL* 3.2 32.1 + - + +
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Residues in contact with GLU 443 (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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301A LYS* 4.0 15.5 + - - -
359A TYR* 2.8 26.6 + - + +
363A HIS* 4.9 2.3 - - - +
439A VAL* 3.0 16.3 + - + +
440A TRP* 2.8 45.6 + - + +
442A ASN* 1.3 77.3 - - - +
444A LEU* 1.3 57.6 + - - +
446A VAL* 2.9 21.6 - - + +
447A GLN* 3.7 11.8 - - - +
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Residues in contact with LEU 444 (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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327A PRO* 3.7 21.5 - - + -
346A LEU* 4.0 17.0 - - + -
356A TYR* 4.4 4.9 - - + +
359A TYR* 3.5 32.3 - - + -
360A ALA* 3.8 26.9 - - + +
440A TRP* 3.0 47.2 + - + +
441A ARG* 3.5 8.3 - - - +
442A ASN 2.9 0.2 - - - -
443A GLU* 1.3 78.0 - - - +
445A ASN* 1.3 59.6 + - - +
446A VAL 3.0 1.8 - - - -
447A GLN* 2.8 8.9 + - + +
448A LYS* 2.8 30.4 + - - +
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Residues in contact with ASN 445 (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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343A GLU* 4.5 6.7 + - - +
441A ARG* 2.9 35.2 + - - +
442A ASN* 3.3 21.6 + - - +
444A LEU* 1.3 76.8 - - - +
446A VAL* 1.3 58.5 + - + +
448A LYS* 3.3 33.6 + - + +
449A GLN* 3.1 25.1 + - - +
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Residues in contact with VAL 446 (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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442A ASN* 3.2 17.5 + - + +
443A GLU* 2.9 30.3 - - + +
445A ASN* 1.3 75.3 - - + +
447A GLN* 1.3 65.4 + - + +
448A LYS 3.1 0.2 - - - -
449A GLN* 3.0 15.8 + - - +
450A LYS* 2.8 30.9 + - - +
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Residues in contact with GLN 447 (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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355A VAL* 4.6 7.3 - - - +
356A TYR* 4.0 16.8 - - + +
359A TYR* 3.3 57.5 + - + -
443A GLU 3.7 7.2 - - - +
444A LEU 2.8 9.5 + - - +
446A VAL* 1.3 84.1 - - + +
448A LYS* 1.3 57.7 + - - +
450A LYS* 4.4 1.8 - - - +
451A PHE* 2.8 63.4 + - - +
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Residues in contact with LYS 448 (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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343A GLU 3.4 20.8 + - - -
344A LEU 5.1 0.6 - - - -
345A SER 3.6 15.3 + - - +
346A LEU* 4.4 11.4 - - - +
347A HIS* 5.3 4.7 - - + -
356A TYR* 3.6 49.1 - - + +
444A LEU* 2.8 13.5 + - - +
445A ASN* 3.3 31.7 + - - +
446A VAL 3.1 0.2 - - - -
447A GLN* 1.3 77.0 - - - +
449A GLN* 1.3 56.5 + - - +
452A PRO* 3.4 25.9 - - + +
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Residues in contact with GLN 449 (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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445A ASN 3.1 13.4 + - - +
446A VAL* 3.0 18.2 + - - +
448A LYS* 1.3 77.8 - - - +
450A LYS* 1.3 65.5 + - - +
452A PRO* 3.4 11.5 - - - +
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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