Contacts of the helix formed by residues 410 - 418 (chain B) in PDB entry 4YC3
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 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B TYR 3.3 9.0 - - - -
404B ALA 3.3 21.8 - - - +
405B THR* 2.9 18.6 + - - +
406B SER* 3.4 24.6 + - - +
409B ALA* 1.3 78.0 - - - +
411B ILE* 1.3 63.8 + - - +
412B SER 3.2 2.7 - - - -
413B THR* 2.7 35.0 + - + +
414B LEU* 4.0 2.4 + - - +
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Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLU* 3.8 39.0 - - + +
320B THR* 4.0 11.7 - - + -
321B LEU* 3.8 26.5 - - + +
324B TYR* 3.9 17.3 - - + -
403B TYR* 3.0 35.5 + - + +
408B HIS 3.1 9.9 + - - +
409B ALA* 3.1 10.7 - - + +
410B LYS* 1.3 75.5 - - - +
412B SER* 1.3 60.8 - - - +
413B THR 3.0 5.9 + - - -
414B LEU* 3.2 39.7 + - + +
417B LEU* 3.7 5.1 - - - +
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Residues in contact with SER 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TYR* 3.4 37.8 + - - -
390B ASN* 4.3 7.6 + - - +
400B LYS* 2.6 45.7 + - - +
403B TYR* 3.2 7.3 + - - -
404B ALA* 3.0 18.4 + - - +
411B ILE* 1.3 80.3 - - - +
413B THR* 1.3 57.2 + - - +
414B LEU 3.4 0.9 - - - -
417B LEU* 3.8 10.9 - - - +
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Residues in contact with THR 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B LYS* 5.7 3.6 - - - +
404B ALA* 3.8 29.4 - - + +
410B LYS* 2.7 33.4 + - + +
411B ILE 3.0 0.4 + - - -
412B SER* 1.3 76.4 - - - +
414B LEU* 1.3 67.3 + - - +
415B PRO* 3.3 7.8 - - - +
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B GLU* 4.3 14.1 - - - +
321B LEU* 4.4 13.5 - - + -
354B ILE* 5.1 1.8 - - + -
355B LEU* 3.9 21.5 - - + -
390B ASN* 5.1 1.2 + - - -
409B ALA 6.2 0.2 - - - +
410B LYS 5.0 0.9 - - - +
411B ILE* 3.2 46.7 + - + +
412B SER 3.4 1.4 - - - +
413B THR* 1.3 78.7 + - - +
415B PRO* 1.3 73.2 - - + +
416B GLN* 3.3 25.0 + - - +
417B LEU* 3.3 25.9 + - + +
418B ASN* 4.2 4.9 - - - +
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Residues in contact with PRO 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B THR 3.4 7.6 - - - +
414B LEU* 1.3 85.7 - - + +
416B GLN* 1.3 70.2 + - + +
418B ASN* 3.0 35.9 + - - +
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Residues in contact with GLN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B GLU* 5.6 0.2 - - - +
354B ILE* 3.6 39.8 - - + +
355B LEU* 4.2 16.1 - - - +
414B LEU* 3.2 17.5 - - + +
415B PRO* 1.3 99.6 - - + +
417B LEU* 1.3 56.0 + - - +
418B ASN 3.1 1.6 - - - -
419B SER* 3.1 31.0 + - - +
422B VAL* 4.2 0.7 - - - +
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B LEU* 4.2 20.4 - - + -
324B TYR* 4.3 11.0 - - + -
325B LEU* 4.6 4.9 - - + -
354B ILE* 4.2 20.6 - - + -
386B VAL* 3.6 30.5 - - + +
387B VAL* 5.8 0.3 - - - +
390B ASN* 3.8 14.1 - - - +
411B ILE 3.7 22.9 - - - +
412B SER* 3.8 19.5 - - - +
414B LEU* 3.3 18.3 + - + +
415B PRO 3.2 1.0 - - - -
416B GLN* 1.3 77.8 - - - +
418B ASN* 1.3 59.5 + - - +
419B SER 3.4 1.6 - - - -
422B VAL* 3.4 28.1 - - + +
423B GLN* 5.3 1.0 + - - -
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Residues in contact with ASN 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B ASN* 3.0 39.5 + - - +
391B GLN* 5.3 7.9 - - - +
414B LEU 4.2 5.5 - - - +
415B PRO* 3.0 20.2 + - - +
417B LEU* 1.3 78.3 + - - +
419B SER* 1.3 64.6 + - - +
423B GLN* 4.4 14.5 + - - +
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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