Contacts of the helix formed by residues 536 - 545 (chain A) in PDB entry 4YCV
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 ASP 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A ILE* 4.4 15.0 + - + +
309A LEU* 4.1 24.3 - - + +
535A LEU* 1.3 75.0 - - - +
537A SER* 1.3 56.6 + - - +
539A PHE* 2.9 22.6 + - + +
540A CYS* 3.0 19.6 + - - -
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Residues in contact with SER 537 (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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535A LEU* 3.7 21.1 - - - +
536A ASP* 1.3 76.1 - - - +
538A ALA* 1.3 61.9 + - - +
540A CYS* 3.3 11.7 + - - +
541A THR* 2.9 35.4 + - - -
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Residues in contact with ALA 538 (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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313A MET* 4.0 22.1 - - + +
535A LEU 3.0 27.9 + - - +
537A SER* 1.3 80.8 + - - +
539A PHE* 1.3 56.0 + - - +
541A THR* 3.8 6.2 - - - -
542A SER* 2.9 28.9 + - - -
235B ARG* 4.9 12.1 - - + +
236B GLN* 6.4 1.8 - - + -
238B TYR* 4.5 2.9 - - + -
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Residues in contact with PHE 539 (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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309A LEU* 4.0 41.5 - - + -
312A LYS* 3.5 44.6 - - + -
313A MET* 3.9 9.5 - - + -
478A LEU* 5.0 1.3 - - + -
507A GLU* 3.6 13.0 - - - -
514A GLN* 4.5 16.2 - - - -
535A LEU 3.4 3.4 + - - +
536A ASP* 2.9 14.6 + - + +
538A ALA* 1.3 77.8 - - - +
540A CYS* 1.3 68.8 + - - +
542A SER* 2.6 24.5 + - - -
543A LEU* 2.9 48.0 + - + +
547A LEU* 5.2 1.3 - - + -
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Residues in contact with CYS 540 (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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511A PRO* 5.0 1.2 - - - +
514A GLN* 5.3 0.4 - - - -
516A GLU* 5.1 3.1 - - - -
517A CYS* 2.0 55.3 - - + -
536A ASP* 3.0 19.2 + - - +
537A SER* 3.3 11.4 + - - +
539A PHE* 1.3 87.4 - - - +
541A THR* 1.3 56.9 - - - +
543A LEU* 3.1 9.1 - - - +
544A GLU* 3.0 31.7 + - - +
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Residues in contact with THR 541 (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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537A SER* 2.9 20.4 + - - -
538A ALA* 3.8 6.5 - - - -
540A CYS* 1.3 73.3 - - - +
542A SER* 1.3 60.4 + - - +
543A LEU 3.0 1.6 - - - -
544A GLU* 2.9 35.2 + - - +
545A TYR* 3.1 28.7 + - + -
219B HIS* 4.8 2.2 - - + +
236B GLN* 4.5 7.4 - - + +
238B TYR* 3.5 16.4 - - - +
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Residues in contact with SER 542 (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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313A MET* 3.4 13.8 - - - +
316A VAL* 3.6 26.8 - - - +
538A ALA 2.9 14.7 + - - -
539A PHE* 2.6 32.7 + - - -
541A THR* 1.3 76.2 - - - +
543A LEU* 1.3 56.7 + - - +
545A TYR* 3.0 22.8 + - - +
546A GLY 3.7 0.7 + - - -
547A LEU 4.1 0.3 + - - -
238B TYR* 3.5 34.9 + - - -
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Residues in contact with LEU 543 (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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316A VAL* 5.8 0.7 - - + -
508A LEU 4.1 17.5 - - - +
509A ASN* 4.3 12.0 - - - +
511A PRO* 4.0 32.6 - - + +
514A GLN* 4.6 15.9 - - + +
517A CYS* 4.9 2.5 - - - -
539A PHE* 2.9 43.8 + - + +
540A CYS* 3.1 15.9 - - - +
541A THR 3.0 0.4 - - - -
542A SER* 1.3 73.6 + - - +
544A GLU* 1.3 58.7 + - - +
545A TYR 3.0 5.2 + - - -
546A GLY* 3.3 12.4 + - - +
547A LEU* 3.6 38.5 + - + +
102B TYR* 5.4 0.5 + - - -
216B ALA 5.2 0.3 - - - +
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Residues in contact with GLU 544 (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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511A PRO* 4.4 13.7 - - + -
512A PHE* 6.4 0.4 - - + -
540A CYS* 3.0 18.5 + - - +
541A THR* 2.9 22.9 + - - +
543A LEU* 1.3 75.0 - - - +
545A TYR* 1.3 56.1 + - - +
546A GLY 3.2 3.1 + - - -
84B PHE* 3.8 19.3 - - + -
218B LEU* 3.1 48.4 + - + +
219B HIS* 3.2 30.1 + - - +
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Residues in contact with TYR 545 (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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316A VAL* 4.2 6.0 - - + +
541A THR* 3.1 29.4 + - + -
542A SER 3.0 14.3 + - - +
544A GLU* 1.3 77.9 - - - +
546A GLY* 1.3 59.0 + - - +
138B ARG* 3.4 24.1 + - - -
217B CYS* 3.5 15.2 - - - -
219B HIS* 3.4 39.0 + + + +
221B LEU* 3.7 27.8 - - + -
222B PRO* 5.3 2.4 - - - +
236B GLN* 3.8 14.4 + - - -
238B TYR* 3.2 32.3 - + + -
239B LEU* 3.6 29.3 - - + +
242B LEU* 5.9 2.0 - - + +
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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