Contacts of the helix formed by residues 269 - 275 (chain D) in PDB entry 4YP8
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 269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267D ASN 3.6 0.6 + - - -
268D GLY* 1.3 73.7 - - - -
270D LEU* 1.3 62.9 + - - +
271D LEU* 3.7 7.8 + - - +
272D ASP* 3.3 30.4 + - - +
273D ARG* 3.1 27.7 + - - +
314D SER 3.9 2.2 - - - -
315D ALA* 3.5 25.5 - - - +
317D ILE 3.4 6.7 - - - -
318D LEU* 3.9 1.3 - - - -
319D LEU* 4.3 1.1 - - - -
501D 4GF 3.0 21.7 - - - -
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Residues in contact with LEU 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D SER* 1.3 68.6 - - - +
271D LEU* 1.4 55.5 + - - +
273D ARG 3.2 0.5 + - - -
274D LEU* 2.8 55.6 + - + +
283D LEU* 3.8 25.4 - - + -
288D ARG* 6.0 0.2 - - + -
291D ILE* 4.0 25.8 - - + -
314D SER* 3.5 15.5 - - - +
317D ILE* 2.8 27.3 + - + +
319D LEU* 4.0 11.3 - - + +
376D VAL* 4.0 21.5 - - + -
380D ILE* 4.0 26.7 - - + -
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Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D SER* 3.7 8.1 - - - +
270D LEU* 1.4 75.0 - - - +
272D ASP* 1.3 72.5 + - - +
274D LEU* 3.2 6.7 + - - +
275D SER* 3.1 25.3 + - - +
314D SER* 3.2 33.6 + - - +
315D ALA* 3.8 25.1 - - + +
354D TYR* 4.1 5.8 - - - +
379D GLU* 3.8 11.4 - - - +
385D PRO* 5.0 14.8 - - + -
501D 4GF 5.8 3.6 - - + -
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Residues in contact with ASP 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D MET 4.9 2.9 - - - +
193D GLY* 5.9 0.7 - - - -
269D SER* 3.3 25.1 + - - +
271D LEU* 1.3 87.4 - - - +
273D ARG* 1.4 77.9 + - - +
275D SER* 3.1 8.3 + - - -
276D CYS 3.0 7.3 + - - -
277D LEU* 2.9 55.4 + - + +
501D 4GF 4.6 24.3 + - - +
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Residues in contact with ARG 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ASN* 2.6 54.1 + - - +
268D GLY* 4.3 1.2 - - - -
269D SER 3.1 11.4 + - - +
270D LEU 3.7 4.3 - - - +
272D ASP* 1.4 96.2 + - - +
274D LEU* 1.4 64.5 + - - +
276D CYS* 3.4 17.5 + - - +
277D LEU* 2.8 34.4 + - - +
278D ASP* 5.1 1.8 + - - +
280D THR* 2.8 36.2 + - - +
281D PRO 4.7 3.1 - - - +
283D LEU* 3.8 34.7 + - + +
319D LEU* 3.5 14.4 - - + -
323D PHE* 4.4 9.0 - - + -
501D 4GF 3.4 23.7 - - - +
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Residues in contact with LEU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D LEU* 2.8 44.2 + - + +
271D LEU* 3.2 6.0 + - - +
273D ARG* 1.4 72.6 - - - +
275D SER* 1.3 59.0 + - - +
276D CYS* 3.7 1.2 + - - -
283D LEU* 4.2 13.5 - - + -
288D ARG* 3.8 34.7 + - + +
314D SER* 4.8 4.5 - - - -
379D GLU* 3.6 42.4 - - + +
380D ILE* 3.9 10.1 - - - +
383D GLY* 3.9 23.3 - - - +
384D LEU 5.6 0.4 - - - +
415D ASP* 4.7 1.4 - - - +
417D LYS* 4.0 17.0 + - - -
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Residues in contact with SER 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A LYS* 5.4 3.1 - - - +
417A LYS* 3.1 22.8 - - - +
271D LEU* 3.1 17.8 + - - +
272D ASP* 3.1 13.9 + - - -
274D LEU* 1.3 76.9 - - - +
276D CYS* 1.4 64.3 + - - +
277D LEU* 3.4 10.8 + - - +
383D GLY 5.2 2.9 - - - -
417D LYS* 5.5 1.6 - - - +
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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