Contacts of the strand formed by residues 280 - 283 (chain D) in PDB entry 5Y1Z
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 LEU 280 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D HIS 4.2 2.9 - - - +
279D PRO* 1.3 76.1 - - - +
281D VAL* 1.3 63.7 + - - +
293D ALA 3.6 3.4 - - - +
294D LYS* 4.6 3.8 - - + -
308D PHE* 4.1 18.6 - - + -
323D LEU* 3.7 1.0 - - - +
324D MET* 2.8 21.4 + - + -
346D MET* 3.7 32.3 - - + -
349D TYR* 3.4 32.8 - - + -
350D VAL* 3.7 15.0 - - + -
360D PHE* 3.7 28.3 - - + -
376D GLN* 2.7 37.8 + - - +
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Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D PRO 4.4 1.3 - - - +
280D LEU* 1.3 81.2 - - - +
282D TRP* 1.3 70.4 + - - +
283D ALA* 4.2 7.2 - - + -
292D PRO* 3.4 6.1 - - - +
293D ALA* 2.9 55.9 + - + +
294D LYS 4.8 0.2 - - - -
295D ALA* 4.2 19.7 - - + +
303D VAL* 5.4 0.2 - - + -
305D ALA* 5.3 2.5 - - + -
321D CYS* 4.5 8.7 - - + -
322D TYR 3.0 14.8 - - - +
323D LEU* 4.5 1.6 - - + -
324D MET* 3.5 8.3 - - - +
369D TYR* 3.6 37.0 - - + -
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Residues in contact with TRP 282 (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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281D VAL* 1.3 73.6 - - - +
283D ALA* 1.3 58.5 + - - +
290D PHE* 3.8 17.1 - - + -
291D TRP 3.7 4.7 - - - -
292D PRO* 3.9 17.9 - - + -
320D ASN 3.3 1.8 - - - +
321D CYS* 3.1 7.1 - - - -
322D TYR* 2.8 35.6 + - + +
323D LEU 3.7 17.7 - - - -
324D MET* 3.4 23.3 - - + +
325D SER* 3.0 29.7 + - - +
327D GLU 3.7 18.6 - - - -
328D ILE* 3.5 23.6 - - + -
330D PHE* 3.7 26.7 - + - -
339D PHE* 4.0 2.5 - + - -
343D MET* 3.8 29.6 - - + -
365D PHE* 3.4 24.6 - + - -
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Residues in contact with ALA 283 (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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281D VAL* 3.7 3.0 - - + -
282D TRP* 1.3 73.7 - - - +
284D LYS* 1.3 59.8 + - - +
285D LEU 4.1 0.9 + - - -
289D PRO 4.0 0.9 - - - +
290D PHE* 3.6 0.8 - - - -
291D TRP* 2.9 35.1 + - - +
293D ALA* 4.2 5.8 - - + -
305D ALA* 4.1 17.9 - - + -
307D PHE* 4.0 22.4 - - + -
316D VAL* 4.2 7.0 - - + -
320D ASN 3.5 4.7 - - - -
321D CYS* 4.1 15.5 - - - -
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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