Contacts of the strand formed by residues 291 - 299 (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 TRP 291 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ARG* 5.7 1.1 - - - -
14B LEU* 4.8 1.3 - - + -
282D TRP* 4.0 5.1 - - - -
283D ALA* 2.9 35.6 + - - +
288D PHE* 3.3 36.6 - + + -
289D PRO* 3.8 11.9 - - + +
290D PHE* 1.3 80.4 - - - +
292D PRO* 1.3 97.9 - - + +
293D ALA* 3.5 0.9 + - - +
307D PHE* 3.6 22.9 - + + +
308D PHE 3.0 21.4 + - - -
310D GLN* 3.1 21.6 + - - -
335D THR* 3.6 22.0 - - - -
338D ILE* 3.9 14.6 - - + -
339D PHE* 3.7 37.9 - + - -
342D ALA* 3.8 20.5 - - + +
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Residues in contact with PRO 292 (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 3.4 8.3 - - - +
282D TRP* 3.9 13.4 - - + -
291D TRP* 1.3 103.0 - - + +
293D ALA* 1.3 59.8 + - - +
307D PHE* 3.6 0.5 - - - -
308D PHE* 3.0 41.8 + - + -
324D MET* 4.1 5.4 - - + -
339D PHE* 4.0 7.4 - - + -
342D ALA* 4.1 10.1 - - + -
343D MET* 3.6 21.3 - - - -
346D MET* 3.9 27.8 - - + -
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Residues in contact with ALA 293 (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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280D LEU* 3.6 6.8 - - - +
281D VAL* 2.9 42.0 + - + -
283D ALA* 4.2 2.2 - - + -
291D TRP 4.1 2.9 - - - +
292D PRO* 1.3 76.3 - - - +
294D LYS* 1.3 62.9 + - - +
305D ALA* 3.8 26.5 - - + -
306D ARG 3.3 15.5 - - - +
307D PHE* 4.0 9.4 - - + -
308D PHE* 3.9 7.6 - - - -
324D MET* 5.1 0.2 - - - +
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Residues in contact with LYS 294 (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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258D CYS* 4.7 13.7 - - - -
269D TRP 5.2 0.2 + - - -
270D PHE* 2.8 66.3 + - + +
272D GLU 4.5 7.7 + - - -
274D CYS* 6.1 1.0 - - - -
278D HIS* 4.1 26.0 - - + -
279D PRO 3.7 5.2 - - - -
280D LEU* 4.6 7.2 - - + -
281D VAL* 4.8 0.7 - - - -
293D ALA* 1.3 72.5 - - - +
295D ALA* 1.3 61.9 + - - +
296D LEU* 3.5 10.5 + - + +
305D ALA* 3.3 6.4 - - - -
306D ARG* 2.8 38.2 + - + +
308D PHE* 3.9 15.7 - - + -
349D TYR* 3.9 19.1 - - + -
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Residues in contact with ALA 295 (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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278D HIS* 3.3 17.5 + - - +
279D PRO* 3.0 24.1 + - + +
281D VAL* 4.2 11.4 - - + +
293D ALA 3.9 1.0 + - - -
294D LYS* 1.3 70.3 - - - +
296D LEU* 1.3 61.3 + - - +
297D ARG 3.6 1.6 - - - -
303D VAL* 3.7 23.3 - - + -
304D ASP 3.9 3.8 - - - -
369D TYR* 3.7 30.5 + - + +
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Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254D VAL* 4.0 25.7 - - + +
255D CYS* 4.8 3.8 - - + -
258D CYS* 4.1 14.4 - - + -
278D HIS* 3.4 49.8 + - + +
294D LYS* 4.1 11.9 - - + +
295D ALA* 1.3 75.9 - - - +
297D ARG* 1.3 65.9 + - + +
304D ASP* 2.8 16.0 + - - +
306D ARG* 3.6 22.2 - - + -
313D ARG* 3.5 32.3 - - + -
503D ZN 4.4 0.2 - - - -
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Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250D ASN* 4.5 3.8 + - - +
254D VAL* 3.3 32.9 - - + +
295D ALA 3.6 1.2 - - - -
296D LEU* 1.3 83.9 - - + +
298D ASP* 1.3 71.6 + - - +
299D LYS* 5.6 5.4 - - - +
303D VAL* 3.5 7.1 - - - +
304D ASP* 2.9 52.4 + - + +
313D ARG* 3.2 3.8 - - - +
315D TRP* 3.6 22.4 - - + -
369D TYR* 5.0 1.6 - - - -
504D SO4 2.8 38.4 + - - -
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Residues in contact with ASP 298 (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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297D ARG* 1.3 83.4 - - - +
299D LYS* 1.3 64.4 + - - +
301D GLY 6.3 0.4 - - - +
302D GLN 3.3 7.9 - - - +
303D VAL* 3.9 3.9 - - + +
315D TRP* 4.7 0.9 - - - -
318D ILE* 4.8 2.3 - - + +
369D TYR* 2.5 43.6 + - - -
371D PRO* 3.7 23.8 - - + +
372D ASN* 3.6 14.9 + - - +
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Residues in contact with LYS 299 (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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297D ARG* 5.6 4.7 - - - +
298D ASP* 1.3 77.3 - - - +
300D ASP* 1.3 95.2 + - - +
301D GLY 3.3 1.7 - - - +
302D GLN* 2.9 28.0 + - - +
315D TRP* 4.0 20.3 - - + -
505D SO4 3.4 20.7 + - - +
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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