Contacts of the strand formed by residues 281 - 290 (chain D) in PDB entry 4RZR
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 PRO 281 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273D TYR* 4.0 17.3 - - + +
276D LEU* 4.0 11.9 - - + -
279D ARG 3.8 7.4 - - - +
280D ILE* 1.4 89.0 - - + +
282D LYS* 1.3 56.3 + - - +
283D ALA 3.9 5.4 - - - +
305D GLY* 3.4 1.7 - - - -
306D ILE* 2.8 35.4 + - + +
337D PHE* 3.5 35.7 - - + -
338D SER 3.4 15.5 - - - +
339D LYS 3.9 0.7 - - - +
340D PHE* 3.6 18.6 - - + -
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Residues in contact with LYS 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 PRO* 1.3 74.3 - - - +
283D ALA* 1.3 57.8 + - - +
301D THR* 3.3 6.0 - - + -
302D PHE* 2.7 47.7 + - - +
303D PRO* 5.0 2.2 - - + -
304D HIS* 3.5 29.4 - - - +
306D ILE* 3.6 7.4 - - - +
339D LYS* 3.0 39.3 + - + +
340D PHE 4.2 10.1 + - - -
341D ILE* 4.1 22.2 - - + +
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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 PRO* 3.6 1.3 - - - +
282D LYS* 1.3 81.3 - - - +
284D ILE* 1.3 60.3 + - - +
285D HIS* 4.8 7.2 - - - +
300D ARG 3.3 6.1 - - - +
301D THR* 3.6 19.3 - - - +
306D ILE* 3.7 2.9 - - - -
337D PHE* 3.4 9.4 - - - -
338D SER* 3.0 50.1 + - - +
339D LYS* 3.9 14.4 - - + -
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Residues in contact with ILE 284 (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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283D ALA* 1.3 76.2 - - - +
285D HIS* 1.3 70.2 + - - +
286D VAL 4.3 0.4 - - - +
299D GLY* 3.0 2.8 - - - -
300D ARG 2.8 41.6 + - - +
302D PHE* 4.3 2.2 - - + -
306D ILE* 3.9 16.8 - - + -
311D ALA* 3.8 27.8 - - - +
314D GLU* 4.1 15.7 - - + -
315D SER* 4.2 14.8 - - - +
318D LEU* 4.1 15.7 - - + -
335D VAL* 3.8 15.3 - - + -
336D ARG 3.5 3.1 - - - -
337D PHE* 3.6 30.3 - - + -
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Residues in contact with HIS 285 (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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283D ALA* 4.8 6.0 - - + +
284D ILE* 1.3 81.2 + - - +
286D VAL* 1.3 64.9 + - - +
287D VAL* 3.8 6.9 + - + +
297D SER* 4.8 10.3 + - - -
298D ARG 3.5 5.7 - - - +
299D GLY* 3.5 21.9 + - - -
300D ARG 5.1 1.2 + - - -
301D THR* 5.6 1.8 + - - -
335D VAL* 3.2 5.2 - - - +
336D ARG* 2.8 53.6 + - + +
338D SER* 4.4 16.6 + - - -
339D LYS* 5.9 2.8 + - - -
6F T 5.2 9.2 - + + -
7F A 4.3 14.2 + + - -
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Residues in contact with VAL 286 (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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265D LEU* 4.3 9.4 - - + -
284D ILE* 5.0 0.4 - - + -
285D HIS* 1.3 72.4 - - - +
287D VAL* 1.3 62.3 + - - +
297D SER* 3.3 5.5 - - - -
298D ARG 2.8 31.5 + - - +
315D SER* 3.5 39.7 - - - +
318D LEU* 3.6 22.1 - - + +
319D LEU* 4.5 10.3 - - + -
322D ILE* 3.8 15.5 - - + +
333D ILE* 3.7 22.7 - - + -
334D GLY 3.3 10.5 - - - +
335D VAL* 4.9 3.6 - - + -
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Residues in contact with VAL 287 (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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248D ILE* 4.3 24.6 - - + +
285D HIS* 4.1 13.2 - - + +
286D VAL* 1.3 75.9 - - - +
288D ALA* 1.3 62.8 + - - +
289D VAL* 4.3 2.0 + - + +
295D ILE* 4.0 27.8 - - + -
296D VAL 3.7 3.1 - - - +
297D SER* 4.2 10.1 - - - -
332D ARG 4.1 0.3 - - - +
333D ILE* 3.5 5.9 - - - +
334D GLY* 2.7 48.4 + - - +
335D VAL 4.6 2.2 - - - +
336D ARG* 4.7 14.6 - - + +
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Residues in contact with ALA 288 (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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286D VAL 4.2 0.4 + - - -
287D VAL* 1.3 74.8 - - - +
289D VAL* 1.3 62.1 + - - +
290D THR* 4.0 2.3 + - + +
294D ASP 3.6 0.9 - - - +
295D ILE* 3.4 4.9 - - - +
296D VAL* 2.7 49.0 + - + +
322D ILE* 4.0 29.4 - - + -
330D ILE* 4.2 21.5 - - + -
332D ARG 3.6 4.7 - - - +
333D ILE* 4.4 3.8 - - + -
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Residues in contact with VAL 289 (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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248D ILE* 4.6 13.9 - - + -
287D VAL* 5.3 3.6 - - + -
288D ALA* 1.3 72.8 - - - +
290D THR* 1.3 63.5 + - - +
293D LEU* 3.8 28.5 - - + +
294D ASP 3.2 8.7 - - - +
295D ILE* 3.5 23.8 - - + -
330D ILE* 3.7 2.3 - - - -
331D ARG* 2.8 31.5 + - + -
332D ARG* 2.9 50.8 + - + +
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Residues in contact with THR 290 (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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288D ALA* 5.1 2.5 - - + +
289D VAL* 1.3 81.0 - - - +
291D GLU* 1.3 57.4 + - - +
292D ASP* 2.4 26.4 + - - -
293D LEU* 2.8 23.0 + - - +
294D ASP* 2.9 21.4 + - - +
296D VAL* 4.0 17.5 - - + -
322D ILE* 6.4 1.1 - - + -
326D ASP* 4.4 5.4 - - - +
328D ARG* 3.6 32.7 + - + +
329D LYS 3.3 15.3 - - - +
330D ILE* 4.3 7.4 - - + +
331D ARG* 3.8 5.6 - - - +
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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