Contacts of the strand formed by residues 302 - 319 (chain A) in PDB entry 3RBH
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 LYS 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 4.7 24.5 + - + +
286A ASP* 3.2 33.2 + - + +
287A ASN 3.1 17.9 - - - +
288A LEU* 5.3 0.9 - - + -
289A THR* 4.6 5.6 - - - -
301A GLY* 1.3 75.7 - - - +
303A GLN* 1.3 60.9 + - - +
304A SER* 4.2 4.6 + - - +
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Residues in contact with GLN 303 (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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286A ASP* 4.4 0.9 - - - -
287A ASN* 2.8 47.7 + - + +
289A THR* 4.6 11.1 - - + +
302A LYS* 1.3 72.5 - - - +
304A SER* 1.3 63.3 + - - +
339A ASP* 6.0 6.3 - - + -
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Residues in contact with SER 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG 3.2 6.3 - - - -
286A ASP* 2.8 26.5 - - - -
302A LYS* 4.0 5.2 + - - +
303A GLN* 1.3 76.1 - - - +
305A GLY* 1.3 57.7 + - - +
339A ASP* 5.8 2.9 - - - +
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Residues in contact with GLY 305 (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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284A ASP* 3.3 3.5 - - - +
285A ARG* 2.9 35.7 + - - +
287A ASN* 5.5 1.7 - - - +
303A GLN 4.0 0.4 + - - -
304A SER* 1.3 76.5 - - - +
306A ASP* 1.3 67.9 + - - -
307A VAL* 4.4 0.5 - - - +
339A ASP* 5.7 8.3 - - - -
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Residues in contact with ASP 306 (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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283A GLY 3.6 7.1 - - - +
284A ASP* 3.8 14.4 - - - +
305A GLY* 1.3 76.0 - - - -
307A VAL* 1.3 64.1 - - - +
308A ASN* 4.2 15.3 + - - +
341A GLU* 3.6 22.5 - - + +
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Residues in contact with VAL 307 (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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252A LEU* 4.2 14.8 - - + -
281A LEU* 4.1 31.2 - - + -
282A THR* 3.1 18.7 - - - -
283A GLY 2.9 13.5 + - - +
284A ASP* 4.4 7.6 - - - -
285A ARG* 4.1 27.1 - - + -
305A GLY 4.4 2.2 - - - +
306A ASP* 1.3 80.0 - - - +
308A ASN* 1.3 75.7 + - - +
309A ALA* 4.4 2.5 - - + -
340A GLY 4.8 7.6 - - - +
341A GLU 3.4 9.9 - - - +
343A GLN 4.3 11.0 - - - +
345A GLN* 5.8 1.8 - - - +
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Residues in contact with ASN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU 3.4 3.8 - - - +
282A THR* 3.0 23.9 + - - -
283A GLY 5.2 0.2 + - - -
306A ASP* 4.2 19.0 + - - +
307A VAL* 1.3 81.4 + - - +
309A ALA* 1.3 59.7 + - - +
341A GLU* 2.8 18.9 + - + +
342A GLU* 3.4 17.0 - - + +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TRP* 3.7 7.6 - - - +
281A LEU* 2.9 36.0 + - + +
307A VAL* 4.4 4.7 - - + -
308A ASN* 1.3 75.5 - - - +
310A PHE* 1.3 64.1 + - - +
334A SER* 3.3 15.9 - - - +
342A GLU* 3.6 5.4 - - - +
343A GLN 3.8 5.6 - - - +
344A PHE* 3.5 28.7 - - + +
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Residues in contact with PHE 310 (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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278A ALA* 3.8 19.7 - - + -
279A THR 3.2 15.9 - - - -
280A TRP* 3.6 44.6 - + + -
309A ALA* 1.3 76.6 - - - +
311A GLY* 1.3 71.8 + - - +
312A VAL* 3.9 25.4 - - + -
332A ARG* 4.1 9.9 + - - +
334A SER* 2.8 39.7 + - - +
344A PHE* 3.3 8.5 - - - -
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Residues in contact with GLY 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA* 3.5 2.1 - - - -
279A THR* 2.7 41.2 + - - -
310A PHE* 1.3 78.9 - - - +
312A VAL* 1.3 61.9 + - - +
332A ARG 3.1 10.1 - - - -
333A GLY* 4.2 2.7 - - - -
344A PHE* 3.6 17.4 - - - -
374A LEU* 5.0 2.7 - - - -
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Residues in contact with VAL 312 (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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277A SER* 3.2 17.7 - - - +
278A ALA* 4.7 3.6 - - + -
310A PHE* 3.9 22.2 - - + -
311A GLY* 1.3 76.1 - - - +
313A ASP* 1.3 74.5 + - - +
314A LEU* 3.7 24.7 - - + -
330A TYR* 4.5 12.1 - - + -
331A ALA* 3.2 3.5 - - - +
332A ARG* 2.8 54.5 + - + +
374A LEU* 3.9 5.1 - - - +
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Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 5.7 0.2 - - - -
159A GLN* 2.7 38.0 + - - +
264A TYR* 4.7 2.6 + - - -
275A TRP* 2.9 31.9 + - - -
276A ALA* 3.3 2.9 - - - -
277A SER* 2.9 41.8 + - - +
312A VAL* 1.3 80.0 - - - +
314A LEU* 1.3 67.2 + - - +
330A TYR 3.4 5.1 - - - +
331A ALA* 3.9 7.1 - - + +
365A ARG* 3.1 24.7 + - - -
366A PHE* 5.3 0.2 - - - -
374A LEU* 4.9 1.8 - - + -
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Residues in contact with LEU 314 (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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275A TRP* 3.3 13.8 + - - +
276A ALA* 3.8 20.0 - - + -
277A SER 4.4 1.3 - - - +
312A VAL* 3.7 23.3 - - + -
313A ASP* 1.3 87.4 + - - +
315A GLY* 1.3 58.9 + - - +
329A GLY* 3.2 2.6 - - - -
330A TYR* 2.7 58.5 + - + +
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Residues in contact with GLY 315 (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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274A TYR* 3.3 6.9 - - - +
275A TRP* 2.9 57.7 + - - +
314A LEU* 1.3 76.6 - - - +
316A LEU* 1.3 66.5 + - - +
328A VAL* 3.4 7.2 - - - -
329A GLY* 4.1 0.2 - - - -
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Residues in contact with LEU 316 (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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272A LEU* 4.6 21.1 - - + -
273A ASN 3.6 3.6 - - - +
274A TYR* 3.9 15.9 - - + -
275A TRP* 4.4 2.2 - - - -
315A GLY* 1.3 82.6 - - - +
317A ARG* 1.3 61.1 + - - +
327A GLY* 3.0 4.7 - - - -
328A VAL* 3.0 49.8 + - + +
383A PHE* 4.0 2.4 - - - -
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Residues in contact with ARG 317 (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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262A ASP 2.9 28.3 + - - -
263A ALA* 2.8 21.0 + - - +
265A ASN 3.6 12.9 + - - +
271A PRO 3.8 0.2 - - - +
272A LEU* 3.4 6.6 - - - +
273A ASN* 2.8 57.4 + - + +
274A TYR* 4.8 0.2 - - - +
275A TRP* 4.3 8.0 - - + -
316A LEU* 1.3 74.6 - - - +
318A TRP* 1.3 66.7 + - - +
319A ASN* 3.5 21.9 + - - +
325A LYS* 4.2 5.1 - - + +
326A ALA 3.6 9.0 - - - +
356A PHE* 2.8 25.6 + - - +
357A THR 3.6 23.6 - - - -
358A GLY* 3.6 14.5 - - - +
383A PHE* 3.9 12.3 - - + -
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Residues in contact with TRP 318 (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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271A PRO* 3.2 21.2 - - + +
272A LEU* 4.6 9.0 - - + -
317A ARG* 1.3 72.5 - - - +
319A ASN* 1.3 77.7 + - - +
320A ILE* 3.1 46.9 + - + +
325A LYS* 3.2 2.6 - - - +
326A ALA* 2.7 40.6 + - + +
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Residues in contact with ASN 319 (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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268A SER* 3.8 11.8 + - - +
270A MSE 2.7 29.2 + - - +
271A PRO* 2.8 18.0 + - + +
273A ASN* 2.8 27.3 + - - +
317A ARG* 3.5 12.1 + - - -
318A TRP* 1.3 78.8 + - - +
320A ILE* 1.3 67.3 + - - +
321A ASP* 3.3 9.7 + - - +
324A TRP 3.8 4.3 - - - -
325A LYS* 2.9 39.7 + - - +
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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