Contacts of the strand formed by residues 304 - 319 (chain C) 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 SER 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285C ARG 3.1 11.7 - - - -
286C ASP* 4.1 12.2 - - - +
303C GLN* 1.3 76.3 - - - +
305C GLY* 1.3 59.0 + - - +
339C ASP* 5.8 1.9 - - - +
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Residues in contact with GLY 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C ASP* 3.3 5.7 - - - +
285C ARG* 2.8 35.4 + - - +
287C ASN* 5.4 0.9 - - - +
303C GLN 3.7 0.8 + - - -
304C SER* 1.3 77.4 - - - +
306C ASP* 1.3 65.1 + - - -
307C VAL* 4.4 0.5 - - - +
339C ASP* 5.7 7.9 - - - -
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Residues in contact with ASP 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C GLY 3.5 10.3 - - - +
284C ASP* 4.2 3.4 - - + +
305C GLY* 1.3 75.7 - - - -
307C VAL* 1.3 64.8 + - - +
308C ASN* 4.2 14.8 - - - +
341C GLU* 3.6 22.3 - - + +
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Residues in contact with VAL 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C LEU* 4.2 15.7 - - + -
281C LEU* 4.0 31.2 - - + -
282C THR* 3.1 19.4 + - - -
283C GLY 2.9 17.1 + - - +
284C ASP* 4.4 7.6 - - - -
285C ARG* 4.2 25.6 - - + -
305C GLY 4.4 2.2 - - - +
306C ASP* 1.3 78.6 - - - +
308C ASN* 1.3 74.5 + - - +
309C ALA* 4.4 1.8 - - + -
340C GLY 4.8 7.2 - - - +
341C GLU* 3.4 9.9 - - - +
343C GLN 4.3 11.0 - - - +
345C GLN* 5.8 1.8 - - - +
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Residues in contact with ASN 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LEU 3.3 3.1 - - - +
282C THR* 3.0 24.0 + - - -
283C GLY 5.3 0.2 + - - -
306C ASP* 4.2 17.2 - - - +
307C VAL* 1.3 82.3 + - - +
309C ALA* 1.3 59.9 + - - +
341C GLU* 2.8 19.3 + - + +
342C GLU* 3.3 17.1 - - + +
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Residues in contact with ALA 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C TRP* 3.6 8.1 - - - +
281C LEU* 2.9 35.6 + - + +
307C VAL* 4.4 2.9 - - + -
308C ASN* 1.3 75.2 - - - +
310C PHE* 1.3 64.7 + - - +
334C SER* 3.3 14.8 - - - +
342C GLU 3.8 5.2 - - - +
343C GLN 3.8 6.3 - - - +
344C PHE* 3.5 31.0 - - + +
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Residues in contact with PHE 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C ALA* 3.8 20.6 - - + -
279C THR 3.2 15.7 - - - -
280C TRP* 3.6 43.3 - + + +
309C ALA* 1.3 77.0 - - - +
311C GLY* 1.3 71.3 + - - +
312C VAL* 3.9 26.0 - - + -
332C ARG* 4.1 9.3 - - - +
333C GLY* 3.6 0.2 - - - -
334C SER* 2.8 40.5 + - - +
344C PHE* 3.3 8.0 - - - -
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Residues in contact with GLY 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C SER 4.7 0.2 - - - -
278C ALA* 3.4 2.6 - - - -
279C THR* 2.7 41.6 + - - +
310C PHE* 1.3 79.9 - - - +
312C VAL* 1.3 60.8 + - - +
332C ARG 3.2 10.1 - - - -
333C GLY* 4.2 0.2 - - - -
344C PHE* 3.5 20.1 - - - -
374C LEU* 5.1 2.7 - - - -
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Residues in contact with VAL 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C SER* 3.3 16.8 - - - +
278C ALA* 4.7 4.3 - - + -
310C PHE* 3.9 22.2 - - + -
311C GLY* 1.3 75.5 - - - +
313C ASP* 1.3 65.1 + - - +
314C LEU* 3.7 25.4 - - + -
330C TYR* 4.4 11.9 - - + -
331C ALA* 3.2 3.7 - - - +
332C ARG* 2.8 54.2 + - + +
374C LEU* 3.9 5.0 - - - +
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Residues in contact with ASP 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C SER* 5.7 0.2 - - - -
159C GLN* 2.7 38.9 + - - +
264C TYR* 4.7 2.1 + - - -
275C TRP* 2.9 32.7 + - - -
276C ALA* 3.3 2.6 - - - -
277C SER* 2.9 43.5 + - - +
312C VAL* 1.3 78.5 - - - +
314C LEU* 1.3 67.1 + - - +
330C TYR 3.4 5.4 - - - +
331C ALA* 3.9 7.6 - - + +
365C ARG* 3.2 23.0 + - - -
374C LEU* 4.9 2.0 - - + -
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C TRP* 3.4 14.7 + - - +
276C ALA* 3.8 20.6 - - + -
277C SER 4.4 1.1 - - - +
312C VAL* 3.7 23.6 - - + -
313C ASP* 1.3 87.2 + - - +
315C GLY* 1.3 58.7 + - - +
329C GLY* 3.2 2.4 - - - -
330C TYR* 2.7 57.7 + - + +
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Residues in contact with GLY 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C TYR* 3.2 7.8 - - - +
275C TRP* 2.9 53.1 + - - +
314C LEU* 1.3 77.2 - - - +
316C LEU* 1.3 65.4 + - - +
328C VAL* 3.3 11.0 - - - -
329C GLY* 4.1 0.2 - - - -
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU* 4.6 20.9 - - + -
273C ASN 3.6 4.3 - - - +
274C TYR* 3.9 16.2 - - + -
275C TRP* 4.3 2.2 - - - -
315C GLY* 1.3 83.0 - - - +
317C ARG* 1.3 60.6 + - - +
327C GLY* 3.0 4.3 - - - -
328C VAL* 2.9 49.4 + - + +
383C PHE* 4.0 2.8 - - - -
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Residues in contact with ARG 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ASP 2.9 27.9 + - - -
263C ALA* 2.8 21.8 + - - +
264C TYR* 4.7 0.2 - - - +
265C ASN 3.6 13.7 + - - +
271C PRO 3.7 0.3 - - - +
272C LEU* 3.4 6.2 - - - +
273C ASN* 2.8 58.3 + - + +
274C TYR* 4.8 0.2 - - - +
275C TRP* 4.3 7.5 - - + -
316C LEU* 1.3 75.2 - - - +
318C TRP* 1.3 65.6 + - - +
319C ASN* 3.5 22.5 + - - +
325C LYS* 4.2 4.9 - - + +
326C ALA 3.5 9.2 - - - +
356C PHE 2.9 23.0 + - - -
357C THR 3.8 22.7 - - - -
358C GLY* 3.6 13.9 - - - -
383C PHE* 4.0 11.7 - - + -
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Residues in contact with TRP 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C PRO* 3.2 25.7 - - + +
272C LEU* 4.7 8.7 - - + -
317C ARG* 1.3 73.5 - - - +
319C ASN* 1.3 73.6 + - - +
320C ILE* 3.1 46.9 + - + +
325C LYS* 3.3 1.9 - - - +
326C ALA* 2.7 41.7 + - + +
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Residues in contact with ASN 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ASN 5.7 0.2 - - - +
268C SER* 3.8 12.0 + - - +
270C MSE 2.8 26.6 + - - +
271C PRO* 2.8 19.9 + - + +
273C ASN* 2.9 25.9 + - - -
317C ARG* 3.5 13.2 + - - -
318C TRP* 1.3 77.9 + - - +
320C ILE* 1.3 65.9 + - - +
321C ASP* 3.3 9.6 + - - +
324C TRP 3.7 0.7 - - - -
325C LYS* 2.9 44.7 + - - +
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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