Contacts of the strand formed by residues 298 - 311 (chain C) in PDB entry 5NXR
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 GLN 298 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287C LYS* 4.7 2.0 - - - -
288C GLY* 2.7 39.9 + - - +
291C LEU* 3.8 9.9 - - + -
295C TYR* 3.8 26.0 - - + +
296C ASP 4.1 1.6 + - - +
297C ASN* 1.3 81.5 + - - +
299C ASP* 1.3 64.2 + - - +
300C LEU* 4.0 1.0 - - - +
330C ASN* 3.1 27.9 + - - +
332C PHE* 3.6 47.9 - - + +
333C THR* 5.9 0.3 - - - +
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Residues in contact with ASP 299 (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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285C GLN* 4.1 5.0 + - - -
286C SER 3.7 6.5 - - - +
287C LYS* 3.5 26.3 - - - +
298C GLN* 1.3 79.6 + - - +
300C LEU* 1.3 59.9 + - - +
301C VAL 4.7 1.1 - - - +
302C LYS* 3.8 35.1 + - + +
326C LEU 5.4 0.9 - - - +
327C LEU* 3.5 29.9 - - + +
328C LYS 5.6 1.4 + - - -
332C PHE* 3.7 18.5 - - - -
338C ILE* 5.0 0.9 - - - +
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Residues in contact with LEU 300 (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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250C SER* 5.9 1.8 - - - -
251C ARG 5.5 2.0 - - - +
252C TYR* 3.8 34.8 - - + -
259C ALA* 4.7 4.3 - - + -
262C THR* 3.8 22.7 - - + -
286C SER* 2.7 31.8 + - - +
288C GLY* 3.8 14.8 - - - +
291C LEU* 4.0 13.5 - - + -
298C GLN 4.1 0.2 - - - +
299C ASP* 1.3 76.2 - - - +
301C VAL* 1.3 66.3 + - + +
327C LEU* 4.4 4.6 - - - +
332C PHE* 3.8 26.5 - - + -
338C ILE* 3.9 26.1 - - + +
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASP* 3.4 34.3 - - + +
118C THR* 4.5 2.7 - - + +
284C ASN* 4.0 5.2 - - + +
285C GLN* 3.1 4.5 - - - +
286C SER* 2.8 47.3 + - - +
299C ASP* 4.9 0.2 - - - +
300C LEU* 1.3 87.0 + - + +
302C LYS* 1.3 65.5 + - - +
303C TYR* 3.7 31.0 - - + -
327C LEU* 4.3 7.0 - - + -
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Residues in contact with LYS 302 (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 TYR* 3.5 26.0 - - - +
284C ASN 3.2 5.2 - - - -
285C GLN* 3.9 23.7 - - + +
299C ASP* 3.8 23.4 + - + +
301C VAL* 1.3 77.3 - - - +
303C TYR* 1.3 62.6 + - - +
325C ASN* 3.3 6.5 - - - +
326C LEU* 2.8 52.2 + - + +
327C LEU* 3.7 19.2 + - + +
405C LDA 6.3 2.1 - - - -
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Residues in contact with TYR 303 (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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111C PHE* 4.2 14.6 - + - -
114C TRP* 3.5 13.9 - - + +
115C GLY* 2.8 21.5 + - - -
117C ASP* 2.4 30.0 + - + -
283C TYR* 3.4 8.1 - - - -
284C ASN* 2.9 48.0 + - + -
301C VAL* 3.7 27.6 - - + -
302C LYS* 1.3 76.7 - - - +
304C ILE* 1.3 74.8 + - - +
305C SER* 4.3 3.4 - - - -
323C LYS* 3.8 36.3 - - + -
324C ILE 3.3 13.5 - - - +
325C ASN* 4.0 7.6 - - - +
326C LEU* 4.2 2.9 - - - +
327C LEU* 6.5 0.2 - - + -
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Residues in contact with ILE 304 (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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281C ILE* 4.6 10.3 - - + -
282C GLY 3.3 10.8 - - - +
283C TYR* 3.7 18.6 - - + -
303C TYR* 1.3 78.9 - - - +
305C SER* 1.3 70.1 + - - +
306C VAL* 4.2 0.9 - - + -
322C TYR 3.6 0.7 - - - +
323C LYS* 3.6 3.1 - - - -
324C ILE* 2.8 45.6 + - + +
326C LEU* 3.8 26.2 - - + +
405C LDA 3.8 42.4 - - + -
425C LDA 4.5 23.8 - - + -
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Residues in contact with SER 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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111C PHE* 3.5 37.2 - - - -
112C PRO* 4.8 2.3 - - - +
114C TRP* 4.3 10.5 - - - -
280C SER* 4.8 2.8 + - - -
281C ILE* 3.2 9.9 - - - +
282C GLY 2.7 36.9 + - - -
303C TYR* 4.3 4.0 - - - -
304C ILE* 1.3 75.9 - - - +
306C VAL* 1.3 62.4 + - - +
321C ASP* 2.8 22.0 + - - -
322C TYR 3.5 3.8 - - - -
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Residues in contact with VAL 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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280C SER 3.7 2.7 - - - -
281C ILE* 3.6 30.5 - - + -
304C ILE* 4.2 1.5 - - + -
305C SER* 1.3 73.4 + - - +
307C GLY* 1.3 55.7 + - - +
320C VAL 4.8 0.2 - - - -
321C ASP* 3.8 2.2 - - - -
322C TYR* 2.8 67.0 + - + +
324C ILE* 4.1 11.2 - - + -
403C LDA 4.4 17.2 - - + +
404C LDA 4.2 21.3 - - + -
425C LDA 4.1 17.9 - - + -
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Residues in contact with GLY 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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112C PRO* 4.3 4.3 - - - -
279C PRO* 3.3 4.3 - - - +
280C SER 2.7 38.6 + - - +
306C VAL* 1.3 74.7 - - - +
308C SER* 1.3 59.0 + - - -
320C VAL 3.0 15.7 - - - -
321C ASP* 4.0 5.5 + - - -
403C LDA 4.1 15.6 - - - +
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PRO* 3.9 4.8 - - - +
277C LEU* 3.4 18.0 - - - +
278C LYS 3.3 18.4 - - - -
279C PRO* 3.3 6.2 - - - +
280C SER 4.3 0.4 - - - +
307C GLY* 1.3 76.6 - - - -
309C TYR* 1.3 80.1 + - - +
319C VAL* 3.2 6.6 - - - +
320C VAL* 2.9 39.0 + - - +
403C LDA 4.2 14.8 - - - -
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Residues in contact with TYR 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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110C VAL* 2.6 30.6 + - - -
111C PHE 2.9 14.4 + - - -
112C PRO* 3.6 23.8 - - + -
270C GLN* 4.2 9.2 - - - -
277C LEU* 3.6 3.2 - - - +
278C LYS* 3.0 46.2 + - + +
280C SER* 4.6 1.6 - - - -
308C SER* 1.3 90.6 + - - +
310C TYR* 1.3 61.1 + - - +
311C TYR* 3.2 44.0 - + + -
317C SER* 5.5 3.8 - - - -
318C ALA 3.4 6.5 - - - +
319C VAL* 3.5 21.3 - - + -
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Residues in contact with TYR 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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275C PHE* 3.6 32.9 + + - -
276C GLY 3.5 12.1 - - - -
277C LEU* 4.0 20.2 - - + -
309C TYR* 1.3 74.1 - - - +
311C TYR* 1.3 61.7 + - - +
312C PHE* 3.5 47.8 + + - -
317C SER* 3.2 4.7 - - - -
318C ALA* 2.7 45.5 + - + +
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Residues in contact with TYR 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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272C LEU* 4.3 12.8 - - + -
275C PHE 4.8 0.9 - - - +
276C GLY* 2.9 37.5 + - - +
278C LYS* 3.2 38.1 + - + -
309C TYR* 3.2 43.5 - + + -
310C TYR* 1.3 75.8 - - - +
312C PHE* 1.3 63.9 - - - +
313C ASN* 4.2 14.5 - - - +
314C LYS* 6.3 0.2 - - - -
316C MET 3.9 2.7 - - - -
317C SER* 4.0 17.5 - - - -
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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