Contacts of the strand formed by residues 280 - 291 (chain C) in PDB entry 5O67
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 ALA 280 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A LEU* 4.7 8.7 - - + -
328A ASN* 5.1 1.3 - - - +
331A MET* 4.2 20.2 - - - -
371A MET* 5.4 0.2 - - + -
276C THR* 3.5 2.9 - - - +
277C PHE* 2.8 41.2 + - + +
279C PRO* 1.3 80.4 - - + +
281C VAL* 1.3 60.4 + - - +
282C LEU* 3.9 3.8 + - + +
323C VAL* 4.4 11.2 - - + -
324C ALA 3.9 3.8 - - - -
325C PHE* 4.0 17.3 - - + -
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Residues in contact with VAL 281 (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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92C VAL* 6.3 0.7 - - + -
95C LEU* 4.1 33.4 - - + -
96C TYR* 4.1 8.5 - - + +
274C VAL* 3.4 33.4 - - + -
275C LYS 3.7 9.9 - - - +
276C THR* 3.8 17.9 - - + +
279C PRO 4.7 3.8 - - - +
280C ALA* 1.3 73.8 - - - +
282C LEU* 1.3 63.6 + - - +
283C PHE* 3.9 5.4 - - + -
323C VAL* 3.4 5.2 - - - -
324C ALA 2.8 44.4 + - - +
325C PHE* 5.4 0.2 - - - -
326C ALA 5.8 0.2 - - - +
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Residues in contact with LEU 282 (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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331A MET* 3.8 18.2 - - + -
371A MET* 4.1 27.8 - - + -
373A ILE* 4.4 13.2 - - + -
274C VAL* 3.3 1.2 - - - -
275C LYS 2.9 36.7 + - - +
277C PHE* 3.6 30.5 - - + -
280C ALA* 3.9 2.4 - - + -
281C VAL* 1.3 72.7 - - - +
283C PHE* 1.3 62.2 - - - +
322C GLY 3.8 11.9 - - - +
323C VAL* 4.1 10.3 - - + -
505C C8E 4.1 33.8 - - + +
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Residues in contact with PHE 283 (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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95C LEU* 5.6 0.2 - - + -
99C ALA* 3.7 31.2 - - + +
273C MET 3.2 13.5 - - - +
274C VAL* 3.9 15.7 - - + -
281C VAL* 3.9 14.8 - - + -
282C LEU* 1.3 76.6 - - - +
284C GLY* 1.3 64.5 + - - +
285C SER* 6.1 0.2 - - - -
321C VAL* 3.6 8.7 - - - +
322C GLY* 2.9 49.4 + - - +
323C VAL 3.6 22.0 - - - -
324C ALA* 3.9 12.3 - - + -
334C SER* 3.9 16.6 - - - -
335C PHE 4.3 0.2 - - - -
336C SER* 4.0 14.8 - - - -
505C C8E 4.1 10.0 + - - +
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Residues in contact with GLY 284 (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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99C ALA 5.6 1.4 - - - +
272C SER* 3.3 2.1 - - - -
273C MET* 2.8 40.0 + - - +
274C VAL* 5.6 0.2 - - - +
283C PHE* 1.3 83.8 - - - +
285C SER* 1.3 63.0 + - - -
320C GLY 3.6 11.7 - - - -
321C VAL* 4.1 8.3 - - - -
505C C8E 4.3 6.3 - - - -
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Residues in contact with SER 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA 5.5 0.7 - - - -
271C LEU 3.2 15.5 - - - -
272C SER* 4.1 5.2 - - - +
273C MET* 5.1 2.6 - - - +
283C PHE* 6.1 0.2 - - - -
284C GLY* 1.3 75.9 - - - -
286C VAL* 1.3 67.3 + - - +
319C PHE* 3.5 2.0 - - - +
320C GLY* 3.1 32.7 + - - +
501C LDA 3.6 46.1 - - - +
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Residues in contact with VAL 286 (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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270C GLY* 3.5 0.5 - - - -
271C LEU* 2.9 55.3 + - + +
273C MET* 5.7 3.6 - - + -
285C SER* 1.3 78.2 - - - +
287C SER* 1.3 68.0 + - - +
317C PHE* 3.9 29.4 - - + -
318C GLN 3.5 13.9 - - - +
319C PHE* 4.0 7.4 - - + +
501C LDA 4.9 3.9 - - - +
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Residues in contact with SER 287 (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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268C THR* 4.3 9.0 - - - +
269C PRO 3.1 19.3 - - - -
270C GLY* 3.7 7.2 - - - -
286C VAL* 1.3 79.7 - - - +
288C TYR* 1.3 60.7 + - - +
317C PHE* 3.6 5.0 - - - -
318C GLN* 2.8 59.0 + - - +
501C LDA 3.6 24.9 - - - +
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Residues in contact with TYR 288 (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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267C ILE* 6.3 0.2 - - + -
268C THR* 3.4 7.0 - - - +
269C PRO* 3.3 52.5 + - + +
287C SER* 1.3 75.0 - - - +
289C THR* 1.3 70.1 + - - +
290C HIS* 4.7 14.6 - - + -
315C ASP* 6.4 0.7 - - + -
316C SER 3.3 14.4 - - - +
317C PHE* 4.4 12.8 - + + -
318C GLN* 4.0 2.5 - - - +
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Residues in contact with THR 289 (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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266C SER* 3.9 15.0 - - - +
267C ILE 3.6 0.2 - - - -
268C THR* 2.9 31.8 + - - +
288C TYR* 1.3 75.9 - - - +
290C HIS* 1.3 61.4 + - - +
291C ASN* 3.8 22.7 - - - +
315C ASP* 3.5 10.6 - - - +
316C SER* 3.0 37.7 + - - +
318C GLN* 3.7 12.2 + - - +
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Residues in contact with HIS 290 (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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266C SER* 3.4 3.1 - - - -
267C ILE* 3.0 45.2 + - + +
288C TYR* 4.2 15.5 + - + -
289C THR* 1.3 71.9 - - - +
291C ASN* 1.3 76.2 + - - +
292C LEU* 3.9 25.9 - - + +
315C ASP* 3.2 21.9 + - - +
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Residues in contact with ASN 291 (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 ASN* 4.4 6.9 + - - -
264C VAL* 4.1 14.1 - - + +
265C TRP 3.6 4.0 - - - -
266C SER* 3.4 18.5 - - - -
289C THR* 3.8 11.1 + - - +
290C HIS* 1.3 90.9 - - - +
292C LEU* 1.3 62.6 + - - +
293C GLU 4.0 1.4 + - - -
312C ARG* 6.1 1.3 - - - +
313C LEU* 3.2 34.6 + - + +
314C GLY 2.8 28.7 + - - -
315C ASP* 3.1 14.0 + - - +
316C SER* 5.7 0.4 + - - -
342C GLN* 4.7 2.8 - - - +
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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