Contacts of the strand formed by residues 277 - 284 (chain C) in PDB entry 4X4R
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 277 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C THR* 1.3 70.8 - - - +
278C VAL* 1.3 60.8 + - - +
279C PHE* 4.0 7.2 - - + -
331C PHE 3.5 2.1 - - - +
332C GLU* 3.3 3.8 - - - -
333C CYS* 2.8 38.3 + - + +
335C ILE 4.1 5.4 - - - +
336C LYS* 3.7 27.9 - - + +
385C PRO* 4.1 14.1 - - + -
386C GLU* 4.1 14.8 - - - +
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C VAL* 3.8 32.2 - - + +
276C THR* 3.6 21.0 + - - +
277C ALA* 1.3 73.3 - - - +
279C PHE* 1.3 65.0 + - - +
331C PHE 3.4 9.2 - - - +
332C GLU* 3.9 11.0 - - + -
386C GLU* 5.0 1.4 + - - -
416C SER* 3.6 14.2 + - - -
417C GLY 4.4 2.3 + - - -
420C LEU* 3.7 18.9 - - + +
421C PHE* 5.5 3.6 - - + -
429C LEU* 3.7 31.6 - - + -
432C MET* 4.6 4.0 - - + -
433C MET* 4.4 7.4 - - - -
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Residues in contact with PHE 279 (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 ALA 4.0 10.3 - - - -
278C VAL* 1.3 76.6 - - - +
280C ALA* 1.3 66.5 + - - +
281C VAL* 5.0 0.2 - - + -
308C LEU* 4.2 4.7 - - + -
329C LEU 3.9 0.2 - - - +
330C LEU* 3.7 1.4 - - - +
331C PHE* 3.0 62.1 + + + +
333C CYS* 4.1 10.1 - - - -
385C PRO* 3.5 28.5 - - + -
386C GLU* 3.7 31.6 - - + +
389C VAL* 3.6 40.4 - - + -
414C ILE* 3.9 16.2 - - + -
415C ILE 3.4 12.6 - - - +
416C SER* 4.2 3.4 - - - -
420C LEU* 4.1 4.7 - - - -
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Residues in contact with ALA 280 (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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279C PHE* 1.3 76.9 - - - +
281C VAL* 1.3 65.5 + - - +
282C LYS 4.0 0.6 + - - +
328C TYR* 4.6 13.2 - - + -
329C LEU 3.1 6.3 - - - +
330C LEU* 3.5 21.8 - - + -
414C ILE* 3.4 8.5 - - - +
415C ILE* 3.0 33.0 + - + +
420C LEU* 3.5 25.4 - - + -
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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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279C PHE* 5.0 1.1 - - + -
280C ALA* 1.3 74.7 - - - +
282C LYS* 1.3 60.3 + - - +
283C PHE* 3.8 19.7 - - + -
304C ILE* 4.3 7.0 - - + -
327C CYS 3.4 6.9 - - - +
328C TYR* 3.4 2.0 - - - -
329C LEU* 3.0 36.6 + - + -
331C PHE* 4.0 17.7 - - + -
389C VAL* 3.7 28.9 - - + -
393C ALA* 5.3 3.6 - - + -
408C ILE* 4.8 7.4 - - + -
412C PHE* 4.0 26.0 - - + -
413C GLU 3.9 1.8 - - - -
414C ILE* 3.8 8.1 - - + -
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Residues in contact with LYS 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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280C ALA 4.0 0.4 + - - -
281C VAL* 1.3 73.0 - - - +
283C PHE* 1.3 62.3 + - - +
326C PHE* 3.5 46.7 - - + -
327C CYS 3.5 4.9 - - - +
328C TYR* 3.5 28.1 + - + -
411C TYR* 5.1 1.2 - - - -
412C PHE* 3.2 7.3 - - - +
413C GLU* 3.0 57.9 + - + +
415C ILE* 4.2 15.3 - - + -
423C GLU* 2.9 34.0 + - - +
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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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281C VAL* 3.8 19.3 - - + -
282C LYS* 1.3 80.2 - - - +
284C ARG* 1.3 74.8 + - - +
286C PRO* 4.4 3.1 - - + -
297C LEU* 4.0 9.9 - - + -
326C PHE* 3.3 12.1 - - - -
327C CYS* 2.8 57.7 + - + -
329C LEU* 4.0 17.3 - - + -
404C VAL* 3.6 35.4 - - + -
407C SER* 3.6 15.3 - - - +
408C ILE* 3.8 20.2 - - + -
411C TYR* 3.7 22.4 - - - +
412C PHE* 4.2 3.6 - - + -
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Residues in contact with ARG 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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283C PHE* 1.3 76.8 - - - +
285C LYS* 1.3 69.9 + - - +
286C PRO* 3.2 5.7 - - - +
325C GLU* 2.7 51.6 + - - +
326C PHE* 4.0 13.0 - - + -
407C SER* 2.7 28.8 + - - +
411C TYR* 4.9 7.8 + - + +
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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