Contacts of the strand formed by residues 278 - 287 (chain A) in PDB entry 5JPM
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 GLY 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A VAL* 3.7 5.9 + - - -
277A GLN* 1.3 75.6 - - - +
279A VAL* 1.3 60.5 + - - -
304A LYS* 4.1 3.9 - - - +
305A LEU* 3.1 35.8 + - - +
344A ILE* 5.4 0.2 - - - -
345A ILE 3.2 13.9 - - - -
346A GLU* 4.1 1.3 - - - -
347A SER* 3.2 15.9 + - - -
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Residues in contact with VAL 279 (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 GLY* 1.3 75.0 - - - -
280A ALA* 1.3 63.0 + - - +
281A TYR* 6.1 0.7 - - + -
302A GLN* 3.7 33.7 - - + +
303A THR 3.3 17.0 - - - +
304A LYS* 4.3 13.7 - - + +
305A LEU* 4.6 1.8 - - - -
343A ALA 3.8 1.4 - - - +
344A ILE* 3.4 2.4 - - - +
345A ILE* 2.9 56.3 + - + +
347A SER* 4.2 4.7 + - - +
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Residues in contact with ALA 280 (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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266A ILE* 4.6 17.0 - - + -
279A VAL* 1.3 75.8 - - - +
281A TYR* 1.3 60.6 + - - +
282A VAL* 3.9 1.8 + - - +
302A GLN* 3.6 1.6 - - - -
303A THR* 2.8 48.6 + - - +
305A LEU* 3.8 23.3 - - + +
310A SER* 5.1 0.4 - - - -
342A ALA* 5.8 0.7 - - + -
343A ALA 3.4 4.9 - - - +
344A ILE* 3.9 16.2 - - + -
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Residues in contact with TYR 281 (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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279A VAL* 4.1 0.4 + - + -
280A ALA* 1.3 71.4 - - - +
282A VAL* 1.3 58.5 + - - +
283A ARG* 4.2 20.8 + - + -
300A GLU* 2.2 46.1 + - + +
301A SER 3.6 14.8 - - - -
302A GLN* 4.1 20.4 - - + +
341A ALA 3.7 1.6 - - - +
342A ALA* 3.3 2.1 - - - -
343A ALA* 2.6 44.7 + - + +
345A ILE* 4.5 8.1 - - + -
681B VAL* 4.3 21.0 + - + +
684B GLN* 3.6 27.1 - - + +
685B LYS 5.4 0.2 + - - -
767B ILE* 3.5 34.8 - - + -
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 5.0 0.4 - - + -
266A ILE* 4.2 19.1 - - + -
280A ALA 5.0 3.8 - - - +
281A TYR* 1.3 74.8 - - - +
283A ARG* 1.3 60.1 + - - +
284A PHE* 3.7 22.6 - - + -
299A LEU 4.6 0.3 - - - +
300A GLU* 3.6 1.2 - - - +
301A SER* 2.6 66.6 + - - +
303A THR* 5.0 0.2 - - - +
312A ILE* 4.1 26.2 - - + -
340A VAL* 3.7 25.4 - - + -
341A ALA 3.4 6.1 - - - +
342A ALA* 4.3 1.6 - - + +
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Residues in contact with ARG 283 (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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281A TYR* 4.2 12.4 + - + -
282A VAL* 1.3 75.5 - - - +
284A PHE* 1.3 64.3 + - - +
295A PHE* 4.0 27.8 - - + -
297A ARG* 5.9 1.3 - - - +
300A GLU* 3.8 35.6 + - + +
339A TYR 3.7 1.9 - - - +
340A VAL* 3.7 2.3 - - - -
341A ALA* 2.9 56.7 + - + +
342A ALA 6.2 0.2 - - - -
343A ALA* 6.1 1.2 - - - +
354A GLU* 3.9 11.5 + - - -
688B ASN* 5.9 3.0 - - - +
767B ILE* 3.3 36.6 + - - +
768B ASP 2.6 31.9 + - - -
769B GLU* 4.1 14.5 + - - +
770B ASP 5.1 1.0 + - - -
772B ILE* 5.1 5.7 - - - +
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Residues in contact with PHE 284 (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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264A LEU* 4.2 10.3 - - + -
282A VAL* 3.7 25.8 - - + -
283A ARG* 1.3 77.7 - - - +
285A GLY* 1.3 59.0 + - - +
295A PHE* 3.7 8.6 - - - -
296A PHE* 2.8 40.9 + - + +
299A LEU* 3.2 33.7 + - + +
300A GLU* 4.9 1.2 - - - +
301A SER* 4.7 5.4 - - - -
312A ILE* 3.6 31.6 - - + -
313A SER 5.7 0.4 - - - -
314A LEU* 4.4 34.3 - - + -
338A LEU* 4.0 10.8 - - + -
339A TYR 3.3 3.1 - - - +
340A VAL* 3.8 29.6 - - + -
360A TRP* 5.6 0.2 - + - -
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Residues in contact with GLY 285 (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 PHE* 1.3 77.0 - - - +
286A LEU* 1.3 57.7 + - - -
294A THR 3.2 13.7 - - - -
295A PHE* 3.9 6.7 - - - -
296A PHE* 3.6 14.3 - - - -
338A LEU* 3.6 11.3 - - - +
339A TYR* 2.7 41.7 + - - +
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Residues in contact with LEU 286 (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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285A GLY* 1.3 78.1 - - - +
287A LEU* 1.3 60.9 + - - +
288A ASP 4.0 0.6 + - - -
292A LYS 3.6 4.3 - - - +
293A LYS* 3.6 2.1 - - - +
294A THR* 2.8 40.2 + - - +
296A PHE* 3.6 23.8 - - + -
319A PHE* 4.7 2.0 - - + -
323A LEU* 3.9 22.2 - - + -
326A LEU* 4.7 6.7 - - + -
328A MET* 4.3 19.5 - - + -
333A LEU* 4.6 6.3 - - + -
336A LEU* 4.3 18.8 - - + -
337A ARG 3.5 1.8 - - - +
338A LEU* 4.4 1.8 - - + -
339A TYR* 4.3 2.2 - - - +
362A PHE* 3.7 35.2 - - + -
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Residues in contact with LEU 287 (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 LEU* 1.3 72.0 - - - +
288A ASP* 1.3 70.0 + - - +
291A GLY* 3.8 18.2 - - - +
292A LYS 3.6 11.4 - - - +
293A LYS* 3.9 17.0 - - + -
336A LEU* 3.6 4.8 - - - -
337A ARG* 2.8 70.5 + - + +
339A TYR* 4.1 16.6 - - + +
358A THR* 3.8 32.3 - - + +
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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