Contacts of the strand formed by residues 374 - 381 (chain D) in PDB entry 1SA0
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 374 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272D PHE* 4.2 12.7 - - - -
274D PRO* 4.0 15.0 - - - -
291D LEU* 3.6 7.9 - - - +
319D PHE* 3.6 1.4 - - - +
320D ARG* 2.8 41.7 + - - +
323D MET* 4.5 0.3 - - - +
360D PRO* 3.6 33.6 - - - +
371D LEU* 4.6 4.3 - - - -
373D MET* 1.3 78.1 - - - +
375D ALA* 1.3 67.0 + - - +
376D THR* 4.7 2.6 - - - +
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Residues in contact with ALA 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D PHE* 3.7 4.6 - - - -
273D ALA* 2.7 36.3 + - + +
291D LEU* 2.9 37.0 - - + -
295D MET* 3.8 14.4 - - + -
318D VAL 3.7 8.5 - - - +
319D PHE* 4.3 8.3 - - + -
374D SER* 1.3 76.2 + - - +
376D THR* 1.3 64.9 + - - +
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Residues in contact with THR 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D THR* 5.1 2.5 - - - +
237D GLY* 3.4 42.6 + - - +
238D VAL* 3.9 10.4 + - - +
271D GLY 3.2 10.5 - - - -
272D PHE* 4.1 16.6 - - + +
295D MET* 3.8 6.9 - - - +
317D ALA* 3.7 2.4 - - - -
318D VAL* 3.1 44.1 + - + +
320D ARG* 5.5 4.3 - - - +
374D SER* 4.7 4.7 - - - +
375D ALA* 1.3 79.6 - - - +
377D PHE* 1.3 65.9 + - - +
378D ILE* 5.3 0.7 - - - +
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Residues in contact with PHE 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 5.3 0.5 - - - +
269D MET* 3.3 18.6 - - + -
270D PRO* 3.1 9.0 - - - +
271D GLY* 2.7 43.8 + - - +
295D MET* 3.4 33.0 - - + +
296D PHE* 3.7 24.0 - + - -
301D MET* 3.3 25.8 - - + -
312D TYR* 3.6 28.5 - + - -
315D VAL* 3.5 31.6 - - + -
316D ALA 3.8 4.5 - - - -
317D ALA* 5.1 0.7 - - + -
376D THR* 1.3 78.6 + - - +
378D ILE* 1.3 67.7 + - - +
379D GLY* 3.7 10.3 - - - -
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Residues in contact with ILE 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D TYR* 3.7 17.7 - - + +
238D VAL* 3.6 34.1 - - + -
255D LEU* 5.4 1.8 - - + -
259D MET* 3.5 23.2 - - + +
268D PHE* 3.8 25.6 - - + -
269D MET 4.1 1.6 - - - -
270D PRO* 4.7 1.6 - - + -
315D VAL* 3.5 3.1 - - - -
316D ALA* 2.7 44.2 + - + +
318D VAL* 5.4 2.2 - - + -
376D THR* 5.3 1.1 - - - +
377D PHE* 1.3 82.8 - - - +
379D GLY* 1.3 59.9 + - - +
701D CN2 3.3 33.9 - - - -
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Residues in contact with GLY 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D PHE 4.0 0.3 - - - +
268D PHE* 3.4 5.1 - - - -
269D MET* 2.8 49.1 + - - +
312D TYR* 4.8 0.9 - - - -
314D THR 4.0 3.6 - - - -
315D VAL* 4.1 3.8 - - - -
377D PHE* 3.7 15.7 - - - -
378D ILE* 1.3 77.2 - - - +
380D ASN* 1.3 61.1 + - - -
381D SER* 3.1 8.5 + - - -
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Residues in contact with ASN 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D MET* 3.1 19.3 - - + +
260D VAL* 4.1 1.2 - - - +
261D PRO* 3.8 7.8 - - - +
266D HIS* 3.4 33.5 - - - +
267D PHE 3.8 10.6 + - - -
268D PHE* 3.7 19.8 - - + -
312D TYR* 3.7 1.3 - - - -
313D LEU* 2.7 50.6 + - + +
314D THR* 3.0 29.1 + - - +
378D ILE 4.3 0.4 - - - -
379D GLY* 1.3 70.3 - - - -
381D SER* 1.3 51.2 + - - +
432D TYR* 4.1 6.9 + - - -
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Residues in contact with SER 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D PHE 4.6 1.4 + - - -
269D MET* 4.3 15.2 - - - +
307D PRO* 4.4 3.1 - - - +
310D GLY 4.2 2.8 + - - -
311D ARG 3.0 16.0 + - - -
312D TYR* 3.6 28.6 - - - +
313D LEU* 5.7 0.2 - - - -
379D GLY 3.1 6.1 + - - -
380D ASN* 1.3 79.0 + - - +
382D THR* 1.3 53.8 + - - +
383D ALA* 2.8 30.7 + - - +
384D ILE* 2.9 25.8 + - - +
432D TYR* 4.5 1.6 - - - -
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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