Contacts of the strand formed by residues 312 - 320 (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 TYR 312 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269D MET* 4.2 2.5 - - + -
296D PHE* 3.9 24.5 + + - -
301D MET* 4.5 1.6 - - - +
307D PRO* 3.1 40.6 - - + +
310D GLY 5.5 0.4 - - - -
311D ARG* 1.3 73.9 - - - +
313D LEU* 1.3 64.6 + - - +
314D THR 4.6 1.6 - - - +
315D VAL* 3.5 20.9 - - + -
342D TYR* 3.0 32.7 + + + +
343D PHE* 3.6 38.3 - + + -
344D VAL* 3.4 25.1 + - - +
350D ASN* 4.2 1.6 - - - +
377D PHE* 3.6 26.5 - + - -
379D GLY* 4.8 1.1 - - - -
380D ASN 3.9 2.0 - - - -
381D SER* 3.6 20.2 - - - +
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Residues in contact with LEU 313 (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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261D PRO* 3.8 28.7 - - + -
262D PHE* 5.2 5.4 - - + -
266D HIS* 4.7 12.6 - - + +
311D ARG 4.0 1.4 + - - -
312D TYR* 1.3 72.7 - - - +
314D THR* 1.3 68.0 + - - +
344D VAL* 4.0 13.2 - - + +
346D TRP* 3.5 34.5 - - + -
347D ILE* 3.8 12.5 - - + +
350D ASN* 3.3 14.3 - - - +
380D ASN* 2.7 38.7 + - + +
381D SER* 4.3 0.2 - - - +
382D THR* 4.4 23.3 - - + -
432D TYR* 5.0 2.9 - - + -
435D TYR* 4.9 8.3 - - + -
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Residues in contact with THR 314 (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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181C VAL* 5.1 1.3 - - + -
404C PHE* 4.2 16.6 - - + -
258D ASN 4.1 9.9 - - - +
259D MET* 2.8 45.0 + - - +
261D PRO* 4.6 1.3 - - + -
312D TYR* 4.7 0.9 - - - -
313D LEU* 1.3 87.9 - - + +
315D VAL* 1.3 63.9 + - - +
347D ILE* 4.3 14.8 - - + -
350D ASN* 3.4 14.4 - - + -
380D ASN* 3.0 27.0 + - - +
701D CN2 4.2 5.2 - - - -
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Residues in contact with VAL 315 (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* 4.1 2.5 - - - -
296D PHE* 4.2 11.4 - - + -
312D TYR* 3.5 37.9 - - + -
314D THR* 1.3 76.2 - - - +
316D ALA* 1.3 68.3 + - - +
317D ALA* 4.6 3.1 - - + +
343D PHE* 4.4 7.6 - - + -
350D ASN 3.0 7.0 + - - +
351D VAL* 3.3 28.3 - - + -
352D LYS 3.2 21.8 + - - -
377D PHE* 3.5 32.8 - - + -
378D ILE 3.5 3.8 - - - +
379D GLY* 4.1 0.9 - - - -
701D CN2 3.3 7.1 - - - +
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Residues in contact with ALA 316 (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* 3.8 24.2 - - + -
315D VAL* 1.3 77.8 - - - +
317D ALA* 1.3 57.6 + - - +
318D VAL* 4.4 2.2 + - - +
352D LYS 3.4 5.4 - - - +
377D PHE* 3.7 0.5 - - - -
378D ILE* 2.7 49.2 + - + +
701D CN2 3.3 32.8 - - + +
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Residues in contact with ALA 317 (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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295D MET* 4.1 18.6 - - - -
296D PHE* 5.6 0.2 - - + -
315D VAL* 4.6 5.8 - - + +
316D ALA* 1.3 74.4 - - - +
318D VAL* 1.3 62.9 + - - +
319D PHE* 4.2 8.3 - - + -
332D MET* 4.6 8.3 - - + -
352D LYS 2.9 8.0 + - - +
353D THR* 3.2 21.2 - - + -
354D ALA* 2.8 25.5 + - - +
376D THR 3.7 10.1 - - - +
377D PHE* 4.9 1.3 - - + -
701D CN2 4.3 2.1 - - - +
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Residues in contact with VAL 318 (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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237D GLY 3.9 15.0 - - - +
238D VAL* 5.2 0.4 - - - -
240D THR* 3.4 25.6 - - - +
241D CYS* 4.2 10.5 - - + +
247D GLN* 5.8 1.3 - - - +
316D ALA 5.0 1.8 - - - +
317D ALA* 1.3 77.8 - - - +
319D PHE* 1.3 71.3 + - - +
320D ARG* 5.0 1.1 - - - -
354D ALA* 3.1 18.4 - - + +
356D CYS* 5.5 3.8 - - + -
375D ALA* 3.7 0.2 - - - -
376D THR* 3.1 44.5 + - + +
378D ILE* 5.4 2.5 - - + -
701D CN2 4.2 25.8 - - - +
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Residues in contact with PHE 319 (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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288D VAL* 4.9 6.1 - - + -
291D LEU* 3.5 23.3 - - + -
292D THR* 3.8 8.7 - - + -
295D MET* 3.7 22.7 - - + -
317D ALA* 4.2 10.8 - - + -
318D VAL* 1.3 84.7 - - - +
320D ARG* 1.3 73.8 + - - +
323D MET* 3.5 26.0 - - + -
328D VAL* 3.7 35.9 - - + -
332D MET* 3.8 22.9 - - + -
353D THR* 4.5 3.1 - - + -
354D ALA 2.8 14.0 + - - -
355D VAL* 3.6 20.0 - - + -
356D CYS 3.6 15.9 + - - -
374D SER 3.5 4.7 - - - -
375D ALA* 4.1 3.4 - - + +
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Residues in contact with ARG 320 (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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27D GLU* 2.7 38.8 + - - +
236D SER* 4.0 6.5 + - - -
237D GLY* 4.5 8.5 - - - +
240D THR* 3.0 39.4 - - - +
244D PHE* 4.2 6.3 - - - -
272D PHE* 5.9 2.0 - - - -
318D VAL* 5.0 2.2 - - - +
319D PHE* 1.3 82.5 - - - +
321D GLY* 1.3 62.1 + - - +
323D MET* 4.1 6.5 - - - +
356D CYS* 3.1 19.1 + - - +
358D ILE* 3.4 32.7 + - - +
359D PRO* 5.1 1.6 - - - -
360D PRO* 3.2 29.1 - - + +
373D MET* 3.7 4.5 - - - -
374D SER* 2.8 54.1 + - - +
376D THR* 5.5 3.3 - - + +
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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