Contacts of the strand formed by residues 370 - 380 (chain B) in PDB entry 1EX0
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 TRP 370 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.7 32.8 + - - +
279B PHE* 3.9 14.1 - + - -
314B CYS* 4.0 1.8 - - + -
339B PHE* 3.2 5.7 - - - -
340B SER* 2.8 42.9 + - - +
342B HIS* 3.7 32.1 + + + +
343B ASP* 4.6 3.6 + - - -
368B SER 4.3 7.1 + - - -
369B VAL* 1.3 75.4 - - - +
371B ASN* 1.3 66.4 + - - +
372B TYR 3.4 24.2 - - - +
373B HIS* 3.5 26.9 - + + -
398B THR* 4.3 9.6 - - + -
560B TYR* 3.4 29.2 - + - -
561B THR* 3.3 43.0 + - + -
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Residues in contact with ASN 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLY 3.5 19.8 - - - +
216B GLU* 4.5 5.7 - - + -
217B VAL 5.1 0.3 + - - -
338B TYR* 3.4 11.1 - - - +
339B PHE* 3.0 30.2 + - - -
369B VAL 3.6 5.5 + - - -
370B TRP* 1.3 70.2 - - - +
372B TYR* 1.3 62.8 + - + +
558B THR* 4.6 2.6 + - - -
559B PHE 4.6 1.1 - - - +
560B TYR* 2.8 23.0 + - + +
562B GLY* 5.2 4.6 - - - +
603B SER* 3.6 29.1 + - - -
604B LEU 5.1 0.2 - - - +
605B HIS* 5.0 2.2 + - - +
624B SER* 2.7 37.2 + - - -
625B THR 4.9 0.2 - - - +
626B VAL* 4.7 3.3 - - - +
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Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE 4.1 1.6 - - - -
214B TYR* 3.4 26.0 - - + +
215B GLY 3.4 24.2 - - - -
314B CYS* 4.7 0.7 - - - -
315B TRP* 3.9 16.8 - + + -
336B THR* 3.5 27.1 - - + -
337B ASN 3.2 9.0 - - - +
338B TYR* 3.8 9.6 - - + -
340B SER* 4.5 0.2 - - - -
370B TRP* 3.4 20.3 - - - +
371B ASN* 1.3 80.2 - - + +
373B HIS* 1.3 68.1 + - - +
374B CYS* 4.0 19.7 - - - -
560B TYR* 3.5 32.0 + + + -
601B GLN* 2.8 40.3 + - - -
716B HIS* 4.4 2.1 + - - -
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Residues in contact with HIS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B CYS* 3.3 26.9 - - + +
336B THR* 3.5 0.5 - - - -
337B ASN* 3.0 32.4 + - - +
340B SER* 3.5 16.8 - - - +
342B HIS* 3.5 9.0 - + - -
370B TRP* 3.5 17.1 - + + -
372B TYR* 1.3 77.9 - - - +
374B CYS* 1.3 81.1 + - - +
375B TRP* 3.6 18.6 - + - -
396B ASP* 2.6 28.3 + - - -
398B THR* 3.5 21.3 - - + -
434B GLU* 3.3 22.2 - - - -
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Residues in contact with CYS 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 4.0 13.7 - - - -
213B PHE 4.1 0.2 - - - -
314B CYS* 3.3 12.5 - - - +
315B TRP* 3.8 38.4 - - - -
318B ALA* 4.3 2.2 - - + -
334B ILE* 4.2 10.8 - - + -
335B VAL 3.2 7.2 - - - +
336B THR* 3.6 21.3 - - - -
372B TYR* 4.0 16.4 - - - -
373B HIS* 1.3 99.4 + - - +
375B TRP* 1.3 61.2 + - - +
396B ASP* 4.0 1.9 - - - +
398B THR* 4.5 0.3 + - - -
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Residues in contact with TRP 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ALA* 4.4 3.8 - - - -
334B ILE* 3.4 6.8 - - - +
335B VAL* 2.8 45.2 + - + +
337B ASN* 3.5 40.2 - - + -
340B SER* 3.8 5.6 - - - -
373B HIS* 3.6 34.3 - + - -
374B CYS* 1.3 72.2 - - - +
376B ASN* 1.3 87.5 + - - +
394B ALA* 3.8 12.7 - - + +
395B VAL 3.7 12.1 - - - +
396B ASP* 3.7 24.0 - - + +
397B SER 5.6 0.4 - - - +
431B VAL* 4.5 9.0 - - + -
434B GLU* 3.8 11.2 - - + -
435B VAL* 3.9 13.2 - - + -
464B ILE* 5.1 2.0 - - + -
481B TYR* 3.0 41.4 + + - -
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Residues in contact with ASN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ALA* 2.9 40.9 + - - -
321B PHE* 3.5 30.3 - - + +
322B ASN* 3.4 27.0 + - - +
325B LEU* 4.8 3.5 - - + +
333B ARG 3.3 5.6 - - - +
334B ILE* 3.7 6.1 - - - +
375B TRP* 1.3 85.6 - - - +
377B GLU* 1.3 67.1 + - - +
394B ALA* 3.6 1.0 - - - -
395B VAL* 2.9 39.3 + - + +
397B SER* 4.7 4.7 + - - -
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Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ALA* 3.1 7.6 - - - +
333B ARG* 2.7 74.3 + - + -
335B VAL* 3.5 19.2 - - + +
376B ASN* 1.3 81.7 - - - +
378B ALA* 1.3 60.3 + - - +
392B TRP* 3.5 27.9 - - + -
393B GLN 3.2 9.6 - - - +
394B ALA* 4.5 1.3 - - - -
395B VAL* 5.7 0.2 - - - -
414B VAL* 3.6 6.6 - - + +
477B ILE* 4.2 1.8 - - - +
480B THR* 4.8 1.0 + - - -
481B TYR* 2.6 41.3 + - - +
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B SER* 4.0 6.1 - - - +
325B LEU* 3.8 23.1 - - + -
330B ILE* 3.9 7.9 - - + -
331B PRO 3.4 5.4 - - - -
332B ALA* 4.4 0.2 - - - +
377B GLU* 1.3 75.0 - - - +
379B TRP* 1.3 59.2 + - - +
380B MET* 3.4 21.3 - - + -
392B TRP* 3.7 3.4 - - - -
393B GLN* 2.9 38.6 + - - +
395B VAL* 4.8 7.2 - - + -
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Residues in contact with TRP 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ALA 5.5 0.2 + - - -
193B VAL* 3.5 41.9 - - - +
194B TYR 2.9 20.3 + - - -
195B LEU* 3.7 29.5 - - + +
196B ASP 6.0 0.2 - - - -
200B GLU* 5.7 3.1 - - - -
330B ILE* 4.1 1.9 - - - +
331B PRO* 2.9 30.7 + - + +
378B ALA* 1.3 71.1 - - - +
380B MET* 1.3 69.7 + - - +
391B GLY* 3.4 39.5 - - - -
392B TRP* 3.5 44.4 - + + -
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Residues in contact with MET 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ALA 3.5 12.1 - - - +
193B VAL* 4.5 0.4 - - + -
255B PRO* 3.7 17.9 - - + +
256B ILE* 3.5 39.7 - - + -
259B SER* 3.5 15.7 - - - +
330B ILE* 4.2 6.3 - - + -
378B ALA* 3.4 41.3 - - + +
379B TRP* 1.3 83.8 - - - +
381B THR* 1.3 77.5 + - - +
382B ARG* 4.4 0.7 - - - -
390B GLY* 3.4 1.7 - - - -
391B GLY* 3.0 28.5 + - - +
393B GLN* 3.6 21.0 + - + -
411B PRO* 5.2 2.0 - - + -
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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