Contacts of the strand formed by residues 392 - 405 (chain B) in PDB entry 2W77
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 GLU 392 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354B ASP* 2.6 32.7 - - - +
355B ASN 3.3 12.3 - - - +
356B ASP* 3.7 21.7 - - - +
357B PRO* 3.7 3.4 - - - -
390B SER* 3.4 8.4 + - - +
391B TRP* 1.3 76.0 - - - +
393B GLN* 1.3 64.4 + - - +
394B TYR* 3.4 28.2 - - - +
423B TYR* 3.4 2.3 - - - -
424B HIS* 3.0 57.7 + - + +
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Residues in contact with GLN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ASP* 3.1 28.5 + - - +
232B SER* 3.2 35.1 - - - +
233B ALA 5.2 0.4 - - - -
234B GLY* 2.9 36.7 + - - +
236B THR* 3.6 6.8 - - - +
237B LEU* 3.6 14.5 - - + +
355B ASN* 2.8 52.7 + - - +
391B TRP* 3.3 34.2 + - + +
392B GLU* 1.3 71.2 + - - +
394B TYR* 1.3 61.3 + - - +
422B GLY 3.6 5.6 - - - +
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Residues in contact with TYR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ALA 4.2 0.8 + - - +
352B TYR* 5.6 8.5 - + + +
353B GLN 3.3 9.4 - - - +
354B ASP* 4.3 7.6 - - - +
392B GLU* 3.4 30.3 - - - +
393B GLN* 1.3 74.2 - - - +
395B THR* 1.3 67.0 + - - +
396B ARG* 4.9 11.9 - - + -
420B ILE* 3.9 23.3 - - + -
421B ASN* 3.6 1.7 - - - -
422B GLY* 2.7 65.3 + - - +
423B TYR 4.0 9.0 - - - -
424B HIS* 5.3 3.1 - - + -
450B GLY 4.2 1.9 + - - -
451B GLU* 2.9 32.6 + - + +
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Residues in contact with THR 395 (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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233B ALA 3.3 25.8 - - - +
234B GLY* 4.3 13.0 - - - +
235B ASN* 5.0 0.9 - - - +
351B ASP* 5.3 1.1 - - - -
352B TYR* 4.6 1.9 - - - -
353B GLN* 2.7 56.5 + - - +
355B ASN* 5.6 1.8 + - - +
394B TYR* 1.3 77.2 - - - +
396B ARG* 1.3 64.9 + - - +
397B THR* 6.1 0.2 - - - -
419B LYS* 4.9 10.8 - - - -
420B ILE 3.1 7.2 - - - +
421B ASN* 3.8 14.1 - - - +
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Residues in contact with ARG 396 (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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351B ASP* 3.2 18.4 - - - +
352B TYR* 3.9 26.6 - - + -
394B TYR* 4.9 11.8 - - + -
395B THR* 1.3 79.3 - - - +
397B THR* 1.3 66.6 + - - +
398B VAL* 5.4 11.0 - - + +
418B HIS 3.8 1.0 - - - +
419B LYS* 3.7 1.9 - - - +
420B ILE* 2.8 61.7 + - + +
451B GLU* 5.5 0.2 + - - -
1819B PO4 3.4 27.7 + - - -
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Residues in contact with THR 397 (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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219B TYR* 6.5 0.4 - - + -
270B ARG* 3.9 10.6 + - - +
350B ALA* 3.1 8.4 - - - +
351B ASP* 2.8 54.0 + - - +
395B THR* 6.1 0.2 - - - -
396B ARG* 1.3 73.6 - - - +
398B VAL* 1.3 71.2 + - - +
399B PHE* 4.1 15.7 - - + -
417B ASP* 4.0 20.6 - - - +
418B HIS 3.4 11.7 - - - +
419B LYS* 3.3 28.7 - - + +
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Residues in contact with VAL 398 (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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349B GLY 3.5 9.2 - - - +
350B ALA* 4.8 9.2 - - + -
396B ARG* 5.4 11.7 - - + +
397B THR* 1.3 78.1 - - - +
399B PHE* 1.3 67.5 + - - +
417B ASP* 3.7 0.3 - - - -
418B HIS* 2.8 53.4 + - + +
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Residues in contact with PHE 399 (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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220B ASP* 5.0 3.1 - - - -
270B ARG* 3.5 48.7 - - - -
333B TYR* 4.4 4.5 - + - -
335B ILE* 4.1 21.8 - - + -
347B THR* 4.6 3.4 - - + -
348B VAL* 3.4 8.0 - - - +
349B GLY* 2.9 63.1 + - - +
350B ALA* 4.2 3.4 - - - -
351B ASP* 4.8 2.0 - - - -
397B THR* 4.1 9.2 - - + -
398B VAL* 1.3 81.1 - - - +
400B ALA* 1.3 66.0 + - - +
401B ASN* 3.7 18.8 - - - +
416B LEU 3.1 13.9 - - - +
417B ASP* 3.3 17.0 - - - +
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Residues in contact with ALA 400 (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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346B LEU* 5.1 6.7 - - + -
347B THR 3.3 10.5 - - - +
348B VAL* 4.6 9.0 - - + -
399B PHE* 1.3 77.6 - - - +
401B ASN* 1.3 65.3 + - - +
414B VAL 3.6 1.4 - - - +
415B GLN* 3.3 4.3 - - - -
416B LEU* 2.6 55.4 + - + +
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Residues in contact with ASN 401 (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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272B LYS* 5.7 6.4 - - - +
345B MET 3.6 1.5 - - - +
346B LEU* 3.3 6.4 - - - +
347B THR* 2.7 51.9 + - - +
399B PHE* 3.7 22.2 - - - +
400B ALA* 1.3 79.3 - - - +
402B LEU* 1.3 62.1 + - - +
403B GLU* 5.3 4.2 + - - +
413B LYS* 3.9 21.7 - - + +
414B VAL 3.2 4.9 - - - -
415B GLN* 3.5 37.3 + - - +
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Residues in contact with LEU 402 (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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340B LEU* 4.0 19.1 - - + -
344B THR* 3.9 27.6 - - + -
345B MET 3.4 10.5 - - - +
346B LEU* 4.2 13.0 - - + -
401B ASN* 1.3 75.4 - - - +
403B GLU* 1.3 61.0 + - - +
404B HIS* 6.0 1.8 - - + -
412B GLY 4.1 0.2 - - - +
413B LYS* 3.4 3.1 - - - +
414B VAL* 2.9 46.8 + - + +
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Residues in contact with GLU 403 (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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136B GLN* 3.4 29.6 - - - +
272B LYS* 5.1 5.2 + - - -
343B ASP 3.9 0.2 - - - +
344B THR* 3.4 7.2 - - - +
345B MET* 3.0 62.7 + - + +
401B ASN* 4.1 5.6 + - - +
402B LEU* 1.3 76.0 - - - +
404B HIS* 1.3 61.9 + - - +
405B ASN* 5.8 3.1 - - - +
411B VAL* 5.2 5.7 - - + +
412B GLY 3.3 12.3 - - - +
413B LYS* 3.4 31.3 + - + +
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Residues in contact with HIS 404 (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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341B ASN* 4.9 1.6 - - - -
343B ASP* 3.2 12.7 + - + -
344B THR* 3.0 32.5 + - + +
402B LEU* 6.0 1.8 - - + -
403B GLU* 1.3 74.5 - - - +
405B ASN* 1.3 81.1 + - - +
406B PHE* 3.5 44.5 + + + -
407B ALA 5.6 0.2 + - - -
411B VAL* 3.5 4.9 - - - +
412B GLY 3.0 33.9 + - - +
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Residues in contact with ASN 405 (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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343B ASP* 3.0 40.0 + - + +
403B GLU* 5.8 3.8 - - - +
404B HIS* 1.3 89.3 + - - +
406B PHE* 1.3 64.3 + - - +
407B ALA 3.8 1.7 + - - -
410B TRP 4.0 3.8 - - - -
411B VAL* 4.3 18.2 - - - +
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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