Contacts of the strand formed by residues 351 - 358 (chain B) in PDB entry 1W1J
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 351 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LEU* 3.1 45.9 + - + +
285B LYS 4.0 8.1 - - - -
286B ASP* 2.8 40.2 + - - -
288B ASP 4.7 0.2 - - - -
289B LEU* 3.3 43.1 - - + +
311B ILE* 4.1 13.2 - - + -
312B ARG 3.3 23.1 - - - -
313B HIS* 3.7 34.1 - + + -
349B GLY 3.7 0.9 - - - -
350B ARG* 1.3 77.6 - - - +
352B ASN* 1.3 71.0 + - - +
440B TYR* 3.8 31.2 - + - -
454B PHE* 4.2 5.8 - + - -
456B GLY 4.3 3.8 - - - -
458B PHE* 3.9 24.7 - + - -
467B HIS* 6.0 0.2 - + - -
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Residues in contact with ASN 352 (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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280B LEU* 3.9 2.0 - - + -
281B ILE 3.7 3.4 - - - -
282B THR* 3.2 21.6 - - - +
283B LEU* 4.7 0.2 - - - -
310B THR 3.5 2.3 - - - +
311B ILE* 3.3 4.2 - - - -
312B ARG* 2.8 39.3 + - + +
314B ILE* 4.3 6.4 - - - +
317B ASP* 3.7 13.2 - - - +
348B LEU* 3.4 17.9 - - - +
349B GLY 3.0 40.8 - - - +
351B TRP* 1.3 76.9 + - - +
353B PHE* 1.3 60.9 + - - +
354B TYR* 3.5 25.2 - - + -
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Residues in contact with PHE 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 4.0 15.5 - + - -
280B LEU* 3.5 2.8 - - - -
281B ILE* 2.8 73.6 + - + +
283B LEU* 4.3 14.1 - - + +
296B ILE* 3.9 26.5 - - + -
305B LEU* 3.6 29.2 - - + -
309B PRO* 3.3 28.5 - - + -
310B THR 3.5 9.2 - - - -
311B ILE* 4.0 11.4 - - + +
352B ASN* 1.3 72.6 - - - +
354B TYR* 1.3 63.5 + - - +
355B GLY* 3.9 1.4 + - - -
371B ILE* 4.9 0.7 - - + -
375B PHE* 3.7 21.5 - + + -
460B VAL* 4.8 0.7 - - + -
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Residues in contact with TYR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR 3.4 6.7 - - - +
280B LEU* 3.9 13.4 - - + +
309B PRO* 3.4 7.2 - - - +
310B THR* 2.9 40.4 + - - +
312B ARG* 3.5 26.9 - - - -
317B ASP* 2.9 21.3 + - - -
348B LEU* 4.2 13.0 - - - +
352B ASN* 3.5 30.7 - - + -
353B PHE* 1.3 74.7 - - - +
355B GLY* 1.3 59.9 + - - +
394B VAL* 3.7 14.0 + - + +
395B LEU* 3.5 49.7 + - + -
398B ARG* 4.2 14.6 - - + +
402B MET* 4.3 13.4 - - + +
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Residues in contact with GLY 355 (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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279B TYR* 3.1 53.1 + - - -
305B LEU* 5.5 0.2 - - - -
307B ASN* 4.6 1.8 - - - -
309B PRO* 4.2 13.2 - - - -
353B PHE* 4.0 1.0 - - - -
354B TYR* 1.3 73.7 - - - +
356B ALA* 1.3 60.2 + - - -
402B MET* 3.1 18.3 - - - +
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Residues in contact with ALA 356 (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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276B TYR* 3.9 13.9 - - + -
277B GLN 3.4 12.1 - - - +
278B SER* 3.9 4.0 - - - -
279B TYR* 3.3 8.7 + - - -
304B ALA 5.7 0.5 - - - +
305B LEU* 5.5 1.9 - - - +
306B GLN* 4.4 6.2 + - - +
307B ASN* 3.7 18.0 + - - +
355B GLY* 1.3 74.7 - - - +
357B LEU* 1.3 63.4 + - - +
358B TYR* 3.4 38.4 - - + +
402B MET* 4.0 8.3 - - + -
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Residues in contact with LEU 357 (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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276B TYR* 3.7 8.0 - - - -
277B GLN* 2.8 52.0 + - + +
279B TYR* 4.1 8.5 - - + -
304B ALA 4.6 1.6 - - - +
306B GLN* 3.6 3.8 - - - +
356B ALA* 1.3 74.8 - - - +
358B TYR* 1.3 66.1 - - - +
364B ARG* 3.7 25.5 - - + +
367B LEU* 3.5 37.9 - - + -
368B TRP* 3.9 32.8 - - + +
371B ILE* 3.8 19.7 - - + -
385B PHE* 5.6 1.6 - - + -
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Residues in contact with TYR 358 (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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303A MET* 6.0 1.3 - - + -
165B TRP* 4.4 7.2 - + - -
188B THR* 3.6 10.4 - - - -
189B PRO* 3.6 21.8 - - + -
270B MET* 4.6 12.1 - - + -
273B PRO* 4.0 22.7 - - + -
275B GLY 3.5 2.7 - - - -
276B TYR* 3.8 14.1 - + - -
306B GLN* 2.9 52.2 + - + +
307B ASN* 3.5 26.3 + - + -
356B ALA* 3.4 26.6 - - + +
357B LEU* 1.3 77.6 - - - +
359B GLY* 1.3 60.2 + - - +
363B ILE* 4.3 8.1 - - - +
364B ARG* 4.4 4.0 - - - +
402B MET* 2.7 42.8 + - - +
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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