Contacts of the helix formed by residues 347 - 357 (chain B) in PDB entry 1WBB
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 ASP 347 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B GLU* 4.3 7.8 - - + +
301B PRO* 4.0 23.4 - - + +
302B MET* 3.8 9.2 - - - +
305B ARG* 3.0 40.5 + - - -
346B GLY* 1.3 68.8 - - - -
348B LEU* 1.3 63.0 + - - +
349B GLU 3.1 0.4 - - - -
350B ARG* 3.2 32.0 + - + +
351B ILE* 3.4 22.6 + - + +
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Residues in contact with LEU 348 (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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302B MET* 4.0 10.0 - - + -
345B VAL* 4.0 12.7 + - + +
346B GLY 3.0 6.5 + - - -
347B ASP* 1.3 74.6 - - - +
349B GLU* 1.3 63.3 + - - +
351B ILE* 3.4 10.7 + - + +
352B LEU* 3.0 38.2 + - + +
368B MET* 4.2 35.2 - - + +
371B ALA* 4.7 9.9 - - + -
372B PHE* 5.6 11.0 - - + -
542B LEU* 4.7 3.4 - - + +
545B SER* 4.4 4.9 - - - +
546B ALA* 3.6 32.8 - - + +
549B LEU* 4.1 15.0 - - + -
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Residues in contact with GLU 349 (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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149B ASP* 4.5 4.7 - - - +
151B SER* 4.0 7.4 - - - +
152B SER* 3.6 35.2 + - - +
302B MET* 3.6 25.4 - - - +
305B ARG* 2.5 29.1 + - - +
306B MET* 5.4 2.4 - - - +
309B ARG* 4.8 14.1 + - - -
347B ASP* 3.1 5.8 + - - +
348B LEU* 1.3 78.9 - - - +
350B ARG* 1.3 60.4 + - + +
352B LEU* 3.4 6.6 + - - +
353B ALA 3.3 18.2 + - - -
546B ALA* 3.9 13.9 - - + +
547B SER* 5.3 7.1 - - - -
550B ALA* 5.1 6.9 - - - +
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Residues in contact with ARG 350 (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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120B SER 4.9 0.3 - - - +
125B LEU* 3.8 40.2 - - - +
126B GLN 3.0 26.3 + - - -
127B GLU* 3.6 11.9 + - - +
129B GLN 3.1 21.8 + - - -
130B ASP* 4.1 8.9 + - - +
131B ASN* 4.6 2.8 - - - +
149B ASP* 5.3 6.5 + - - -
151B SER* 4.0 19.3 + - - +
305B ARG* 3.6 28.2 - - - +
347B ASP* 3.2 28.4 + - + +
349B GLU* 1.3 77.5 + - - +
351B ILE* 1.3 64.9 + - + +
353B ALA* 3.3 20.2 - - - +
354B ARG* 3.5 27.1 + - - +
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Residues in contact with ILE 351 (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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345B VAL 5.7 1.6 - - - +
346B GLY* 6.2 0.4 - - - -
347B ASP* 3.4 26.0 + - + +
348B LEU* 3.7 14.4 - - + +
350B ARG* 1.3 74.1 - - - +
352B LEU* 1.3 68.0 + - - +
354B ARG* 3.0 26.4 + - - +
355B LEU* 3.0 9.9 + - - +
360B ALA* 4.9 1.2 - - + +
364B ASP* 3.4 38.1 - - + +
367B ARG* 4.0 33.0 - - + +
368B MET* 3.6 34.1 - - + +
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Residues in contact with LEU 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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254B HIS* 5.9 1.1 - - - -
348B LEU* 3.0 39.4 + - + +
349B GLU* 3.5 7.4 - - - +
350B ARG 3.3 0.2 - - - -
351B ILE* 1.3 77.7 - - - +
353B ALA* 1.3 61.3 + - - +
355B LEU* 3.2 11.3 + - + +
356B ALA* 3.0 21.7 + - - +
368B MET* 4.2 19.5 - - + -
539B LEU* 4.0 14.9 - - + +
542B LEU* 3.4 56.3 - - + +
543B GLN* 4.0 10.8 - - + +
546B ALA* 3.7 15.0 - - + -
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Residues in contact with ALA 353 (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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120B SER* 4.8 7.6 - - - -
150B ILE 4.7 2.5 - - - +
151B SER* 3.0 48.2 + - - +
254B HIS* 4.5 8.2 + - + +
349B GLU 3.3 4.2 + - - +
350B ARG 3.3 13.2 - - - +
351B ILE 3.1 0.4 - - - -
352B LEU* 1.3 79.4 - - - +
354B ARG* 1.3 57.2 + - - +
356B ALA* 3.1 6.2 + - - +
357B LEU* 3.1 32.9 + - + +
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Residues in contact with ARG 354 (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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120B SER* 2.9 35.2 + - - +
121B ASP* 4.4 10.8 - - - +
122B GLU* 3.7 38.6 + - - +
125B LEU* 5.3 0.8 - - - +
350B ARG* 3.5 23.3 + - - +
351B ILE* 3.0 21.2 + - - +
353B ALA* 1.3 73.3 - - - +
355B LEU* 1.3 59.9 + - - +
357B LEU* 3.9 2.5 - - - +
358B ARG* 3.1 3.8 + - - -
359B THR* 2.9 53.3 + - - +
360B ALA* 3.0 17.5 + - + +
361B ARG* 5.5 3.8 - - - +
364B ASP* 2.9 38.8 + - - +
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Residues in contact with LEU 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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351B ILE 3.0 11.5 + - - +
352B LEU* 3.2 17.2 + - + +
354B ARG* 1.3 77.0 - - - +
356B ALA* 1.3 59.9 + - - +
358B ARG* 3.4 13.3 + - - +
360B ALA* 4.0 2.2 - - + +
365B LEU* 4.4 2.7 - - + -
368B MET* 4.3 14.1 - - + -
532B PHE* 3.6 31.8 - - + -
535B LEU* 3.8 42.2 - - + -
536B LEU* 3.5 23.3 - - + +
539B LEU* 4.1 20.9 - - + -
542B LEU* 4.1 15.7 - - + -
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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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250B THR* 4.9 2.3 - - - +
251B THR* 4.3 3.1 + - - +
253B PRO* 3.7 21.8 - - + +
254B HIS* 3.7 38.6 - - + +
352B LEU 3.0 12.3 + - - +
353B ALA 3.1 8.9 + - - +
355B LEU* 1.3 77.3 - - - +
357B LEU* 1.3 61.2 + - - +
358B ARG* 3.7 5.5 + - - +
536B LEU* 4.1 11.4 - - - +
539B LEU* 4.0 11.2 - - + +
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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
----------------------------------------------------------
120B SER* 3.4 32.1 - - - +
150B ILE* 5.1 6.3 - - + +
248B GLN* 4.1 17.0 - - - +
250B THR* 4.3 22.2 + - + +
251B THR 4.0 8.5 - - - +
252B LEU* 3.6 31.6 - - + -
254B HIS* 4.2 14.4 - - + +
353B ALA* 3.1 20.2 + - + +
354B ARG* 5.1 0.4 - - - -
355B LEU 3.3 0.2 - - - -
356B ALA* 1.3 78.1 - - - +
358B ARG* 1.3 71.3 + - - +
359B THR* 3.5 22.8 + - + +
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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