Contacts of the strand formed by residues 355 - 361 (chain B) in PDB entry 3HYW
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 ALA 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348B ILE* 3.6 13.9 - - + -
349B ALA 3.3 13.9 - - - +
350B ASP* 3.8 4.9 - - - -
351B PHE* 3.6 9.2 - - - -
354B ASP* 1.3 81.3 - - - +
356B GLY* 1.3 61.1 + - - +
374B MET* 3.3 4.4 - - - +
375B GLY 3.0 28.0 + - - +
378B ALA* 3.6 11.1 - - - +
379B HIS* 3.5 25.1 - - - +
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Residues in contact with GLY 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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205B LEU* 5.4 1.6 - - - -
347B CSS 3.6 1.2 - - - +
348B ILE* 3.2 6.5 - - - +
349B ALA 2.8 37.3 + - - -
351B PHE* 3.2 18.9 - - - -
355B ALA* 1.3 72.8 - - - +
357B PHE* 1.3 60.7 + - - -
358B PHE* 3.8 14.9 - - - -
373B LYS 3.4 8.1 - - - -
374B MET* 4.4 2.9 - - - -
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Residues in contact with PHE 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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346B ILE* 3.5 28.3 - - + -
347B CSS 3.6 1.6 - - - -
348B ILE* 3.9 22.2 - - + +
355B ALA 3.9 0.8 + - - -
356B GLY* 1.3 71.0 - - - -
358B PHE* 1.3 60.3 + - - +
359B PHE* 3.9 23.6 - - + -
371B ILE* 4.0 25.4 - - + -
372B THR* 3.3 5.5 - - - -
373B LYS* 2.8 42.7 + - + +
377B TRP* 3.6 37.9 - + + -
378B ALA* 4.3 7.0 - - + -
381B PHE* 5.3 3.4 - + - -
411B LEU* 4.6 6.3 - - + -
500B DCQ 5.3 0.2 - - - -
600B LMT 4.0 35.9 - - + -
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Residues in contact with PHE 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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194B PHE* 4.2 20.4 - + - -
199B ILE* 3.9 25.1 - - + +
202B SER* 3.7 29.4 - - - -
205B LEU* 4.3 27.4 - - + -
206B VAL* 4.7 4.7 - - + -
345B ALA 3.6 1.7 - - - +
346B ILE* 3.6 0.5 - - - -
347B CSS 2.7 50.4 + - + +
349B ALA* 4.3 13.5 - - + -
351B PHE* 5.1 2.9 - + - -
356B GLY* 3.8 26.7 - - - -
357B PHE* 1.3 79.4 - - - +
359B PHE* 1.3 59.8 + - - +
371B ILE 3.3 4.0 - - - -
372B THR* 3.8 21.5 - - + -
802B PS9 4.4 11.9 - - - -
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Residues in contact with PHE 359 (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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199B ILE* 3.5 3.5 - - - +
315B MET* 4.8 0.4 - - - -
344B SER* 4.4 5.2 - - - -
345B ALA 3.3 16.4 - - - -
346B ILE* 3.8 16.6 - - + -
357B PHE* 3.9 21.7 - - + -
358B PHE* 1.3 74.9 - - - +
360B ALA* 1.3 63.6 + - - +
361B ASP* 3.5 31.4 - - + -
369B ARG* 4.5 14.8 - - + -
370B VAL* 3.1 11.4 - - - +
371B ILE* 2.7 55.4 + - + +
411B LEU* 3.8 30.1 - - + -
413B VAL* 3.6 31.6 - - + -
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Residues in contact with ALA 360 (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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199B ILE* 4.2 23.3 - - + +
344B SER* 3.3 4.3 - - - -
345B ALA* 2.9 34.9 + - + +
358B PHE 4.2 0.4 - - - -
359B PHE* 1.3 76.9 - - - +
361B ASP* 1.3 60.3 + - - +
362B PRO 3.6 5.8 - - - +
363B VAL* 4.1 13.9 - - + -
367B ARG* 3.9 24.2 - - - +
369B ARG 3.8 4.3 - - - -
370B VAL* 4.1 1.6 - - + -
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Residues in contact with ASP 361 (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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342B ARG* 2.6 41.9 + - - +
344B SER* 3.3 17.6 - - - -
359B PHE* 3.5 28.4 - - + -
360B ALA* 1.3 74.5 - - - +
362B PRO* 1.3 53.8 + - - +
367B ARG* 3.6 1.2 - - - +
368B GLU* 2.7 33.1 + - - +
369B ARG* 3.0 29.6 + - + +
411B LEU 4.9 0.5 - - - +
412B LYS 4.3 13.5 - - - +
413B VAL* 4.9 4.5 - - - -
414B HIS 5.7 0.2 + - - -
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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