Contacts of the strand formed by residues 355 - 361 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348F ILE* 3.7 19.5 - - + -
349F ALA 3.2 15.0 - - - +
350F ASP* 3.7 7.9 - - - -
351F PHE* 3.8 8.3 - - - -
354F ASP* 1.3 79.0 - - - +
356F GLY* 1.3 61.2 + - - +
374F MET* 3.4 4.0 - - - +
375F GLY 3.1 29.6 + - - +
378F ALA* 3.6 4.7 - - - +
379F HIS* 3.5 23.1 - - - +
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Residues in contact with GLY 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F LEU* 5.6 1.8 - - - -
347F CSS 3.8 0.5 - - - +
348F ILE* 3.3 7.4 - - - +
349F ALA 2.8 35.7 + - - -
351F PHE* 3.3 17.9 - - - -
355F ALA* 1.3 73.6 - - - +
357F PHE* 1.3 60.3 + - - -
358F PHE* 4.1 14.9 - - - -
373F LYS 3.4 7.6 - - - -
374F MET* 4.5 3.1 - - - -
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Residues in contact with PHE 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346F ILE* 3.5 31.2 - - + -
347F CSS 3.7 1.8 - - - -
348F ILE* 3.8 21.3 - - + -
355F ALA 4.0 0.6 + - - -
356F GLY* 1.3 72.5 - - - -
358F PHE* 1.3 63.1 + - - +
359F PHE* 3.9 25.8 - - + -
371F ILE* 3.9 24.9 - - + -
372F THR* 3.4 4.2 - - - -
373F LYS* 2.7 43.6 + - + +
377F TRP* 3.6 38.6 - + + -
378F ALA* 4.2 6.7 - - + -
381F PHE* 5.5 4.3 - + - -
411F LEU* 4.8 3.6 - - + -
600F LMT 4.1 31.6 - - + -
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Residues in contact with PHE 358 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194F PHE* 4.1 21.3 - + - -
199F ILE* 4.1 26.5 - - + -
202F SER* 3.7 26.0 - - - -
205F LEU* 4.3 32.1 - - + -
206F VAL* 4.9 3.6 - - + -
345F ALA 3.6 1.0 - - - +
346F ILE* 3.5 3.1 - - - +
347F CSS 2.7 53.9 + - + +
349F ALA* 4.3 12.8 - - + -
351F PHE* 5.3 3.1 - + - -
356F GLY* 4.1 21.8 - - - -
357F PHE* 1.3 78.6 - - - +
359F PHE* 1.3 60.6 + - - +
360F ALA 4.2 0.4 - - - -
371F ILE 3.4 2.0 - - - -
372F THR* 4.0 17.5 - - + -
800F PS9 4.6 14.4 - - - -
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Residues in contact with PHE 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F ILE* 3.7 3.0 - - - +
315F MET* 4.7 1.1 - - - -
344F SER* 4.5 5.4 - - - -
345F ALA 3.3 18.2 - - - -
346F ILE* 3.7 16.8 - - + -
357F PHE* 3.9 20.6 - - + -
358F PHE* 1.3 74.5 - - - +
360F ALA* 1.3 66.7 + - - +
361F ASP* 3.6 28.5 - - + -
369F ARG* 4.7 12.6 - - + -
370F VAL* 3.0 12.6 - - - +
371F ILE* 2.8 51.9 + - + +
411F LEU* 4.0 36.6 - - + -
413F VAL* 3.8 30.7 - - + -
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Residues in contact with ALA 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F ILE* 4.2 22.0 - - + +
344F SER* 3.4 5.2 - - - -
345F ALA* 3.0 34.1 + - + +
359F PHE* 1.3 77.0 - - - +
361F ASP* 1.3 60.8 + - - +
362F PRO 3.6 5.7 - - - +
363F VAL* 4.0 14.6 - - + -
367F ARG* 3.7 25.6 - - - +
369F ARG 3.9 3.4 - - - -
370F VAL* 4.1 1.3 - - - -
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Residues in contact with ASP 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342F ARG* 2.7 39.2 + - - +
344F SER* 3.4 15.9 - - - -
359F PHE* 3.6 27.4 - - + -
360F ALA* 1.3 74.9 - - - +
362F PRO* 1.4 55.3 + - - +
367F ARG* 4.2 1.1 - - - +
368F GLU* 2.7 31.6 + - - +
369F ARG* 2.9 37.4 + - + +
411F LEU 4.9 0.7 - - - +
412F LYS 4.5 9.9 - - - +
413F VAL* 5.5 3.4 - - - -
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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