Contacts of the strand formed by residues 355 - 361 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348D ILE* 3.7 7.6 - - + -
349D ALA 3.2 14.1 - - - +
350D ASP* 3.7 9.4 - - - -
351D PHE* 3.6 9.6 - - - -
354D ASP* 1.3 79.6 + - - +
356D GLY* 1.3 62.0 + - - +
374D MET* 3.4 4.5 - - - +
375D GLY 3.1 28.9 + - - +
378D ALA* 3.6 10.6 - - + +
379D HIS* 3.4 26.0 - - - +
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Residues in contact with GLY 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 5.6 1.3 - - - -
347D CSS 3.7 0.7 - - - +
348D ILE* 3.2 8.1 - - - +
349D ALA 2.8 37.8 + - - -
351D PHE* 3.2 17.7 - - - -
355D ALA* 1.3 72.6 - - - +
357D PHE* 1.3 61.9 + - - -
358D PHE* 3.8 14.3 - - - -
373D LYS 3.6 6.7 - - - -
374D MET* 4.4 3.4 - - - -
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Residues in contact with PHE 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ILE* 3.4 30.3 - - + -
347D CSS 3.7 2.0 - - - -
348D ILE* 3.9 21.1 - - + -
355D ALA 4.0 0.6 + - - -
356D GLY* 1.3 72.5 - - - -
358D PHE* 1.3 61.4 + - - +
359D PHE* 3.9 23.6 - - + -
371D ILE* 4.0 19.5 - - + -
372D THR* 3.4 4.0 - - - -
373D LYS* 2.7 45.0 + - + +
377D TRP* 3.6 40.6 - + + -
378D ALA* 4.3 5.8 - - + -
381D PHE* 5.5 3.4 - + - -
411D LEU* 4.7 2.2 - - + -
600D LMT 3.7 42.0 - - + -
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Residues in contact with PHE 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D PHE* 4.1 28.3 - + - -
199D ILE* 4.1 21.1 - - + -
202D SER* 3.9 23.6 - - - -
205D LEU* 3.9 25.1 - - + -
206D VAL* 4.8 2.0 - - + -
345D ALA 3.7 1.0 - - - +
346D ILE* 3.4 1.7 - - - +
347D CSS 2.6 55.3 + - + +
349D ALA* 4.3 17.5 - - + -
351D PHE* 5.0 3.1 - + - -
356D GLY* 3.8 26.2 - - - -
357D PHE* 1.3 76.2 - - - +
359D PHE* 1.3 59.0 + - - +
371D ILE 3.4 2.5 - - - -
372D THR* 3.9 27.6 - - + -
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Residues in contact with PHE 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ILE* 3.6 4.8 - - - +
315D MET* 4.8 1.1 - - - -
344D SER* 4.4 3.6 - - - -
345D ALA 3.2 19.1 - - - -
346D ILE* 3.7 19.7 - - + -
357D PHE* 3.9 21.7 - - + -
358D PHE* 1.3 73.9 - - - +
360D ALA* 1.3 67.6 + - - +
361D ASP* 3.6 27.1 - - + -
369D ARG* 4.6 12.8 - - + -
370D VAL* 3.1 10.5 - - - +
371D ILE* 2.8 59.7 + - + +
411D LEU* 3.8 28.3 - - + -
413D VAL* 3.6 29.4 - - + -
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Residues in contact with ALA 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ILE* 4.2 18.4 - - + +
344D SER* 3.4 5.2 - - - -
345D ALA* 3.0 31.4 + - + +
358D PHE 4.3 0.2 - - - -
359D PHE* 1.3 77.7 - - - +
361D ASP* 1.3 60.4 + - - +
362D PRO 3.8 1.6 - - - -
363D VAL* 3.7 17.8 + - + -
367D ARG* 3.7 26.9 - - - +
369D ARG 3.8 4.3 - - - -
370D VAL* 4.1 4.5 - - + -
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Residues in contact with ASP 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ARG* 2.7 40.3 + - - +
344D SER* 3.2 18.7 - - - -
359D PHE* 3.6 24.6 - - + -
360D ALA* 1.3 75.2 - - - +
362D PRO* 1.3 56.5 + - - +
367D ARG* 3.5 1.2 - - - +
368D GLU* 2.6 31.8 + - - +
369D ARG* 2.9 37.3 + - + +
411D LEU 4.9 0.5 - - - +
412D LYS 4.4 9.0 - - - +
413D VAL* 4.7 5.3 - - - +
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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