Contacts of the strand formed by residues 363 - 368 (chain D) in PDB entry 3FZ7
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 TYR 363 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D ILE* 3.2 37.2 - - + -
358D ALA* 4.4 2.7 - - - -
360D LEU* 4.0 1.9 + - + -
361D GLY* 3.1 31.2 + - - -
362D PRO* 1.3 79.3 - - - +
364D GLU* 1.3 60.7 + - - +
365D PHE* 3.7 22.7 + - + -
380D PHE* 3.7 22.9 - + + -
381D LYS 3.3 6.5 - - - +
382D LEU* 3.7 20.9 - - + -
383D LYS* 3.2 21.7 - - - +
390D TYR* 2.7 31.0 + - - -
392D LEU* 4.6 3.8 - - + -
441D TYR* 2.9 35.8 + + - -
445D LEU* 4.2 1.6 - - - +
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Residues in contact with GLU 364 (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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363D TYR* 1.3 73.4 - - - +
365D PHE* 1.3 70.5 + - - +
366D ILE* 3.9 4.2 + - - +
380D PHE* 3.2 3.1 - - - -
381D LYS* 2.7 75.5 + - + +
383D LYS* 3.9 17.3 - - + +
384D ASP* 4.3 7.4 + - - +
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Residues in contact with PHE 365 (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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354D ALA* 3.6 22.2 - - - -
357D ILE* 3.8 11.2 - - + -
358D ALA* 3.5 31.0 - - + -
363D TYR* 3.7 24.5 - - + -
364D GLU* 1.3 84.4 - - - +
366D ILE* 1.3 62.8 + - - +
367D CYS 4.0 4.3 - - - -
368D THR* 3.5 32.8 - - + -
378D VAL* 3.7 20.0 - - + -
379D CYS 3.6 6.5 - - - -
380D PHE* 3.6 21.5 - + + -
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Residues in contact with ILE 366 (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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187D LEU* 3.7 35.0 - - + -
188D PHE* 4.3 2.5 - - + -
214D THR* 3.9 11.7 - - - -
216D ASN* 3.0 37.0 - - - +
364D GLU* 4.7 8.3 - - - +
365D PHE* 1.3 77.2 - - - +
367D CYS* 1.3 58.5 + - - +
368D THR* 5.5 0.9 - - - -
373D GLU* 5.4 1.2 - - - +
379D CYS* 2.8 15.6 + - - +
380D PHE 4.9 2.5 - - - -
381D LYS* 4.4 19.5 - - + -
411D LEU* 4.1 7.6 - - + -
418D ILE* 5.3 0.2 - - + -
420D VAL* 3.6 30.5 - - + -
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Residues in contact with CYS 367 (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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214D THR 3.2 26.5 - - - +
215D GLY* 3.8 22.0 - - - -
216D ASN* 3.9 11.7 - - - +
365D PHE* 3.7 0.5 - - - -
366D ILE* 1.3 78.8 - - - +
368D THR* 1.3 68.2 + - - +
369D GLY* 3.7 4.5 - - - -
370D ARG 5.6 1.1 - - - -
373D GLU* 5.2 6.5 - - - -
374D GLY* 5.1 4.3 - - - -
375D ILE 4.4 6.7 - - - -
377D ALA 3.5 17.3 - - - +
378D VAL* 3.5 5.5 - - - +
379D CYS* 2.9 34.3 + - + +
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Residues in contact with THR 368 (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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350D ALA 4.7 0.9 - - - -
351D ALA* 3.4 7.6 - - - -
354D ALA* 3.6 16.6 - - + +
355D ASP* 5.9 0.2 - - - +
365D PHE* 3.5 33.0 - - + -
366D ILE 5.5 0.2 - - - -
367D CYS* 1.3 79.1 - - - +
369D GLY* 1.3 61.1 + - - +
370D ARG* 2.7 51.7 + - - +
373D GLU* 4.0 13.8 + - - -
377D ALA 3.9 1.6 - - - -
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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