Contacts of the strand formed by residues 377 - 382 (chain B) 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 ALA 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B THR 4.5 3.4 - - - +
215B GLY* 4.4 12.6 - - - -
350B ALA* 4.0 1.5 - - - +
367B CYS* 3.5 9.8 - - - -
369B GLY 3.0 23.8 + - - -
375B ILE* 2.6 20.7 + - + +
376B PRO* 1.3 75.0 - - - +
378B VAL* 1.3 66.6 + - - +
379B CYS 4.0 0.2 - - - -
422B ARG* 4.8 7.0 - - + -
423B ILE 3.3 12.1 - - - +
424B MET* 4.0 17.3 - - + -
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ALA* 3.4 32.5 - - + +
353B LEU* 3.9 16.4 - - + -
354B ALA* 3.9 16.6 - - + +
357B ILE* 4.8 5.4 - - + -
365B PHE* 3.7 28.9 - - + -
367B CYS 3.4 6.5 - - - +
368B THR 5.2 0.2 - - - -
377B ALA* 1.3 75.9 - - - +
379B CYS* 1.3 62.3 + - - +
380B PHE* 4.0 12.9 - - + -
421B MET 3.7 0.9 - - - +
422B ARG* 3.3 2.6 - - - +
423B ILE* 2.7 48.5 + - + +
425B CYS* 4.9 0.9 - - - -
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Residues in contact with CYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR 3.8 20.6 - - - -
214B THR* 3.4 28.5 - - - +
365B PHE* 3.7 1.1 - - - -
366B ILE* 2.8 41.6 + - + -
367B CYS* 3.0 18.4 + - + +
378B VAL* 1.3 73.4 - - - +
380B PHE* 1.3 61.5 + - - +
420B VAL* 3.8 22.4 - - - -
421B MET 3.2 11.2 - - - +
422B ARG* 4.4 6.7 - - + -
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Residues in contact with PHE 380 (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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357B ILE* 3.8 22.4 - - + -
363B TYR* 3.6 35.7 - + + -
364B GLU 3.4 13.7 - - - +
365B PHE* 3.5 20.2 - + + -
366B ILE* 4.3 2.9 - - - +
378B VAL* 4.0 14.1 - - + -
379B CYS* 1.3 79.0 - - - +
381B LYS* 1.3 62.1 + - - +
392B LEU* 3.8 12.4 - - + +
420B VAL* 3.2 7.4 - - - -
421B MET* 2.8 69.3 + - + +
423B ILE* 4.4 8.7 - - + -
441B TYR* 3.5 27.6 - + - -
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Residues in contact with LYS 381 (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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363B TYR* 3.3 6.1 - - - +
364B GLU* 2.7 71.0 + - + +
366B ILE* 4.7 10.5 - - + -
380B PHE* 1.3 78.3 - - - +
382B LEU* 1.3 81.3 + - - +
384B ASP* 2.7 32.9 + - - +
392B LEU* 3.9 4.7 - - - -
418B ILE* 3.8 42.2 - - + +
419B VAL 3.4 19.7 - - - +
420B VAL* 4.6 2.2 - - + -
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Residues in contact with LEU 382 (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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362B PRO* 3.5 7.4 - - + +
363B TYR* 3.7 26.5 - - + -
381B LYS* 1.3 99.0 + - - +
383B LYS* 1.3 67.5 + - - +
384B ASP* 3.3 0.3 + - - -
387B ASP* 5.9 0.9 - - - +
388B PRO* 3.6 33.7 - - + -
390B TYR* 3.6 27.8 - - + +
391B THR* 4.3 11.9 - - - -
392B LEU* 3.9 17.2 - - + +
419B VAL 4.6 0.8 + - - -
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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