Contacts of the strand formed by residues 382 - 390 (chain A) in PDB entry 5FBQ
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 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A LEU* 2.8 46.1 + - - +
320A ILE* 4.3 5.3 - - + +
321A GLY* 3.9 22.9 - - - -
324A LEU* 4.4 8.1 - - + -
337A LEU* 3.8 24.5 - - + -
341A LEU* 5.0 2.0 - - + -
372A VAL 3.8 10.8 - - - +
373A VAL* 3.9 19.1 - - + +
374A LEU* 4.5 1.8 - - - +
380A ALA 4.5 3.6 - - - +
381A PRO* 1.3 77.5 - - - +
383A LEU* 1.3 58.9 + - - +
384A ILE* 3.3 31.8 + - + -
561A VAL 4.0 0.5 - - - +
562A ILE* 3.6 3.9 - - - -
563A VAL* 2.8 63.0 + - + +
565A CYS* 5.9 0.7 - - + -
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ALA* 3.6 1.6 - - - +
372A VAL* 2.9 44.0 + - + +
374A LEU* 4.2 21.8 - - + +
382A TYR* 1.3 70.2 - - - +
384A ILE* 1.3 76.2 + - - +
385A TYR* 3.7 38.8 - - + +
560A SER* 5.3 1.6 - - - -
561A VAL 3.8 6.7 - - - +
562A ILE* 3.8 27.1 - - + +
612A PRO* 4.2 9.9 - - + -
801A 5W6 4.0 29.2 - - + +
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Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 6.5 0.7 - - + -
317A LEU* 4.6 26.0 - - + -
341A LEU* 4.4 9.0 - - + -
366A VAL* 4.9 13.9 - - + -
371A ALA* 4.2 15.9 - - + -
382A TYR* 3.3 31.2 - - + +
383A LEU* 1.3 83.4 - - - +
385A TYR* 1.3 66.5 + - - +
386A VAL* 3.8 22.4 - - + -
560A SER* 3.4 5.5 - - - -
561A VAL* 3.1 46.5 + - + +
563A VAL* 4.9 3.4 - - + -
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Residues in contact with TYR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A VAL* 3.6 11.8 - - - +
367A PRO* 3.0 37.6 + - + +
370A GLN* 3.3 43.5 - - + -
371A ALA* 4.5 2.2 - - - +
372A VAL* 5.6 2.2 - - + +
383A LEU* 3.7 21.8 - - + +
384A ILE* 1.3 76.0 - - - +
386A VAL* 1.3 64.5 + - - +
537A TRP* 3.8 30.1 - + - -
540A LYS* 3.4 33.6 + - + +
544A ILE* 4.5 5.2 - - + -
558A LEU* 4.6 10.3 - - + -
559A LEU 3.5 6.1 - - - +
560A SER* 4.3 7.6 - - - -
801A 5W6 3.5 25.2 + - + -
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 6.0 4.0 - - + -
354A LEU* 4.1 24.0 - - + -
363A VAL* 3.5 41.3 - - + -
365A ARG 3.5 4.3 - - - +
366A VAL* 4.6 6.5 - - + -
384A ILE* 3.8 27.6 - - + +
385A TYR* 1.3 79.9 - - - +
387A GLU* 1.3 67.4 + - - +
388A VAL* 4.0 4.9 - - + -
558A LEU* 3.3 6.5 - - - +
559A LEU* 2.7 45.5 + - + +
560A SER* 5.5 0.2 - - - -
561A VAL* 5.0 1.3 - - + -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A VAL* 3.4 1.7 - - - -
364A VAL* 2.6 40.3 + - + -
365A ARG* 2.4 70.5 + - + +
367A PRO* 4.0 6.4 - - + +
386A VAL* 1.3 71.4 - - - +
388A VAL* 1.3 63.2 + - - +
544A ILE* 3.9 8.1 - - - +
548A SER* 2.4 29.1 + - - -
550A TYR* 4.1 2.6 - - - -
556A TRP* 3.1 20.0 + - + +
557A ARG 3.8 3.6 - - - -
558A LEU* 3.4 20.6 - - + -
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A PHE* 4.7 5.4 - - + -
361A HIS* 3.2 38.1 - - + +
362A HIS 3.0 10.3 - - - +
363A VAL* 3.7 11.9 - - + -
364A VAL* 3.5 3.6 - - - +
386A VAL* 4.0 5.8 - - + -
387A GLU* 1.3 81.2 - - - +
389A LEU* 1.3 64.9 + - - +
390A GLU 5.2 0.4 - - - +
555A ASN 3.8 0.2 - - - +
556A TRP* 3.5 5.4 - - - -
557A ARG* 3.0 51.2 + - + +
559A LEU* 3.8 29.8 - - + -
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A HIS* 4.3 1.8 - - - -
362A HIS* 2.8 30.8 + - - +
364A VAL* 3.6 25.3 - - + +
388A VAL* 1.3 71.9 - - - +
390A GLU* 1.3 66.3 + - - +
391A CYS* 4.0 3.1 - - - -
400A PRO* 4.3 26.0 - - + -
550A TYR* 4.5 12.1 - - + -
553A LEU* 4.4 20.4 - - + -
555A ASN* 3.1 45.3 - - + +
556A TRP* 3.6 20.0 - - + +
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A PHE* 4.1 31.5 - - + +
360A ASP 4.2 3.1 - - - -
361A HIS* 4.2 4.5 - - - -
388A VAL* 4.1 2.4 - - - +
389A LEU* 1.3 74.6 - - - +
391A CYS* 1.3 75.7 + - - +
555A ASN* 2.7 42.0 + - - +
557A ARG* 3.5 37.7 + - + +
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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