Contacts of the strand formed by residues 391 - 398 (chain A) in PDB entry 2FY5
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 LEU 391 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 4.1 26.0 - - + -
287A LEU* 3.8 14.8 - - + +
290A LEU* 3.8 25.6 - - + -
291A HIS* 3.6 26.7 - - + +
387A ILE 3.2 16.7 + - - +
388A VAL 3.7 10.0 + - - +
389A LYS 3.5 1.9 - - - +
390A ASN* 1.3 74.5 - - - +
392A ASP* 1.3 72.8 + - - +
393A PHE* 3.7 14.0 + - + -
554A PRO* 5.2 2.0 - - + -
576A SER* 4.2 13.2 - - - -
577A SER 3.9 7.9 - - - +
578A PHE* 4.7 3.8 - - + -
579A HIS* 3.8 10.4 - - - -
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Residues in contact with ASP 392 (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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390A ASN 3.4 0.8 + - - -
391A LEU* 1.3 71.8 - - - +
393A PHE* 1.3 60.3 + - - +
394A ILE* 5.9 0.2 - - - +
576A SER* 3.4 1.4 - - - -
577A SER* 2.9 36.4 + - - +
578A PHE 4.6 0.6 - - - -
579A HIS* 3.5 40.2 + - + +
584A THR 4.9 0.7 - - - +
585A SER* 3.8 6.6 + - - -
586A SER* 2.8 53.9 + - - -
587A SER* 4.6 5.0 + - - -
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Residues in contact with PHE 393 (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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283A THR* 3.5 29.0 - - + +
286A ALA* 3.4 24.5 - - + -
287A LEU* 3.7 24.4 - - + +
290A LEU* 4.3 11.4 - - + -
391A LEU* 3.7 12.2 + - + -
392A ASP* 1.3 78.3 + - - +
394A ILE* 1.3 72.9 + - - +
395A VAL* 3.7 15.9 - - + -
551A CYS* 3.4 38.4 - - + -
552A TYR 4.8 3.1 - - - -
574A CYS* 4.1 21.5 - - + -
575A ILE 3.5 18.8 - - - -
576A SER* 3.8 15.0 - - - -
586A SER* 4.8 0.4 - - - -
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Residues in contact with ILE 394 (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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283A THR* 3.9 10.8 - - + +
392A ASP* 5.9 0.2 - - - +
393A PHE* 1.3 80.8 - - - +
395A VAL* 1.3 75.2 + - - +
396A TYR* 5.1 3.4 - - + +
573A PHE 3.7 0.7 - - - +
574A CYS* 3.7 1.9 - - - -
575A ILE* 3.0 41.7 + - + +
586A SER* 3.7 26.2 - - - +
587A SER* 4.5 22.2 - - - +
590A ALA* 4.5 13.2 - - + -
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Residues in contact with VAL 395 (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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282A ASP* 3.8 27.8 - - + +
283A THR* 3.2 35.8 + - - +
393A PHE* 3.7 19.3 - - + -
394A ILE* 1.3 80.7 - - - +
396A TYR* 1.3 59.3 + - - +
397A LYS* 4.1 1.5 + - + -
549A PHE* 4.2 12.1 - - + -
572A LEU* 3.8 31.4 - - + -
573A PHE 3.6 3.8 - - - +
574A CYS* 4.5 5.6 - - - +
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Residues in contact with TYR 396 (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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394A ILE* 3.8 6.4 + - + +
395A VAL* 1.3 74.3 - - - +
397A LYS* 1.3 72.2 + - - +
398A PHE* 3.3 30.3 - - + -
571A ILE 3.9 0.2 - - - +
572A LEU* 3.5 3.0 - - - +
573A PHE* 2.5 64.2 + + + +
575A ILE* 5.0 1.6 - - + -
590A ALA* 3.8 44.6 - - + -
593A VAL* 4.4 5.4 - - + -
594A GLU* 2.9 50.8 + - + +
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Residues in contact with LYS 397 (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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395A VAL* 4.1 2.6 + - + -
396A TYR* 1.3 85.2 - - - +
398A PHE* 1.3 65.8 + - - +
399A ASP* 3.6 18.6 + - + +
570A THR* 4.0 29.0 - - - +
571A ILE 3.8 2.7 - - - +
572A LEU* 3.5 23.1 - - + -
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Residues in contact with PHE 398 (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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396A TYR* 3.3 31.9 - - + -
397A LYS* 1.3 70.9 - - - +
399A ASP* 1.3 59.5 + - - +
400A ASN* 3.5 23.8 - - + -
401A TYR* 3.5 52.9 - + - -
570A THR* 3.3 8.0 - - - -
571A ILE* 2.9 45.4 + - + +
573A PHE* 4.3 2.9 - - + -
594A GLU* 4.2 14.1 - - + -
597A LEU* 3.3 47.8 - - + -
598A ILE* 4.2 11.0 - - + -
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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