Contacts of the strand formed by residues 504 - 509 (chain B) in PDB entry 5FS9
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 THR 504 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B PRO* 4.1 19.5 - - + +
499B ASP 4.7 0.4 - - - +
500B SER* 5.0 4.9 - - - +
502B LEU 3.6 9.5 + - - +
503B PRO* 1.3 76.7 - - - +
505B VAL* 1.3 66.7 - - - +
506B GLY 4.3 0.4 - - - -
565B ILE* 4.0 11.7 - - + -
566B PHE 3.1 9.4 - - - +
567B TYR* 3.3 42.6 - - + -
568B LEU* 5.0 0.4 - - - -
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Residues in contact with VAL 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B THR* 1.3 77.7 - - - +
506B GLY* 1.3 61.1 + - - +
507B VAL* 4.5 6.1 - - + -
565B ILE* 3.4 3.2 - - - -
566B PHE* 2.8 40.4 + - + +
568B LEU* 4.1 13.5 - - + -
601B LEU* 3.7 39.9 - - + -
617B ARG* 3.5 38.4 - - - +
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Residues in contact with GLY 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B PRO* 5.7 2.2 - - - +
504B THR 4.3 0.4 - - - -
505B VAL* 1.3 75.3 - - - +
507B VAL* 1.3 60.4 + - - -
508B PHE* 3.8 24.0 - - - -
564B VAL 3.3 7.6 - - - -
565B ILE* 4.1 10.7 - - - +
617B ARG* 3.7 20.5 + - - +
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B VAL* 4.5 5.6 - - + -
506B GLY* 1.3 76.8 - - - +
508B PHE* 1.3 67.1 + - - +
563B GLY* 3.2 2.1 - - - -
564B VAL* 2.8 37.3 + - + +
566B PHE* 4.2 15.9 - - + -
601B LEU 4.4 5.4 - - - +
602B ASN* 3.5 27.6 - - - +
605B ALA* 3.9 24.2 - - + -
610B ILE* 3.7 21.3 - - + +
612B GLU* 5.0 4.7 - - + -
617B ARG* 4.5 12.6 - - - +
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Residues in contact with PHE 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B PRO* 5.1 4.9 - - + -
347B TYR* 4.1 31.2 - + + -
348B LEU* 4.6 10.1 - - + -
506B GLY* 3.8 22.7 - - - -
507B VAL* 1.3 76.7 - - - +
509B ALA* 1.3 64.2 + - - +
560B TYR* 3.6 39.8 - + + -
562B LYS 3.4 4.7 - - - +
563B GLY* 4.0 7.2 - - - -
565B ILE* 4.2 31.9 - - + -
579B TRP* 3.8 33.2 - + + -
610B ILE* 4.1 2.1 - - - +
612B GLU* 3.4 18.2 - - - +
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Residues in contact with ALA 509 (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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508B PHE* 1.3 75.7 - - - +
510B LYS* 1.3 61.5 + - - +
560B TYR* 3.3 13.9 - - - -
561B GLY 2.7 27.9 + - - -
562B LYS* 2.9 18.3 + - - +
610B ILE* 3.8 26.0 - - + -
611B HIS 5.3 0.7 - - - +
612B GLU* 3.3 24.9 - - + +
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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