Contacts of the strand formed by residues 594 - 598 (chain A) in PDB entry 5I4E
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 PHE 594 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A LEU* 5.2 2.0 - - + -
550A LEU* 4.6 9.2 - - + -
568A PHE* 4.3 17.7 - + - -
569A VAL* 5.1 5.6 - - + -
572A VAL* 4.8 7.4 - - + -
582A PHE* 3.4 42.2 - + + -
583A GLN 3.6 6.7 - - - +
585A PRO* 4.6 4.0 - - + -
592A ALA* 3.5 2.8 - - - +
593A ASP* 1.3 93.4 - - + +
595A SER* 1.3 63.6 + - - +
596A VAL* 4.2 11.7 - - + -
604A ASP* 3.6 2.6 - - - -
605A TYR* 2.8 55.3 + + + -
607A ALA* 4.4 4.9 - - + -
610A TRP* 3.4 37.9 - + - -
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Residues in contact with SER 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LYS 3.7 0.2 - - - +
582A PHE* 3.5 7.6 - - - -
583A GLN* 2.9 54.5 + - - +
584A ARG 5.7 0.5 + - - -
585A PRO* 6.0 1.4 - - - +
590A ASP* 5.4 6.8 + - - +
592A ALA* 5.6 0.5 - - - +
594A PHE* 1.3 74.4 + - - +
596A VAL* 1.3 66.7 + - - +
597A LEU* 6.0 0.2 - - - -
602A LYS* 3.9 17.8 + - - +
603A VAL 3.4 5.6 - - - -
604A ASP* 2.7 27.5 + - - +
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Residues in contact with VAL 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 4.7 2.7 - - + -
537A CYS* 3.8 18.4 - - - -
540A LEU* 4.3 10.3 - - + -
541A ILE* 4.6 5.2 - - + -
550A LEU* 4.0 24.7 - - + -
581A LYS 3.4 6.1 - - - +
582A PHE* 4.8 1.1 - - + -
594A PHE* 4.2 7.2 - - + -
595A SER* 1.3 78.6 - - - +
597A LEU* 1.4 62.3 + - - +
598A HIS* 3.2 40.7 + - + +
602A LYS* 4.5 1.3 - - - -
603A VAL 3.0 31.9 + - - -
605A TYR* 3.8 19.3 - - + -
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Residues in contact with LEU 597 (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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500A GLU* 4.6 0.2 - - - +
537A CYS* 3.9 10.9 - - - +
580A PRO 3.4 24.2 - - - +
581A LYS* 2.8 49.9 + - + +
582A PHE 6.3 0.2 - - - -
583A GLN* 4.8 15.0 - - + +
595A SER 6.0 0.2 - - - -
596A VAL* 1.4 69.4 - - - +
598A HIS* 1.3 66.0 + - - +
601A GLY 4.3 1.8 - - - -
602A LYS* 3.7 35.9 - - + +
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Residues in contact with HIS 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A PHE* 3.7 20.4 - + + -
493A LEU* 4.6 3.1 - - + -
496A ASN* 3.9 15.3 + - + +
500A GLU* 3.4 17.4 + - - +
537A CYS* 4.1 3.4 - - - -
541A ILE* 4.4 12.7 - - + +
596A VAL* 3.2 33.0 + - + +
597A LEU* 1.3 78.0 - - - +
599A TYR* 1.3 66.7 + - + +
600A ALA 3.1 2.0 - - - +
601A GLY* 3.0 22.9 + - - +
603A VAL* 2.9 32.8 - - + -
605A TYR* 2.6 35.9 + + - -
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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
------------------------------------------------------------
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