Contacts of the strand formed by residues 577 - 581 (chain A) in PDB entry 4KSC
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 577 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLN* 5.4 8.5 - - + +
386A GLY 5.1 5.2 - - - +
388A LEU* 3.7 13.5 - - + +
414A LYS 5.1 1.3 - - - -
415A SER* 3.9 14.8 - - - -
416A GLY* 3.2 28.0 - - - +
417A GLN 4.1 7.2 - - - -
546A LYS* 2.5 26.2 + - + +
547A ILE* 3.1 20.5 - - + +
548A LEU 3.0 19.6 + - - -
576A ARG* 1.3 71.6 - - - +
578A THR* 1.3 58.3 + - - +
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Residues in contact with THR 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 5.2 4.8 - - - +
413A VAL* 4.6 4.0 - - - +
417A GLN 3.5 7.9 + - - +
418A THR* 3.6 30.5 - - + -
419A VAL* 3.6 19.6 + - - +
547A ILE* 5.1 2.0 - - - -
548A LEU* 2.4 40.9 + - - +
550A LEU* 3.5 15.9 - - - +
573A ARG* 4.1 18.8 - - + -
576A ARG 3.7 9.2 - - - +
577A THR* 1.3 75.8 - - - +
579A ILE* 1.3 65.9 + - - +
580A VAL* 5.5 1.6 - - + +
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Residues in contact with ILE 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 4.6 16.2 - - + -
390A PHE* 4.9 14.1 - - + -
411A LEU* 4.7 11.0 - - + -
413A VAL* 5.6 1.1 - - + -
419A VAL* 3.5 22.7 - - + +
421A LEU* 3.6 34.1 - - + -
432A THR* 4.8 5.2 - - - +
433A VAL* 5.0 8.7 - - + +
436A MET* 5.7 2.2 - - + -
548A LEU 3.0 4.7 + - - +
549A LEU* 3.6 30.1 - - + +
550A LEU 3.1 21.8 + - - +
578A THR* 1.3 81.1 + - - +
580A VAL* 1.3 61.8 + - - +
581A ILE* 4.2 9.3 + - + +
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Residues in contact with VAL 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A THR* 5.3 7.4 - - - -
419A VAL 3.2 16.2 + - - +
420A ALA* 3.6 8.7 - - + +
421A LEU 3.4 21.1 + - - +
550A LEU* 3.4 36.1 - - + +
552A GLU 5.7 0.2 - - - +
553A ALA 6.2 0.4 - - - +
573A ARG* 4.4 23.1 - - - +
578A THR* 5.2 1.8 - - + +
579A ILE* 1.3 74.6 - - - +
581A ILE* 1.3 71.9 + - - +
582A ALA* 4.4 7.5 + - + +
587A THR* 5.4 8.1 - - - +
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Residues in contact with ILE 581 (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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421A LEU* 3.3 53.8 - - + +
422A VAL* 5.4 0.2 - - - -
429A LYS* 3.6 35.0 - - + +
430A SER* 4.9 1.3 - - - +
432A THR* 4.1 0.4 - - - +
433A VAL* 3.4 31.4 - - + -
550A LEU 2.8 11.6 + - - +
551A ASP* 4.2 13.5 - - - +
552A GLU* 2.4 42.6 + - + +
579A ILE* 4.2 6.5 - - + -
580A VAL* 1.3 77.1 - - - +
582A ALA* 1.3 61.7 + - - +
583A HIS* 6.0 0.4 - - + +
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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