Contacts of the strand formed by residues 551 - 558 (chain A) in PDB entry 1OAK
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 VAL 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A CYS* 3.5 34.3 - - - +
511A ARG 3.6 15.7 - - - +
513A LEU* 3.3 28.0 - - + +
515A LEU* 4.6 0.9 - - + -
544A LEU* 4.1 26.7 - - + -
545A ARG* 3.1 16.0 + - + +
546A ILE* 3.1 8.8 - - - +
547A SER 2.9 23.7 + - - -
550A TRP* 1.3 81.6 - - - +
552A ARG* 1.3 69.0 + - - +
553A VAL* 4.3 3.4 - - + -
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Residues in contact with ARG 552 (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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513A LEU 2.8 6.9 + - - +
514A ASP* 2.8 46.5 + - - +
515A LEU 2.8 25.5 + - - -
546A ILE* 5.5 1.1 - - - -
547A SER 3.6 15.9 - - - +
548A GLN* 3.2 30.8 + - - +
551A VAL* 1.3 75.9 - - - +
553A VAL* 1.3 64.1 + - - +
568A LEU* 3.4 36.3 + - + +
569A LYS* 3.5 30.3 - - - +
610A ASP* 5.0 11.5 - - - +
611A ARG* 3.2 37.3 - - - +
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Residues in contact with VAL 553 (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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515A LEU* 3.2 7.9 - - + +
517A PHE* 4.0 26.2 - - + -
541A MET* 4.2 11.7 - - + -
544A LEU* 4.2 18.6 - - + -
546A ILE* 4.1 26.9 - - + +
551A VAL* 4.3 3.8 - - + -
552A ARG* 1.3 82.2 - - - +
554A ALA* 1.3 60.0 + - - +
555A VAL* 5.4 0.4 - - + -
566A ILE* 3.3 17.9 - - + +
567A GLY 3.5 12.5 - - - +
568A LEU* 3.7 3.8 + - - +
577A LEU* 4.1 24.9 - - + +
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Residues in contact with ALA 554 (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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515A LEU 3.0 4.4 + - - -
516A VAL* 4.2 18.4 - - + -
517A PHE* 2.8 28.0 + - - +
553A VAL* 1.3 76.4 - - - +
555A VAL* 1.3 64.9 + - - +
556A VAL* 4.2 1.6 - - + -
566A ILE* 3.0 17.9 - - - +
567A GLY* 4.1 0.9 - - - -
568A LEU* 3.8 25.6 - - + +
605A ILE* 5.0 7.6 - - + -
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Residues in contact with VAL 555 (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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517A PHE* 3.6 22.4 - - + +
519A LEU* 4.2 19.1 - - + -
537A VAL* 4.5 12.1 - - + -
541A MET* 4.5 6.3 - - - -
553A VAL* 5.4 1.1 - - + -
554A ALA* 1.3 80.0 - - - +
556A VAL* 1.3 64.6 + - - +
565A TYR* 2.8 31.1 + - + -
566A ILE* 2.9 41.5 + - + +
581A ALA* 4.7 5.6 - - + -
584A VAL* 4.2 25.1 - - + -
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Residues in contact with VAL 556 (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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516A VAL* 4.8 2.0 - - + -
517A PHE 2.9 8.5 + - - +
518A LEU* 3.4 24.6 - - + -
519A LEU* 2.7 35.9 + - - +
554A ALA* 5.0 0.7 - - + -
555A VAL* 1.3 86.4 - - - +
557A GLU* 1.3 58.0 + - - +
558A TYR 4.1 0.2 + - - -
562A SER* 3.6 31.4 - - - +
563A HIS 3.2 11.9 - - - +
564A ALA* 4.1 12.1 - - + -
566A ILE 4.8 2.5 - - - +
597A VAL* 4.5 5.2 - - + -
600A TYR* 4.2 17.9 - - + -
605A ILE* 4.3 10.3 - - + -
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Residues in contact with GLU 557 (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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519A LEU* 3.4 11.9 - - + +
521A GLY* 3.6 11.8 - - - -
530A PHE* 4.1 16.6 - - + -
556A VAL* 1.3 75.2 - - - +
558A TYR* 1.3 68.3 + - - +
559A HIS* 2.6 25.7 + - - -
561A GLY 4.0 0.3 - - - +
562A SER* 3.5 2.1 - - - -
563A HIS* 2.8 56.1 + - - +
565A TYR* 3.7 24.5 + - + -
584A VAL* 4.3 7.6 - - + -
585A LYS 4.2 4.1 - - - +
587A ALA* 3.6 25.2 - - + +
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Residues in contact with TYR 558 (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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518A LEU* 3.5 14.6 - - + -
519A LEU 2.8 45.7 + - - -
520A ASP* 3.4 8.0 - - - +
521A GLY 2.8 25.5 + - - -
556A VAL 4.7 0.2 - - - -
557A GLU* 1.3 80.7 + - - +
559A HIS* 1.3 58.9 + - - +
561A GLY 3.4 7.6 - - - +
562A SER* 4.6 1.6 - - - +
592A ALA* 3.2 32.3 - - + +
593A SER 3.6 6.5 - - - +
594A THR* 3.7 11.4 - - + +
597A VAL* 3.3 47.1 - - + -
620A LEU* 3.9 15.4 - - + +
621A LEU 3.1 14.6 + - - -
622A MET* 3.3 21.0 - - - +
624A SER* 5.4 0.7 + - - -
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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