Contacts of the strand formed by residues 526 - 540 (chain A) in PDB entry 3HI7
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 LYS 526 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A VAL 4.7 0.5 - - - +
524A GLY 3.5 1.3 - - - +
525A THR* 1.3 78.5 - - - +
527A ASN* 1.3 70.7 + - - +
581A SER* 4.4 0.7 + - - -
582A PRO* 3.6 19.0 - - + +
662A ASN* 3.1 52.5 + - - +
663A GLU* 3.7 14.1 - - - +
664A ASP* 4.3 2.9 - - - +
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Residues in contact with ASN 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A LEU* 3.5 15.8 - - - +
521A ASP* 3.6 1.4 - - - -
522A VAL* 2.9 56.2 + - - +
524A GLY 3.6 2.0 + - - -
525A THR 3.9 4.8 - - - +
526A LYS* 1.3 87.1 + - - +
528A SER* 1.3 67.7 + - - +
579A PHE* 5.1 4.0 - - + +
580A THR 3.1 17.8 + - - +
581A SER* 4.1 0.6 - - - +
582A PRO* 5.2 1.3 - - - -
660A ILE 3.8 0.5 - - - +
662A ASN* 3.1 7.1 + - - -
663A GLU 2.9 32.5 + - - +
665A LEU* 3.7 16.8 + - + +
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Residues in contact with SER 528 (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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527A ASN* 1.3 72.6 - - - +
529A PHE* 1.3 64.6 + - - +
558A GLN* 5.8 3.1 - - - -
559A TYR 5.5 2.2 - - - -
579A PHE* 3.4 4.7 - - - -
580A THR* 2.8 41.8 + - - -
660A ILE 4.0 6.1 - - - -
661A GLU* 3.9 5.3 - - - +
662A ASN* 3.1 23.6 + - - +
665A LEU* 3.6 11.0 - - - +
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Residues in contact with PHE 529 (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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528A SER* 1.3 79.4 - - - +
530A GLN* 1.3 62.3 + - - +
531A THR* 3.5 27.1 - - + -
558A GLN* 4.4 2.3 - - - +
559A TYR* 3.4 47.1 + + - +
565A ALA* 3.8 15.9 - - + -
567A PHE* 3.7 29.6 - + - -
577A LEU* 4.2 3.4 - - + -
578A LEU 3.2 30.3 - - - -
579A PHE* 3.5 36.1 - + + -
580A THR* 5.4 0.2 - - - -
622A LEU* 3.9 13.0 - - + -
624A VAL* 4.4 3.8 - - + -
660A ILE* 4.6 12.7 + - + -
665A LEU* 3.9 13.6 - - + +
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Residues in contact with GLN 530 (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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528A SER* 6.3 0.2 - - - -
529A PHE* 1.3 76.9 - - - +
531A THR* 1.3 68.5 + - - +
532A LEU* 3.8 17.4 - - - +
556A GLN* 4.9 2.0 - - - +
557A THR 3.3 14.1 - - - +
558A GLN* 3.1 31.9 + - - +
559A TYR* 3.9 2.0 - - - -
578A LEU* 2.9 58.0 + - + +
580A THR* 3.7 25.5 - - + +
590A LYS* 6.0 3.0 - - - +
592A SER* 5.1 1.2 + - - -
699A PHE* 5.8 0.2 - - - -
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Residues in contact with THR 531 (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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529A PHE* 3.5 23.3 - - + -
530A GLN* 1.3 80.9 - - - +
532A LEU* 1.3 67.4 + - - +
555A GLU 3.9 0.2 - - - +
556A GLN* 3.5 3.1 - - - -
557A THR* 2.8 41.8 + - - -
559A TYR* 2.8 32.1 + - + +
567A PHE* 4.3 0.7 - - + -
574A PRO* 3.7 17.4 - - + +
576A TYR 3.1 14.6 - - - +
577A LEU* 3.8 12.8 - - + -
578A LEU* 5.3 0.2 - - - -
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Residues in contact with LEU 532 (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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530A GLN* 3.8 18.8 - - - +
531A THR* 1.3 86.1 - - - +
533A GLN* 1.3 60.8 + - - +
554A LEU* 4.1 10.5 - - + -
555A GLU 3.2 5.2 - - - +
556A GLN* 3.9 20.2 - - + -
574A PRO* 4.4 3.9 - - - +
575A LYS* 4.2 6.2 + - - +
576A TYR* 3.2 33.7 + - + +
578A LEU* 3.6 25.1 - - + -
699A PHE* 3.8 24.0 - - + -
674B LEU* 5.0 0.2 - - - +
676B ILE* 3.6 30.3 - - + -
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Residues in contact with GLN 533 (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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532A LEU* 1.3 76.1 - - - +
534A MET* 1.3 64.3 + - - +
554A LEU* 3.8 7.7 - - - +
555A GLU* 2.8 56.1 + - - +
557A THR* 6.1 0.2 - - - +
574A PRO* 5.8 4.5 - - + -
575A LYS* 5.9 1.1 - - - +
674B LEU* 4.6 7.4 - - - -
676B ILE* 5.0 0.7 - - - -
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Residues in contact with MET 534 (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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533A GLN* 1.3 78.2 - - - +
535A LYS* 1.3 76.7 + - - +
536A LEU* 3.9 9.2 - - + -
552A PRO* 3.6 32.1 - - + -
553A THR 3.4 7.9 - - - +
509B ILE* 4.1 8.3 - - + -
511B THR* 4.8 4.7 - - - +
603B GLN 4.7 4.0 - - - +
604B VAL* 3.8 46.4 - - + +
674B LEU* 4.0 28.5 - - + +
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Residues in contact with LYS 535 (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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533A GLN 3.9 0.6 + - - -
534A MET* 1.3 78.4 - - - +
536A LEU* 1.3 73.1 + - - +
553A THR* 2.6 49.0 + - - +
555A GLU* 3.1 36.8 - - + +
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Residues in contact with LEU 536 (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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534A MET* 3.9 14.3 - - + -
535A LYS* 1.3 92.3 + - - +
537A GLU* 1.3 63.4 + - - +
550A VAL* 4.0 7.9 - - + -
551A GLN* 3.2 31.4 - - - +
552A PRO* 3.7 8.7 - - + -
553A THR* 4.7 0.4 - - - -
604B VAL 3.4 27.8 - - - +
605B LEU* 4.6 7.4 - - + -
606B PRO* 3.6 32.1 - - + -
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Residues in contact with GLU 537 (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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535A LYS 3.7 0.2 + - - -
536A LEU* 1.3 75.8 - - - +
538A ASN* 1.3 60.5 + - - +
539A ILE* 3.7 30.0 - - + +
550A VAL* 3.2 7.0 - - - +
551A GLN* 2.9 66.2 + - + +
553A THR* 3.5 21.3 - - + -
496B ARG* 2.9 29.0 + - - +
497B HIS* 3.2 7.6 + - - -
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Residues in contact with ASN 538 (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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537A GLU* 1.3 74.4 - - - +
539A ILE* 1.3 62.8 + - - +
548A ARG* 2.9 32.8 + - - +
549A VAL 3.4 3.4 - - - -
550A VAL* 3.7 12.5 - - + +
1D NAG 1.4 66.6 + - - +
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Residues in contact with ILE 539 (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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537A GLU* 3.7 38.8 - - + +
538A ASN* 1.3 77.7 + - - +
540A THR* 1.3 72.9 + - - +
542A PRO* 4.8 4.7 - - + -
548A ARG* 3.3 14.6 + - - +
549A VAL* 2.8 52.8 + - + +
551A GLN* 4.2 10.8 - - - +
367B MET* 4.5 13.9 - - + -
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Residues in contact with THR 540 (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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539A ILE* 1.3 81.6 - - - +
541A ASN* 1.3 76.9 + - - +
542A PRO* 3.1 13.2 - - + +
545A PRO* 3.6 31.9 - - + +
547A HIS 3.8 2.0 - - - +
548A ARG* 3.1 22.9 + - - +
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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