Contacts of the strand formed by residues 534 - 540 (chain A) in PDB entry 7EHI
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 GLN 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A ALA* 4.3 0.8 - - - +
529A VAL* 3.7 4.5 - - - +
530A ILE* 3.0 40.2 + - + +
531A GLY* 3.1 27.0 + - - +
532A GLU 3.3 16.1 + - - +
533A ARG* 1.3 80.5 - - - +
535A ILE* 1.3 61.8 + - - +
550A PHE 3.4 7.2 - - - +
551A ASN* 3.5 23.7 + - - +
553A GLY* 5.7 0.8 - - - -
555A THR* 4.0 16.6 + - - -
556A ASP 4.5 1.2 + - - -
557A LEU* 3.6 38.2 - - + +
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Residues in contact with ILE 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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403A TYR* 3.8 33.2 - - + +
410A ALA* 3.5 28.9 - - + +
413A LEU* 3.9 19.1 - - + -
414A VAL* 4.5 12.8 - - + -
461A PHE* 4.0 14.4 - - + -
527A PHE* 5.4 0.2 - - - -
528A ASP 3.5 10.8 - - - +
529A VAL* 4.9 0.7 - - + -
530A ILE* 4.2 4.2 - - - +
534A GLN* 1.3 72.2 - - - +
536A ARG* 1.3 64.1 + - - +
537A LEU* 3.9 28.9 - - + +
548A GLY 3.6 1.4 - - - +
549A VAL* 3.4 3.1 - - - +
550A PHE* 2.9 39.4 + - + +
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Residues in contact with ARG 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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526A ILE 3.8 2.1 - - - +
527A PHE* 3.8 0.7 - - - -
528A ASP* 2.8 71.9 + - - +
530A ILE* 3.5 36.9 - - + +
535A ILE* 1.3 74.3 - - - +
537A LEU* 1.3 58.0 + - - +
538A THR* 3.9 8.7 - - - +
547A VAL* 3.5 32.1 - - + -
548A GLY 3.4 2.5 - - - -
549A VAL* 3.9 16.0 - - + +
584A TRP* 5.7 2.0 - - - -
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Residues in contact with LEU 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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461A PHE* 3.6 36.3 - - + +
464A MET* 3.8 37.2 - - + +
465A GLN* 3.4 23.8 - - - +
525A ILE* 5.4 4.7 - - + -
526A ILE 3.6 2.2 - - - +
527A PHE* 3.2 36.3 - - + -
535A ILE* 3.9 9.6 - - + -
536A ARG* 1.3 74.4 - - - +
538A THR* 1.3 61.0 + - - +
539A ARG* 6.2 1.8 - - + -
546A ILE 3.8 0.7 - - - +
547A VAL* 3.3 3.5 - - - +
548A GLY 2.8 40.3 + - - +
550A PHE* 4.2 4.3 - - + -
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Residues in contact with THR 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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524A LYS 3.6 0.3 - - - +
525A ILE* 3.3 8.3 - - - +
526A ILE* 2.9 50.3 + - + -
528A ASP* 4.7 3.8 + - - -
536A ARG* 3.9 19.9 + - - -
537A LEU* 1.3 75.6 + - - +
539A ARG* 1.3 67.1 + - - +
540A GLU* 3.5 18.6 - - + +
545A ARG* 3.4 34.0 - - + -
546A ILE 3.4 3.6 - - - +
547A VAL* 4.0 7.2 - - + +
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Residues in contact with ARG 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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430A ARG* 5.8 5.3 - - - +
464A MET* 2.9 46.6 + - + +
465A GLN 3.1 18.2 + - - -
466A PRO* 3.8 19.2 + - - +
513A ARG* 4.4 1.8 - - - +
517A ILE* 3.7 25.9 + - + +
520A LEU* 4.0 6.3 - - + +
523A ASP* 3.0 40.9 + - - +
524A LYS 3.2 4.7 - - - -
525A ILE* 3.7 29.8 - - - +
537A LEU* 5.8 2.0 - - + -
538A THR* 1.3 72.9 - - - +
540A GLU* 1.3 62.1 + - - +
545A ARG* 3.5 0.5 - - - -
546A ILE* 2.9 56.0 + - + +
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Residues in contact with GLU 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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520A LEU* 5.0 0.9 - - - -
522A ASP 4.7 0.2 - - - +
523A ASP* 3.2 7.1 - - - +
524A LYS* 2.8 47.1 + - + +
526A ILE* 3.9 16.1 - - + +
538A THR* 3.5 13.2 - - + +
539A ARG* 1.3 77.9 - - - +
541A ASP* 1.3 65.7 + - - +
544A THR 3.4 11.7 - - - +
545A ARG* 2.9 46.6 + - + -
588A VAL* 4.3 8.3 - - + +
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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