Contacts of the strand formed by residues 543 - 551 (chain A) in PDB entry 4JPB
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 ILE 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A LEU* 3.5 37.5 + - + +
542A ALA* 1.3 74.8 - - - +
544A ILE* 1.3 75.6 + - - +
634A ASP* 3.3 30.5 - - + +
635A ILE 3.5 11.2 - - - +
636A VAL* 4.0 20.9 - - + -
637A ILE* 5.4 0.3 - - - +
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Residues in contact with ILE 544 (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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543A ILE* 1.3 84.2 - - - +
545A GLN* 1.3 72.3 + - - +
546A ALA* 4.7 5.6 - - + -
559A PRO* 3.6 31.9 - - + -
561A ALA* 6.4 0.9 - - + -
634A ASP* 3.6 1.8 - - - -
635A ILE* 3.1 46.7 + - + +
637A ILE* 3.4 38.6 - - + -
664A ILE* 5.0 7.0 - - + -
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Residues in contact with GLN 545 (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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544A ILE* 1.3 78.7 - - - +
546A ALA* 1.3 55.9 + - - +
560A ILE* 2.8 42.9 + - + +
561A ALA 4.5 0.5 + - - -
632A GLN* 2.8 29.0 + - - +
633A ASP 3.2 7.9 - - - +
634A ASP* 3.9 15.9 - - - +
141B THR* 5.6 0.5 - - - +
145B ALA* 3.5 28.6 - - - +
149B GLU* 5.1 8.7 + - - +
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE* 4.7 2.7 - - + -
545A GLN* 1.3 75.8 - - - +
547A LEU* 1.3 62.3 + - - +
548A LEU* 3.6 3.4 + - + +
557A ALA* 4.3 7.9 - - + -
558A ILE 3.4 15.7 - - - +
559A PRO* 3.8 8.7 - - + -
560A ILE* 3.7 3.1 - - - +
632A GLN* 3.5 5.4 - - - +
633A ASP* 2.7 41.3 + - - +
635A ILE* 3.7 29.4 - - + -
664A ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 547 (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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546A ALA* 1.3 70.3 - - - +
548A LEU* 1.3 76.4 + - - +
549A VAL* 3.7 4.1 + - + +
556A TYR 3.7 0.2 - - - +
557A ALA* 3.4 3.1 - - - -
558A ILE* 2.8 39.4 + - + +
560A ILE* 4.5 5.3 - - + +
563A ILE* 3.6 33.0 - - + -
566A ILE* 3.6 24.2 - - + -
613A VAL* 3.6 21.3 - - + -
629A LEU* 3.7 16.8 - - + -
631A GLY* 3.4 20.2 - - - +
632A GLN* 4.3 6.1 - - + +
138B LEU* 4.6 11.4 - - + -
142B ILE* 5.4 2.2 - - + -
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Residues in contact with LEU 548 (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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546A ALA 3.9 10.8 - - - +
547A LEU* 1.3 81.7 - - - +
549A VAL* 1.3 60.6 + - - +
555A VAL* 4.2 11.2 - - + -
556A TYR 3.7 2.2 - - - +
557A ALA* 4.2 16.2 - - + -
629A LEU 3.9 0.3 - - - -
630A LEU* 3.1 43.7 + - + +
631A GLY 2.7 22.4 + - - +
633A ASP* 4.1 24.2 - - + +
635A ILE* 4.4 11.0 - - + -
656A LEU* 3.6 41.3 - - + -
662A ALA* 5.2 0.2 - - + -
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Residues in contact with VAL 549 (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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547A LEU* 3.7 4.9 + - + +
548A LEU* 1.3 73.2 - - - +
550A LYS* 1.3 60.9 + - - +
555A VAL* 3.4 7.6 - - - +
556A TYR* 2.8 53.4 + - + +
558A ILE* 4.5 14.8 - - + -
595A LEU* 4.3 8.5 - - + -
613A VAL* 4.7 7.6 - - + -
626A VAL* 3.4 39.3 - - + -
628A ASP 3.3 18.4 - - - +
629A LEU* 3.7 16.4 - - + -
630A LEU* 4.4 2.2 - - - +
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Residues in contact with LYS 550 (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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549A VAL* 1.3 78.7 - - - +
551A VAL* 1.3 64.0 + - - +
552A ASN 4.1 11.0 + - - +
553A ASN* 3.6 37.8 + - - +
554A LEU 3.3 12.3 - - - +
555A VAL* 4.1 14.4 - - + +
556A TYR* 5.1 0.2 - - - -
626A VAL* 3.8 2.4 - - - +
627A ASP* 3.0 28.8 + - + +
628A ASP* 3.0 34.4 + - + +
630A LEU* 3.7 28.9 - - + -
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Residues in contact with VAL 551 (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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550A LYS* 1.3 75.7 - - - +
552A ASN* 1.3 64.5 + - - +
553A ASN 2.9 0.7 + - - -
554A LEU* 2.8 39.0 + - - +
556A TYR* 4.2 12.4 - - + -
595A LEU* 3.6 39.9 - - + -
596A TRP* 4.1 33.4 - - + +
599A LEU* 6.2 0.2 - - + -
601A ILE* 4.2 24.0 - - + -
603A HIS* 4.9 0.7 - - + -
626A VAL* 5.0 0.4 - - - -
627A ASP* 3.3 10.1 - - - +
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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