Contacts of the strand formed by residues 628 - 636 (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 ASP 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A VAL* 3.3 10.2 - - - +
550A LYS* 3.0 51.5 + - + +
611A GLU* 4.2 4.0 - - - -
626A VAL* 4.5 2.5 - - - -
627A ASP* 1.3 99.2 - - + +
629A LEU* 1.3 60.0 + - - +
630A LEU* 3.4 8.5 + - + +
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Residues in contact with LEU 629 (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 36.1 - - + -
549A VAL* 3.7 16.8 - - + -
566A ILE* 4.1 21.5 - - + -
611A GLU* 3.4 48.9 + - + +
612A ALA 4.8 0.4 - - - +
613A VAL* 4.6 3.8 - - + -
626A VAL* 4.4 7.4 - - + -
628A ASP* 1.3 68.2 - - - +
630A LEU* 1.3 65.3 + - - +
631A GLY* 3.2 4.7 + - - -
134B ASN* 4.4 16.4 + - - +
135B ILE* 5.0 4.0 - - + -
138B LEU* 4.3 18.4 - - + +
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Residues in contact with LEU 630 (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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548A LEU* 3.1 42.8 + - + +
549A VAL* 4.2 2.7 - - - +
550A LYS* 3.7 33.4 - - + -
555A VAL* 4.2 27.8 - - + -
628A ASP* 3.4 9.5 + - + +
629A LEU* 1.3 73.1 - - - +
631A GLY* 1.3 54.7 + - - +
656A LEU* 5.3 2.5 - - + -
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Residues in contact with GLY 631 (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* 3.8 9.1 - - - +
548A LEU* 2.7 39.6 + - - +
629A LEU 3.2 5.8 + - - -
630A LEU* 1.3 78.5 - - - +
632A GLN* 1.3 62.3 + - - -
633A ASP* 5.1 0.7 - - - -
138B LEU* 4.5 9.0 - - - -
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Residues in contact with GLN 632 (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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545A GLN* 2.8 38.6 + - - +
546A ALA 3.5 7.2 - - - +
547A LEU* 4.4 4.5 - - + +
560A ILE* 3.3 31.2 - - + +
631A GLY* 1.3 72.9 - - - -
633A ASP* 1.3 82.8 + - - +
634A ASP* 4.6 4.9 + - - +
138B LEU* 3.9 21.2 - - + +
141B THR* 4.1 24.8 + - + +
142B ILE* 5.7 0.9 - - + -
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Residues in contact with ASP 633 (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 3.8 0.5 - - - +
545A GLN* 3.2 3.0 - - - -
546A ALA* 2.7 42.5 + - - +
548A LEU* 4.1 28.2 - - + +
631A GLY 4.7 0.7 - - - +
632A GLN* 1.3 84.9 + - - +
634A ASP* 1.3 93.5 + - - +
635A ILE* 3.9 9.2 + - + +
656A LEU* 4.8 4.9 - - - +
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Residues in contact with ASP 634 (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* 3.3 25.3 - - + +
544A ILE 3.6 3.2 - - - +
545A GLN* 3.9 21.8 - - - +
632A GLN* 4.6 5.2 - - - +
633A ASP* 1.3 90.8 + - - +
635A ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 635 (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* 3.5 7.5 - - - +
544A ILE* 3.1 43.0 + - + +
546A ALA* 3.7 25.8 - - + -
548A LEU* 4.4 9.9 - - + -
557A ALA* 3.8 19.1 - - + -
633A ASP* 4.3 12.6 - - - +
634A ASP* 1.3 79.9 - - - +
636A VAL* 1.3 65.6 + - - +
637A ILE 4.8 0.7 - - - +
654A ALA* 3.7 15.7 - - + -
655A ILE 5.7 2.9 - - - +
656A LEU* 4.2 24.0 - - + -
664A ILE* 4.1 15.7 - - + -
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Residues in contact with VAL 636 (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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541A LEU* 4.0 29.8 - - + -
542A ALA 3.6 14.4 - - - +
543A ILE* 4.0 15.5 - - + -
634A ASP 5.7 0.2 - - - +
635A ILE* 1.3 75.3 - - - +
637A ILE* 1.3 65.8 + - - +
638A LYS* 3.1 20.8 + - + +
653A ALA 3.8 4.2 - - - +
654A ALA* 3.9 10.8 - - - +
655A ILE 4.7 8.9 + - - +
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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