Contacts of the strand formed by residues 555 - 564 (chain A) in PDB entry 4P3N
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 TYR 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A SER* 5.0 2.1 + - - -
494A PHE* 5.1 2.0 - - - -
495A LYS* 3.6 56.2 - - + +
547A GLN* 4.0 27.4 + - + +
548A ILE 3.2 16.4 - - - -
549A LYS* 3.6 34.6 - - + +
553A GLY 4.3 7.2 - - - -
554A ARG* 1.3 73.9 - - - +
556A HIS* 1.3 69.9 + - - +
682C ILE* 4.5 11.8 - - - +
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Residues in contact with HIS 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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547A GLN* 3.2 8.5 - - - +
548A ILE* 2.9 43.8 + - + +
550A ASP* 2.6 34.1 + - + +
554A ARG* 3.4 24.6 + - + -
555A TYR* 1.3 79.2 + - - +
557A GLN* 1.3 61.7 + - - +
558A CYS* 3.5 3.5 + - - -
599A ARG* 5.1 1.6 - - - +
603A ILE* 3.7 46.0 - - + +
606A GLU* 4.5 15.7 - - - -
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Residues in contact with GLN 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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545A ASP* 3.7 31.0 + - - +
546A ILE 3.5 12.1 + - - +
547A GLN* 3.9 25.3 - - - +
556A HIS* 1.3 69.3 - - - +
558A CYS* 1.3 60.3 + - - +
559A ALA 2.7 29.9 + - - -
560A THR* 4.7 2.4 - - - -
599A ARG* 2.6 40.0 + - - +
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Residues in contact with CYS 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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487A TYR* 4.0 6.1 - - + +
546A ILE 3.8 2.4 + - - +
548A ILE* 3.7 23.3 - - + -
556A HIS* 3.5 3.6 + - - -
557A GLN* 1.3 79.2 + - - +
559A ALA* 1.3 66.7 + - - +
560A THR* 3.8 3.5 + - - +
592A ALA* 3.9 3.1 - - - +
593A ILE 3.8 14.1 - - - +
594A LEU 4.0 15.3 - - - +
595A GLY* 3.6 19.9 + - - +
599A ARG* 3.6 14.4 - - - +
600A MET* 4.8 5.2 - - - -
603A ILE* 3.6 31.6 - - - -
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Residues in contact with ALA 559 (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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483A LEU* 3.5 24.9 - - + -
487A TYR* 3.1 20.6 + - - +
546A ILE* 3.4 31.7 + - + -
557A GLN* 2.7 26.3 + - - -
558A CYS* 1.3 78.7 - - - +
560A THR* 1.3 59.5 + - - +
592A ALA 3.0 11.7 - - - +
593A ILE 3.6 1.6 - - - +
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Residues in contact with THR 560 (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 LYS* 4.7 4.2 - - - +
544A ILE 3.7 6.2 + - - -
545A ASP* 3.1 19.7 + - - -
546A ILE* 4.5 0.9 - - - -
557A GLN* 4.7 2.0 - - - -
558A CYS 5.0 2.7 - - - +
559A ALA* 1.3 77.2 - - - +
561A ILE* 1.3 74.6 + - - +
562A GLN* 4.3 9.9 - - + +
590A HIS* 5.1 5.6 - - + +
591A ARG* 3.2 7.0 - - - +
592A ALA* 2.9 46.9 + - + +
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Residues in contact with ILE 561 (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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476A ILE* 3.7 27.8 - - + -
479A CYS* 3.7 31.6 - - + -
480A LEU* 4.3 14.8 - - + -
483A LEU* 4.2 23.6 - - + -
543A LYS* 3.3 3.3 - - - +
544A ILE* 2.7 60.1 + - + +
546A ILE* 5.1 0.7 - - + -
560A THR* 1.3 78.9 + - - +
562A GLN* 1.3 61.4 + - - +
563A LEU* 4.4 2.4 - - + +
589A VAL* 3.8 17.5 - - + -
590A HIS 3.5 2.9 - - - +
591A ARG* 4.9 3.4 - - + -
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Residues in contact with GLN 562 (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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538A ALA* 3.9 6.9 - - - +
540A TYR* 3.2 27.5 + - + +
541A GLY 3.2 21.4 + - - -
542A PRO 3.4 3.9 + - - -
543A LYS* 3.2 30.2 + - + +
560A THR* 4.3 9.9 - - + +
561A ILE* 1.3 76.8 - - - +
563A LEU* 1.3 85.1 + - - +
589A VAL* 3.5 2.3 - - - -
590A HIS* 2.9 65.1 + - + +
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Residues in contact with LEU 563 (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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472A ILE* 3.7 35.2 - - + -
476A ILE* 4.3 15.3 - - + -
515A ALA* 3.8 22.0 - - + -
519A LEU* 4.3 12.3 - - + -
540A TYR* 3.6 0.7 - - - +
541A GLY* 3.1 13.2 - - - -
542A PRO* 3.0 32.1 + - + +
543A LYS* 5.8 0.4 - - - -
561A ILE* 5.0 0.9 - - + -
562A GLN* 1.3 102.2 + - - +
564A ASP* 1.3 59.5 + - - +
565A PHE* 4.2 3.1 - - + -
587A VAL* 4.4 6.7 - - + -
588A ILE 3.5 2.5 - - - +
589A VAL* 3.6 33.2 - - + -
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Residues in contact with ASP 564 (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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540A TYR* 3.6 20.7 - - + +
563A LEU* 1.3 73.1 - - - +
565A PHE* 1.3 62.9 + - - +
566A GLN* 2.8 34.5 + - - +
567A LEU* 3.0 29.2 + - - +
568A PRO* 3.5 7.5 - - - +
587A VAL* 4.0 0.7 - - - +
588A ILE* 2.8 40.3 + - + +
590A HIS* 2.9 33.4 + - + +
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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