Contacts of the strand formed by residues 601 - 606 (chain A) in PDB entry 1P4J
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 ARG 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561A SER* 3.7 4.5 - - - -
562A LEU* 3.4 28.3 - - + +
564A ASP* 2.5 35.5 + - + +
582A HIS* 3.9 12.7 - - - -
586A LEU* 3.9 21.2 - - - +
599A VAL* 3.6 12.3 - - + +
600A PRO* 1.3 81.1 - - - +
602A THR* 1.3 63.7 + - - +
603A VAL* 3.9 6.5 - - + +
638A ASP 5.1 0.7 - - - +
639A ARG 3.1 8.3 + - - +
640A LEU* 3.4 17.2 + - + +
641A ARG* 3.2 22.7 + - - +
662A LEU* 3.6 8.5 - - - +
784A GLN* 2.7 37.0 + - - +
787A VAL* 4.7 1.2 - - - +
788A SER* 3.0 26.6 + - - +
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Residues in contact with THR 602 (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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557A ILE* 4.5 21.7 - - + +
558A ASN* 3.9 12.8 + - - +
561A SER* 2.7 23.8 + - - -
562A LEU 2.9 6.1 + - - -
563A PHE* 3.6 13.0 - - + -
564A ASP 2.9 24.7 + - - +
601A ARG* 1.3 73.6 + - - +
603A VAL* 1.3 61.2 + - - +
604A MET* 3.6 29.7 + - + +
641A ARG* 3.8 17.8 - - + +
643A ILE* 4.5 5.4 - - + -
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Residues in contact with VAL 603 (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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564A ASP* 3.2 29.2 - - + +
579A ASN* 4.1 15.0 - - - +
582A HIS* 6.0 1.1 - - - +
583A VAL* 3.8 29.4 - - + -
586A LEU* 5.5 2.9 - - + -
601A ARG* 4.5 8.5 - - + +
602A THR* 1.3 72.3 - - - +
604A MET* 1.3 61.6 + - - +
605A ILE* 4.3 15.6 - - + +
640A LEU* 4.2 21.8 - - + -
641A ARG 3.0 11.0 + - - +
642A VAL* 3.5 8.0 - - + +
643A ILE* 3.0 26.7 + - - +
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Residues in contact with MET 604 (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 PHE* 3.6 28.9 - - + -
549A LEU* 4.9 3.6 - - + -
557A ILE* 5.0 2.7 - - + -
563A PHE* 3.5 48.0 - - + -
564A ASP 2.6 9.4 + - - +
565A VAL* 3.3 20.5 - - + +
566A GLN 2.8 26.5 + - - +
602A THR* 3.7 24.9 - - + +
603A VAL* 1.3 76.0 - - - +
605A ILE* 1.3 64.2 + - - +
643A ILE* 3.4 10.3 - - + -
645A LEU* 3.8 29.4 - - + -
656A VAL* 4.4 1.1 - - + -
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Residues in contact with ILE 605 (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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566A GLN* 3.3 13.5 - - + +
567A VAL* 4.8 0.2 - - - -
570A ILE* 5.1 1.1 - - + -
576A GLN* 4.2 19.3 - - + +
579A ASN* 3.7 36.1 - - + +
580A CYS* 4.7 8.1 - - - +
583A VAL* 5.3 3.6 - - + -
603A VAL* 4.3 13.2 - - + +
604A MET* 1.3 79.8 - - - +
606A GLY* 1.3 64.3 + - - +
623A ILE* 3.6 47.6 - - + -
642A VAL* 5.7 3.8 - - + -
643A ILE 3.0 6.8 + - - +
644A PHE* 3.1 13.0 - - + -
645A LEU* 2.8 24.1 + - - +
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Residues in contact with GLY 606 (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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566A GLN 3.1 8.7 + - - +
567A VAL* 3.4 9.6 - - - +
568A LYS 3.0 24.9 + - - +
570A ILE* 4.5 6.2 - - - +
576A GLN* 5.4 0.9 + - - -
605A ILE* 1.3 76.3 - - - +
607A GLY* 1.3 57.8 + - - -
644A PHE* 4.2 5.6 - - - -
645A LEU* 3.5 22.9 - - - -
648A TYR* 4.1 6.5 - - - -
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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