Contacts of the strand formed by residues 594 - 601 (chain A) in PDB entry 4U6R
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 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A MET* 3.3 9.2 - - - +
591A PHE* 2.8 46.4 + - - +
592A ASP* 3.7 17.8 + - - +
593A ASN* 1.3 75.2 - - - +
595A ASP* 1.3 70.7 + - - +
596A VAL* 4.2 4.2 - - + +
627A ARG* 4.0 7.2 - - - +
629A PHE* 3.8 42.5 - - + -
1004A SO4 2.9 50.7 + - - -
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Residues in contact with ASP 595 (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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588A ARG* 5.1 6.5 + - - -
589A GLY 3.6 5.1 - - - +
590A MET* 3.6 18.9 - - - +
593A ASN 4.4 0.2 + - - -
594A ARG* 1.3 75.1 - - - +
596A VAL* 1.3 64.5 + - - +
629A PHE* 4.8 1.7 - - - -
643A GLU* 4.2 3.5 - - - +
644A LEU* 3.3 44.5 + - + +
698A MET* 5.6 8.3 - - + +
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Residues in contact with VAL 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A ILE* 5.3 0.4 - - + -
588A ARG* 3.7 4.0 - - - +
589A GLY 2.9 46.4 + - - -
590A MET 3.6 13.5 - - - +
591A PHE* 3.9 18.4 - - + +
594A ARG* 4.2 4.3 - - + +
595A ASP* 1.3 79.9 - - - +
597A ALA* 1.3 59.0 + - - +
598A VAL* 3.7 18.2 - - + -
629A PHE* 3.7 23.3 - - + -
641A ALA* 4.1 14.6 - - + -
642A ILE 3.1 14.8 - - - +
644A LEU* 3.8 11.2 - - - +
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Residues in contact with ALA 597 (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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577A LEU* 4.0 14.1 - - + -
586A VAL* 4.1 2.0 - - + -
587A TYR 3.5 4.7 - - - -
596A VAL* 1.3 72.6 - - - +
598A VAL* 1.3 60.9 + - - +
599A LYS 4.0 0.4 - - - -
640A ILE 3.2 2.1 - - - +
641A ALA* 3.2 3.8 - - - -
642A ILE* 2.7 36.5 + - + +
643A GLU 4.5 0.2 - - - +
644A LEU* 4.1 2.5 - - + +
1001A 3E4 3.6 51.3 - - + +
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Residues in contact with VAL 598 (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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569A ILE* 3.9 23.3 - - + -
571A PHE* 4.6 9.6 - - + -
585A ILE 3.6 1.4 - - - +
586A VAL* 3.3 4.1 - - - +
587A TYR* 2.8 50.3 + - + +
589A GLY* 4.5 8.5 - - - -
596A VAL* 3.7 24.7 - - + +
597A ALA* 1.3 76.9 - - - +
599A LYS* 1.3 60.1 + - - +
600A ARG 3.7 0.9 + - - -
639A TYR* 4.0 36.6 - - + -
640A ILE 3.1 8.3 - - - +
641A ALA* 4.3 3.4 - - + -
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Residues in contact with LYS 599 (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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580A GLY* 4.5 13.6 - - - -
581A ALA* 4.8 3.0 - - - +
584A THR* 3.9 29.0 - - - +
585A ILE 3.3 5.6 - - - +
586A VAL* 3.9 17.9 - - + -
598A VAL* 1.3 71.8 - - - +
600A ARG* 1.3 61.2 + - - +
601A ILE* 3.8 19.4 + - + -
638A GLN 3.5 1.4 - - - +
639A TYR* 3.4 3.8 - - - -
640A ILE* 2.8 39.4 + - + +
711A ASP* 5.1 3.4 + - - -
1001A 3E4 3.2 67.5 + - + -
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Residues in contact with ARG 600 (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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571A PHE* 5.6 0.4 - - - -
583A GLY 4.1 2.0 + - - +
584A THR* 3.4 8.3 - - - -
585A ILE* 2.7 51.2 + - + +
587A TYR* 3.7 30.4 + - + -
598A VAL 3.7 1.6 + - - -
599A LYS* 1.3 73.4 - - - +
601A ILE* 1.3 62.9 + - - +
637A PHE* 3.5 57.0 - - + -
638A GLN 3.3 3.1 - - - -
639A TYR* 3.5 30.0 + - + -
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Residues in contact with ILE 601 (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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583A GLY 4.5 4.5 - - - -
584A THR* 3.8 15.0 - - + -
599A LYS* 3.8 26.7 - - + +
600A ARG* 1.3 80.8 - - - +
602A LEU* 1.3 63.7 + - - +
605A CYS* 3.7 25.1 - - + +
606A PHE* 3.4 3.3 - - + -
609A ALA* 3.6 31.2 - - + -
637A PHE* 3.5 10.5 - - - -
638A GLN* 2.9 62.0 + - + +
640A ILE* 4.8 8.1 - - + -
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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