Contacts of the strand formed by residues 597 - 605 (chain A) in PDB entry 3RLN
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 LYS 597 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A VAL* 3.2 5.5 - - - -
591A TYR* 2.9 56.9 + - + +
592A GLU* 3.0 26.7 + - + +
595A GLU* 3.5 43.1 + - + +
596A GLN* 1.3 77.5 - - - +
598A LYS* 1.3 59.2 + - - +
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Residues in contact with LYS 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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588A SER* 5.3 2.7 - - - -
589A PHE* 3.2 13.5 - - - +
590A VAL* 3.9 22.2 - - + -
591A TYR* 3.4 7.9 - - - -
596A GLN* 3.5 20.4 + - - +
597A LYS* 1.3 80.1 - - - +
599A MET* 1.3 64.2 + - - +
616A PHE* 4.1 18.0 - - - +
618A ILE* 3.6 37.0 - - + +
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Residues in contact with MET 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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588A SER* 3.2 2.3 - - - -
589A PHE* 2.9 55.0 + - + +
591A TYR* 3.7 16.4 - - + -
598A LYS* 1.3 77.6 - - - +
600A PHE* 1.3 66.6 + - - +
601A HIS* 3.7 21.8 - - + +
614A LYS* 3.7 32.8 - - + -
615A VAL 3.1 13.2 - - - +
616A PHE* 3.9 13.5 - - + -
618A ILE* 3.9 8.1 - - - -
755A HIS* 3.4 33.7 - - + -
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Residues in contact with PHE 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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585A ALA* 4.3 3.6 - - + -
586A THR* 3.7 24.5 - - - +
587A GLU 3.7 11.0 - - - +
588A SER* 3.9 7.2 - - - +
589A PHE* 4.3 1.3 - - - -
599A MET* 1.3 78.2 - - - +
601A HIS* 1.3 74.6 + - - +
602A ALA* 4.5 2.0 - - + -
614A LYS* 3.8 1.7 - - - -
615A VAL* 2.9 70.4 + - + +
617A ASN 4.0 6.5 - - - -
618A ILE* 4.0 8.7 - - + -
621A LYS* 3.7 47.3 - - + -
624A PHE* 3.5 36.6 - + + -
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Residues in contact with HIS 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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585A ALA* 3.2 4.9 - - - +
586A THR* 2.8 42.5 + - + +
589A PHE* 3.8 19.9 - + - -
599A MET* 3.7 19.8 - - + +
600A PHE* 1.3 76.2 - - - +
602A ALA* 1.3 63.5 + - - +
613A VAL 3.4 11.7 + - - +
614A LYS* 4.0 15.2 - - + +
641A PHE* 4.9 4.2 - - - -
736A THR* 3.5 28.7 - - + +
737A CYS* 3.7 20.8 - - + +
755A HIS 2.7 29.1 + - - -
757A HIS* 4.1 6.2 - - + +
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Residues in contact with ALA 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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582A VAL* 4.9 1.3 - - + -
584A ASN* 3.2 15.5 - - - +
585A ALA* 4.0 7.2 - - + +
600A PHE* 4.3 4.9 + - + -
601A HIS* 1.3 76.4 - - - +
603A THR* 1.3 66.2 + - - +
604A VAL* 4.8 0.2 - - + -
612A ARG* 3.7 2.6 - - - +
613A VAL* 2.8 42.2 + - + +
624A PHE* 3.7 31.0 - - + -
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Residues in contact with THR 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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582A VAL* 3.9 0.7 - - - +
583A LEU* 2.8 32.2 + - + +
584A ASN* 2.9 32.6 + - - +
602A ALA* 1.3 75.9 + - - +
604A VAL* 1.3 65.9 + - - +
610A VAL* 3.5 25.6 - - + -
611A PHE 3.6 5.2 - - - +
612A ARG* 2.6 36.8 + - - +
669A ALA* 4.0 12.6 - - + -
688A ASN* 4.7 1.0 + - - -
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Residues in contact with VAL 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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580A VAL* 3.7 32.1 - - + -
581A MET 3.4 11.2 - - - +
582A VAL* 4.1 12.3 - - + -
583A LEU* 4.3 2.5 - - - +
603A THR* 1.3 80.6 - - - +
605A ALA* 1.3 63.4 + - - +
610A VAL* 3.4 6.4 - - - +
611A PHE* 2.9 50.8 + - + +
613A VAL* 3.6 24.5 - - + -
624A PHE* 4.3 18.6 - - + -
632A ILE* 4.9 4.3 - - + -
642A LEU* 5.3 2.7 - - + -
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Residues in contact with ALA 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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580A VAL* 3.3 6.9 - - - -
581A MET* 3.0 33.4 + - - +
583A LEU* 4.1 22.0 - - + -
604A VAL* 1.3 77.9 - - - +
606A THR* 1.3 68.4 + - - +
609A GLU 3.1 11.9 - - - +
610A VAL* 4.5 2.9 - - + -
611A PHE* 5.2 0.2 - - - -
659A MET* 4.4 2.4 - - - +
661A ILE* 3.7 17.8 - - + +
665A LEU* 4.3 7.0 - - + -
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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