Contacts of the strand formed by residues 602 - 609 (chain A) in PDB entry 3MXN
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 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A THR* 5.7 1.4 - - - +
542A ASP 5.5 0.7 - - - -
544A ASP* 3.4 29.1 + - - +
595A SER 3.9 0.3 - - - +
596A PHE* 3.6 5.2 - - - -
597A ASN* 2.8 37.0 + - + +
600A LEU* 3.1 38.8 - - + +
601A SER* 1.3 79.5 - - - +
603A ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 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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541A LEU* 3.8 26.7 - - + -
542A ASP 3.6 19.5 + - - +
543A VAL* 3.5 4.8 - - + -
544A ASP* 2.9 31.6 + - - +
594A ILE* 3.9 8.1 - - + -
595A SER 3.2 9.9 - - - +
596A PHE* 4.2 7.9 - - + -
602A LYS* 1.3 77.9 - - - +
604A MET* 1.3 59.8 + - - +
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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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544A ASP* 3.5 26.9 - - + +
545A PHE 5.3 4.5 - - - +
546A VAL* 3.8 32.8 - - + +
594A ILE* 3.4 2.5 - - - -
595A SER* 2.9 38.4 + - - +
603A ALA* 1.3 76.2 - - - +
605A VAL* 1.3 65.5 + - - +
606A LEU* 3.4 15.5 + - + +
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Residues in contact with VAL 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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543A VAL* 3.8 26.0 - - + -
544A ASP 2.7 20.0 + - - +
545A PHE* 3.8 17.5 - - + -
546A VAL* 3.1 29.8 + - - +
549A ILE* 3.7 10.0 - - + +
592A MET* 4.3 11.2 - - + -
593A THR 3.5 6.3 - - - +
594A ILE* 4.1 16.2 - - + +
604A MET* 1.3 70.3 - - - +
606A LEU* 1.3 60.0 + - - +
607A ALA 3.6 19.5 - - - +
608A LEU* 3.8 19.7 - - + -
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Residues in contact with LEU 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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507A THR* 4.3 19.3 - - + +
546A VAL* 3.7 34.0 - - + +
549A ILE* 4.0 4.0 - - - +
593A THR* 2.8 21.7 + - + +
595A SER* 3.9 22.2 - - - +
604A MET* 3.8 24.2 - - + +
605A VAL* 1.3 73.7 - - - +
607A ALA* 1.3 60.4 + - + +
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Residues in contact with ALA 607 (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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549A ILE* 3.9 6.0 - - - +
591A LEU 4.5 0.2 - - - -
592A MET* 3.5 4.3 - - - -
593A THR* 2.9 40.8 + - + +
605A VAL* 3.6 3.0 - - - +
606A LEU* 1.3 82.8 - - + +
608A LEU* 1.3 71.9 + - - +
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Residues in contact with LEU 608 (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* 4.5 3.8 - - + -
549A ILE* 3.7 34.8 - - + +
553A LEU* 5.0 10.1 - - + -
588A LEU* 4.1 31.4 - - + -
590A CYS* 3.9 13.7 - - - -
591A LEU 3.3 2.2 - - - -
592A MET* 3.8 25.4 - - + -
605A VAL* 3.8 12.3 - - + -
607A ALA* 1.3 87.6 - - - +
609A GLN* 1.3 62.4 + - - +
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Residues in contact with GLN 609 (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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509A LYS* 3.0 31.1 + - - +
590A CYS* 3.4 4.8 - - - +
591A LEU* 2.8 44.6 + - + +
608A LEU* 1.3 75.8 - - - +
610A ASP* 1.3 73.0 + - - +
612A ASN* 4.1 9.3 - - - +
615A HIS* 3.2 27.4 + - - -
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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