Contacts of the strand formed by residues 606 - 612 (chain A) in PDB entry 1M9S
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 GLN 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602A THR* 3.3 6.7 - - - -
603A ILE 2.7 40.2 + - - +
604A GLU* 3.4 4.6 - - + +
605A GLY* 1.3 75.5 - - - +
607A LEU* 1.3 61.3 + - - +
608A TRP* 3.8 6.6 - - - +
622A LYS* 3.0 46.3 + - + +
624A ALA* 5.3 7.3 - - - +
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Residues in contact with LEU 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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600A GLN* 3.7 22.7 - - - +
601A ALA 4.0 6.5 - - - +
602A THR* 4.2 12.3 - - + +
605A GLY 4.2 0.4 + - - -
606A GLN* 1.3 73.4 - - - +
608A TRP* 1.3 67.4 + - - +
609A TYR* 3.6 35.2 - - + +
622A LYS* 3.6 7.4 - - - +
623A ALA* 2.9 30.5 + - + +
624A ALA* 4.3 1.7 + - - +
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Residues in contact with TRP 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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571A SER 5.7 0.2 - - - -
573A TYR* 3.9 13.9 - + - -
575A VAL 4.5 0.2 - - - -
576A PRO* 3.5 47.0 + - + -
577A VAL 3.8 1.3 - - - -
578A ALA* 3.6 33.9 - - + -
600A GLN* 3.4 0.9 - - - +
601A ALA 3.0 35.4 + - - +
603A ILE* 4.3 14.8 + - + +
606A GLN* 3.8 17.4 - - - +
607A LEU* 1.3 80.4 - - - +
609A TYR* 1.3 70.9 + - - +
620A TRP* 3.9 11.9 - - + -
621A THR* 3.5 36.3 - - - -
622A LYS* 3.4 45.4 - - + +
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Residues in contact with TYR 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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557A THR* 6.0 0.2 - - - -
559A LEU* 3.6 14.2 - - + +
561A ARG* 3.3 44.5 + - + -
597A VAL* 3.4 33.4 - - + -
599A CYS 3.9 2.5 - - - -
600A GLN* 3.9 16.6 - - + -
607A LEU* 3.6 32.3 - - + +
608A TRP* 1.3 84.8 - - - +
610A ARG* 1.3 61.0 + - - +
611A ILE* 3.7 7.8 + - + -
620A TRP* 3.5 5.8 - - - -
621A THR* 2.8 35.9 + - - +
623A ALA* 3.4 28.2 - - + +
626A LEU* 4.4 5.6 - - + -
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Residues in contact with ARG 610 (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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554A GLU* 4.4 9.7 + - - -
597A VAL* 3.7 0.7 - - - -
598A ASP* 2.6 61.1 + - - +
599A CYS* 3.2 31.3 + - + +
609A TYR* 1.3 71.9 - - - +
611A ILE* 1.3 59.4 + - - +
612A ARG* 5.9 2.0 - - - +
617A PHE* 3.8 27.8 - - + -
619A GLY 3.2 12.6 - - - +
620A TRP* 3.3 41.1 - - + +
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Residues in contact with ILE 611 (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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572A TYR* 5.5 0.2 - - + -
587A LEU* 4.0 16.6 - - + -
590A TYR* 6.1 0.2 - - + -
595A LEU* 3.6 32.1 - - + -
596A ILE 3.5 3.6 - - - +
597A VAL* 3.9 17.7 - - + -
598A ASP* 4.5 0.2 - - - -
609A TYR* 3.7 2.9 + - + -
610A ARG* 1.3 74.1 - - - +
612A ARG* 1.3 64.4 + - - +
617A PHE* 4.0 3.5 - - - -
618A ILE* 3.2 25.7 + - + -
619A GLY 2.8 40.4 + - - +
621A THR* 3.7 23.6 - - + -
626A LEU* 3.5 28.0 - - + -
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Residues in contact with ARG 612 (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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595A LEU* 3.9 1.1 - - - -
596A ILE* 2.9 51.0 + - + +
598A ASP* 3.7 24.2 + - - +
610A ARG* 5.9 1.6 - - - +
611A ILE* 1.3 79.1 - - - +
613A THR* 1.3 70.2 + - - +
615A SER 5.5 3.6 + - - -
616A THR 3.6 10.9 - - - +
617A PHE* 3.8 31.3 - - + +
618A ILE* 3.8 9.0 - - - +
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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