Contacts of the strand formed by residues 555 - 563 (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 LYS 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552A SER 5.8 1.3 - - - +
553A MET 3.2 10.9 + - - +
554A GLU* 1.3 71.7 - - - +
556A PRO* 1.3 67.3 - - + +
599A CYS* 3.8 2.0 - - - -
600A GLN* 2.8 63.0 + - + +
602A THR* 4.4 24.2 + - - +
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Residues in contact with PRO 556 (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 3.8 6.3 - - - +
555A LYS* 1.3 90.1 - - + +
557A THR* 1.3 73.5 + - - +
598A ASP 3.7 8.3 - - - +
599A CYS* 4.0 11.2 - - + -
600A GLN* 4.0 0.9 + - - -
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Residues in contact with THR 557 (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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556A PRO* 1.3 79.3 - - - +
558A ARG* 1.3 70.6 + - - +
559A LEU* 4.5 7.5 + - + +
597A VAL* 4.6 4.3 + - - +
598A ASP* 2.6 31.8 + - - +
599A CYS 3.9 5.2 + - - -
600A GLN* 2.8 42.6 + - - +
609A TYR* 6.0 0.2 - - - -
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Residues in contact with ARG 558 (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* 1.3 84.1 + - - +
559A LEU* 1.3 63.7 + - - +
560A THR* 2.8 29.5 + - - -
594A LYS* 5.7 1.2 - - - +
596A ILE* 3.4 46.8 - - - +
597A VAL 3.4 4.2 + - - -
598A ASP* 5.2 3.4 - - - +
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Residues in contact with LEU 559 (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* 4.5 5.6 - - + -
558A ARG* 1.3 81.8 + - - +
560A THR* 1.3 79.0 + - - +
561A ARG* 3.2 41.1 - - + +
597A VAL* 2.7 46.0 + - + +
609A TYR* 3.6 17.0 - - + +
628A ALA* 5.2 4.0 - - + -
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Residues in contact with THR 560 (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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558A ARG* 2.8 26.5 + - - -
559A LEU* 1.3 84.2 - - - +
561A ARG* 1.3 83.6 + - - +
562A TYR* 4.6 12.8 - - + +
594A LYS* 4.2 27.3 - - + -
595A LEU 3.5 11.2 - - - +
628A ALA* 3.8 11.7 - - - +
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Residues in contact with ARG 561 (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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559A LEU* 3.2 28.9 - - + +
560A THR* 1.3 85.2 - - - +
562A TYR* 1.3 70.6 + - - +
595A LEU* 2.8 36.8 + - + +
597A VAL* 3.5 21.5 - - + -
609A TYR* 3.3 26.1 + - + -
623A ALA 6.2 0.2 - - - -
626A LEU* 3.5 29.6 - - + -
627A ARG* 3.0 22.5 - - - +
628A ALA* 3.0 31.6 - - - +
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Residues in contact with TYR 562 (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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560A THR* 4.6 11.8 - - + +
561A ARG* 1.3 78.3 - - - +
563A VAL* 1.3 65.6 + - - +
592A ASN* 5.4 4.9 - - - -
593A GLN 3.5 27.6 - - - +
594A LYS* 4.3 26.1 - - + +
595A LEU* 4.1 5.2 - - - -
626A LEU* 3.3 9.7 - - - +
627A ARG* 2.7 68.5 + - + +
628A ALA 3.9 17.0 - - - -
629A GLN 4.4 7.4 - - - -
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Residues in contact with VAL 563 (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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562A TYR* 1.3 80.3 - - - +
564A SER* 1.3 76.3 + - - +
565A ALA 3.8 2.1 + - - -
568A ALA* 4.7 5.6 - - + -
587A LEU* 3.8 37.0 - - + +
590A TYR* 4.2 28.9 - - + +
591A LYS* 4.9 10.1 - - - -
592A ASN* 5.0 5.3 + - - +
593A GLN 5.0 1.5 + - - +
595A LEU* 3.5 25.1 - - + -
625A ASN 4.2 7.6 - - - +
626A LEU* 4.8 1.8 - - + -
627A ARG* 4.6 9.2 - - - +
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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