Contacts of the strand formed by residues 595 - 603 (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 LEU 595 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A THR* 3.5 7.7 - - - +
561A ARG* 2.8 50.8 + - - +
562A TYR 4.1 9.0 - - - -
563A VAL* 3.5 30.3 - - + -
587A LEU* 5.4 0.2 - - + -
590A TYR* 4.7 8.5 - - + -
593A GLN* 4.3 8.3 - - + +
594A LYS* 1.3 80.9 - - - +
596A ILE* 1.3 61.1 + - - +
597A VAL 3.9 0.2 - - - -
611A ILE* 3.6 32.5 - - + -
612A ARG 4.0 2.5 - - - +
613A THR* 4.2 5.2 - - - +
618A ILE* 3.3 32.8 - - + -
626A LEU* 4.3 10.5 - - + -
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Residues in contact with ILE 596 (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* 3.4 46.9 - - - +
560A THR* 5.1 0.7 - - - +
594A LYS* 5.2 15.7 - - + +
595A LEU* 1.3 73.7 - - - +
597A VAL* 1.3 66.5 + - - +
598A ASP* 3.5 6.2 + - + +
611A ILE* 3.5 3.0 - - - -
612A ARG* 2.9 52.5 + - + +
613A THR 4.7 0.4 - - - +
614A SER* 4.0 33.2 - - - +
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Residues in contact with VAL 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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557A THR* 4.6 3.5 + - - +
558A ARG* 3.4 5.0 + - - -
559A LEU* 2.7 47.4 + - + +
561A ARG* 3.5 34.8 - - + +
595A LEU 4.7 0.4 - - - +
596A ILE* 1.3 72.1 - - - +
598A ASP* 1.3 57.7 + - - +
599A CYS 3.2 23.3 - - - +
609A TYR* 3.4 35.4 - - + -
610A ARG 3.7 6.1 - - - +
611A ILE* 3.9 18.2 - - + -
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Residues in contact with ASP 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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556A PRO* 3.6 3.0 - - - +
557A THR* 2.6 47.0 + - - +
558A ARG* 4.6 3.8 - - - +
596A ILE* 3.5 7.8 + - + +
597A VAL* 1.3 74.4 - - - +
599A CYS* 1.3 59.5 + - - +
610A ARG* 2.6 63.9 + - - +
612A ARG* 3.7 34.0 - - - +
617A PHE* 5.6 1.1 - - - -
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Residues in contact with CYS 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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554A GLU* 3.9 17.9 - - - -
555A LYS 3.8 14.4 - - - -
556A PRO* 4.0 11.0 - - + -
557A THR* 3.9 0.8 + - - -
597A VAL* 3.2 13.0 - - - +
598A ASP* 1.3 83.6 + - - +
600A GLN* 1.3 80.2 + - - +
610A ARG* 3.2 54.3 + - + +
620A TRP* 3.7 14.6 - - - -
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Residues in contact with GLN 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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554A GLU* 3.4 3.3 - - - -
555A LYS* 2.8 61.0 + - + +
556A PRO 4.0 2.0 + - - -
557A THR* 2.8 38.8 + - - +
599A CYS* 1.3 82.5 - - - +
601A ALA* 1.3 63.9 + - - +
602A THR* 5.5 0.3 + - - -
607A LEU* 3.7 18.7 - - - +
608A TRP 3.4 14.6 - - - +
609A TYR* 3.9 13.8 - - + -
620A TRP* 3.5 7.4 - - - -
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Residues in contact with ALA 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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553A MET 3.3 24.5 - - - +
554A GLU* 4.0 6.7 - - + -
555A LYS* 4.8 3.8 - - - +
576A PRO* 4.4 5.2 - - + -
600A GLN* 1.3 82.2 + - - +
602A THR* 1.3 64.3 + - - +
603A ILE* 3.8 15.8 + - + -
607A LEU* 4.0 2.7 - - - +
608A TRP* 3.0 33.8 + - - +
620A TRP* 3.7 13.9 - - + -
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Residues in contact with THR 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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553A MET* 3.5 24.4 + - - +
555A LYS* 4.4 19.1 + - - +
600A GLN* 5.5 0.3 + - - -
601A ALA* 1.3 72.8 - - - +
603A ILE* 1.3 60.9 + - - +
604A GLU 4.3 0.3 + - - -
605A GLY* 4.1 22.4 - - - +
606A GLN 3.3 14.4 - - - +
607A LEU* 4.2 13.4 - - + +
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Residues in contact with ILE 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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548A PHE* 3.6 27.4 - - + +
549A TYR* 3.7 25.8 - - + -
553A MET* 4.1 16.4 - - + -
576A PRO* 3.6 35.4 - - + +
601A ALA* 3.8 15.7 + - + +
602A THR* 1.3 80.9 - - - +
604A GLU* 1.3 72.8 + - + +
605A GLY 2.7 5.5 + - - -
606A GLN* 2.7 38.0 + - - +
608A TRP* 4.3 12.6 + - + +
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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