Contacts of the strand formed by residues 594 - 597 (chain A) in PDB entry 1MWR
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 594 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A GLN* 4.6 1.2 - - - +
579A VAL* 3.1 31.2 - - + +
580A ASN* 4.5 4.2 - - - +
587A ILE* 3.3 39.7 - - + +
588A TYR* 6.4 0.2 - - - -
589A ARG* 4.1 18.4 - - + +
591A TYR* 5.8 0.7 - - + +
592A ALA* 3.5 21.9 + - + -
593A ASN* 1.3 75.5 + - - +
595A ILE* 1.3 64.1 + - - +
619A SER* 5.6 0.7 - - - -
620A TYR 3.4 13.7 - - - +
621A ASP* 4.0 10.1 - - + -
653A TYR* 3.9 41.5 - - + -
657A TYR* 5.9 0.2 - - - +
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Residues in contact with ILE 595 (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 THR* 3.4 26.0 - - + +
575A MSE 3.6 23.3 - - + +
576A GLN* 3.6 26.2 - - + +
579A VAL* 3.5 9.2 - - - -
593A ASN* 4.0 11.9 - - - +
594A LEU* 1.3 76.9 - - - +
596A GLY* 1.3 59.0 + - - +
619A SER* 3.3 21.7 - - - -
620A TYR* 3.1 56.0 + - + +
622A LYS* 4.4 16.6 - - + -
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Residues in contact with GLY 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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575A MSE 2.9 23.4 + - - +
578A VAL* 3.1 29.9 - - - +
579A VAL* 3.7 2.6 - - - +
595A ILE* 1.3 77.7 - - - +
597A LYS* 1.3 60.5 + - - -
617A PHE* 4.1 9.0 - - - -
618A ILE 3.0 14.1 - - - -
619A SER* 4.1 1.1 - - - -
620A TYR* 5.8 0.9 - - - -
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Residues in contact with LYS 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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403A SER 3.5 15.4 + - - +
404A THR* 4.7 3.6 - - + +
406A LYS* 4.0 16.6 - - - -
407A ILE* 3.6 20.2 - - + -
459A ILE* 4.2 27.9 + - + +
462A SER* 2.9 26.4 + - - +
467A PHE* 5.3 1.1 - - - -
535A TYR* 3.6 39.5 - - + +
575A MSE 4.8 4.2 - - - -
578A VAL* 4.7 0.7 - - + -
596A GLY* 1.3 73.5 - - - -
598A SER* 1.3 94.3 + - - +
616A TRP* 4.1 0.7 - - - +
617A PHE* 3.5 5.0 - - - -
618A ILE* 2.9 32.9 + - + +
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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