Contacts of the strand formed by residues 594 - 601 (chain B) in PDB entry 1MWT
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576B GLN* 4.3 0.9 + - - -
579B VAL* 3.2 32.6 - - + +
580B ASN* 4.2 6.8 - - - +
587B ILE* 3.3 31.4 - - + +
589B ARG* 4.0 19.3 - - + +
591B TYR* 6.1 0.2 - - + -
592B ALA* 3.3 19.1 + - + +
593B ASN* 1.3 76.0 - - - +
595B ILE* 1.3 63.2 + - - +
619B SER* 5.6 0.7 - - - -
620B TYR 3.4 3.4 - - - +
621B ASP* 3.8 20.6 - - + -
650B GLY* 5.6 0.2 - - - -
653B TYR* 3.7 55.2 - - + -
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Residues in contact with ILE 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B THR* 3.9 22.9 - - + +
575B MET* 3.7 24.9 - - + +
576B GLN* 3.7 22.0 - - - +
579B VAL* 3.4 10.8 - - - -
593B ASN 3.3 12.8 - - - +
594B LEU* 1.3 80.8 - - - +
596B GLY* 1.3 59.9 + - - +
619B SER* 3.1 21.5 - - - -
620B TYR* 3.1 51.7 + - + +
622B LYS* 3.9 20.4 - - + -
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Residues in contact with GLY 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B MET* 3.2 43.6 + - - +
578B VAL* 3.4 11.8 - - - +
579B VAL* 3.6 3.6 - - - +
595B ILE* 1.3 78.8 - - - +
597B LYS* 1.3 61.3 + - - -
617B PHE* 4.4 5.8 - - - -
618B ILE 2.9 14.1 - - - -
619B SER* 4.0 2.0 - - - -
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Residues in contact with LYS 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B SER* 3.4 19.1 + - - +
404B THR* 4.2 4.5 - - + +
406B LYS* 4.0 16.6 - - - -
407B ILE* 4.5 10.1 - - + -
459B ILE* 4.1 34.5 - - + +
462B SER* 3.0 28.9 + - - -
535B TYR* 3.8 33.7 - - + +
575B MET* 4.2 2.7 - - + +
578B VAL* 4.6 3.8 - - + -
596B GLY* 1.3 75.2 - - - +
598B SER* 1.3 92.2 + - - +
616B TRP 4.6 0.2 - - - -
617B PHE* 3.3 9.9 - - - -
618B ILE* 2.8 32.8 + - + +
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Residues in contact with SER 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B SER* 3.2 4.9 - - - -
404B THR* 4.6 2.7 - - - -
462B SER* 4.9 1.6 - - - -
578B VAL* 4.5 5.4 - - - +
583B HIS* 3.3 23.2 + - - -
597B LYS* 1.3 110.4 + - - +
599B GLY* 1.3 60.5 + - - +
616B TRP 3.5 6.7 - - - -
617B PHE* 3.6 19.3 - - - -
642B ALA* 3.7 9.2 - - - -
708B PNM 2.6 25.0 + - - -
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Residues in contact with GLY 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B SER* 3.3 20.6 - - - -
404B THR 4.5 0.7 - - - -
598B SER* 1.3 80.8 - - - +
600B THR* 1.3 64.8 + - - -
615B GLY* 3.8 0.5 - - - -
616B TRP* 3.0 39.8 + - - +
642B ALA* 3.4 6.6 - - - +
708B PNM 3.6 4.4 + - - -
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Residues in contact with THR 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B SER 4.3 0.4 - - - +
599B GLY* 1.3 74.1 - - - -
601B ALA* 1.3 67.3 + - - +
613B GLN* 3.3 26.9 + - - +
614B ILE 2.9 13.4 + - - -
615B GLY* 4.9 0.4 - - - -
636B VAL* 4.2 4.0 - - - +
641B MET* 4.3 4.1 - - + +
642B ALA 4.5 10.1 - - - -
708B PNM 2.9 81.2 + - + +
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Residues in contact with ALA 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B SER* 3.8 35.0 - - - +
402B GLY* 4.1 12.2 - - - -
521B GLN* 4.0 12.1 - - - +
600B THR* 1.3 80.9 - - - +
602B GLU* 1.3 63.7 + - - +
603B LEU* 6.3 0.4 - - + -
613B GLN* 3.2 8.3 - - - +
614B ILE* 3.0 40.0 + - + -
616B TRP* 4.8 2.1 - - + -
708B PNM 4.2 0.8 + - - -
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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