Contacts of the strand formed by residues 614 - 621 (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 ILE 614 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344B TYR* 5.5 2.9 - - + -
399B THR* 5.9 4.5 - - - +
400B SER 5.4 0.9 - - - +
600B THR* 2.9 26.3 + - - -
601B ALA* 3.0 25.3 + - + -
603B LEU* 4.4 20.6 - - + -
613B GLN* 1.3 73.9 - - - +
615B GLY* 1.3 72.7 + - - +
616B TRP* 4.0 9.1 - - - +
632B ASN* 3.7 23.3 - - - +
633B VAL 3.4 5.8 - - - +
634B LYS* 3.3 44.2 - - + -
636B VAL* 3.9 2.2 - - - -
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Residues in contact with GLY 615 (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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599B GLY 3.9 4.3 - - - -
600B THR* 4.6 0.4 - - - -
614B ILE* 1.3 77.9 - - - +
616B TRP* 1.3 65.4 + - - -
632B ASN* 3.4 5.5 - - - -
633B VAL 2.5 33.4 + - - +
636B VAL* 3.6 14.4 - - - +
641B MET 4.7 1.3 - - - -
642B ALA* 4.9 0.7 - - - -
645B ASN* 3.1 23.0 + - - -
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Residues in contact with TRP 616 (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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399B THR* 3.9 12.8 + - - -
400B SER 2.8 27.0 + - - -
401B PRO* 3.6 18.6 + - + -
402B GLY* 4.5 4.5 - - - -
404B THR* 3.9 21.3 - - + -
526B ILE 5.3 0.4 - - - -
528B PRO* 4.1 25.6 - - + -
531B ILE* 3.7 28.5 - - + -
597B LYS 4.6 0.2 - - - -
598B SER* 3.5 2.7 - - - -
599B GLY 3.0 37.3 + - - +
601B ALA 4.8 2.7 - - - -
614B ILE* 4.0 14.2 - - + +
615B GLY* 1.3 79.2 - - - -
617B PHE* 1.3 67.4 + - - +
618B ILE* 4.8 3.4 - - + -
630B ALA* 4.4 22.2 - - + -
631B ILE 3.4 9.0 - - - -
632B ASN* 3.1 36.6 - - + +
642B ALA* 4.0 6.3 - - - +
645B ASN* 3.3 4.4 - - - +
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Residues in contact with PHE 617 (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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404B THR* 5.5 0.2 - - - -
578B VAL* 4.3 9.9 - - + -
579B VAL* 4.5 3.6 - - + -
583B HIS* 3.9 15.9 - + + -
587B ILE* 3.5 37.9 - - + -
596B GLY* 4.4 2.9 - - - -
597B LYS 3.3 20.6 - - - -
598B SER* 3.6 26.5 - - - -
616B TRP* 1.3 74.4 - - - +
618B ILE* 1.3 79.2 + - - +
619B SER* 3.8 5.9 + - - -
629B MET 3.7 1.2 - - - +
630B ALA* 3.4 1.7 - - - -
631B ILE* 2.9 34.5 + - + +
642B ALA 4.2 3.8 - - - -
645B ASN* 3.6 20.4 - - + -
646B ALA* 3.9 19.5 - - + +
649B SER* 3.9 15.1 + - - +
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Residues in contact with ILE 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B THR* 3.7 23.8 - - + -
531B ILE* 3.5 32.3 - - + -
532B LEU* 4.0 14.6 - - + -
535B TYR* 3.6 38.1 - - + -
575B MET* 5.3 1.8 - - + -
596B GLY* 2.9 4.3 - - - -
597B LYS* 2.8 34.2 + - + +
616B TRP* 4.8 4.9 - - + -
617B PHE* 1.3 78.2 - - - +
619B SER* 1.3 69.0 + - - +
620B TYR* 5.9 0.9 - - + -
628B MET* 5.4 3.6 - - + -
629B MET 3.2 8.5 - - - +
630B ALA* 3.8 19.3 - - + -
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Residues in contact with SER 619 (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* 5.7 0.2 - - - -
587B ILE* 3.9 10.9 - - - +
594B LEU* 5.6 0.7 - - - -
595B ILE 3.1 16.6 - - - -
596B GLY* 4.0 0.7 - - - -
617B PHE* 3.8 17.6 + - - -
618B ILE* 1.3 82.0 - - - +
620B TYR* 1.3 68.6 + - - +
628B MET* 3.4 2.0 - - - +
629B MET* 2.9 38.6 + - - +
649B SER* 4.3 1.0 + - - -
653B TYR* 2.8 26.1 + - - -
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Residues in contact with TYR 620 (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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538B LEU* 3.9 8.3 - - + +
539B GLU* 3.4 41.5 + - + +
572B THR* 3.6 13.2 - - - +
575B MET* 4.4 13.0 - - + -
594B LEU* 3.4 4.3 - - - -
595B ILE* 3.1 57.4 + - + +
618B ILE* 5.9 1.3 - - + -
619B SER* 1.3 79.6 - - - +
621B ASP* 1.3 71.4 + - - +
622B LYS* 3.4 13.7 + - + +
625B PRO* 3.7 12.1 - - + -
627B MET 3.0 23.3 - - - +
628B MET* 3.4 33.0 - - + -
653B TYR* 3.0 11.9 - - - -
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Residues in contact with ASP 621 (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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591B TYR 5.2 0.2 - - - +
592B ALA* 3.6 14.5 - - - +
593B ASN 3.0 18.5 + - - -
594B LEU* 3.8 14.0 - - + +
620B TYR* 1.3 73.3 - - - +
622B LYS* 1.3 55.9 + - - +
623B ASP* 2.9 15.3 + - - +
624B ASN* 2.9 26.7 + - - +
625B PRO* 2.7 34.0 - - - +
626B ASN* 5.7 0.2 - - - +
627B MET 4.5 1.6 + - - -
653B TYR* 4.3 4.2 + - + -
657B TYR* 2.5 37.8 + - + +
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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