Contacts of the helix formed by residues 641 - 658 (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 MET 641 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B TYR* 3.5 37.0 - - + +
600B THR* 4.3 7.0 - - + +
613B GLN* 3.2 26.0 - - - +
636B VAL* 2.8 36.0 + - - +
637B GLN 4.6 6.5 - - - +
639B LYS 3.4 0.4 - - - -
640B GLY* 1.3 83.8 - - - +
642B ALA* 1.3 65.5 + - + +
644B TYR* 3.2 19.9 + - - +
645B ASN* 3.4 5.4 - - - +
708B PNM 4.0 35.0 - - + +
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Residues in contact with ALA 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B HIS* 4.9 4.7 - - + +
598B SER* 3.7 18.6 - - - -
599B GLY 3.4 19.1 - - - +
600B THR* 4.5 1.8 - - - -
616B TRP 4.0 3.1 - - - +
617B PHE* 4.2 2.9 - - - -
641B MET* 1.3 76.1 - - - +
643B SER* 1.3 64.0 + - - +
644B TYR 3.1 2.7 - - - -
645B ASN* 3.1 13.3 + - - +
646B ALA* 3.0 21.4 + - - +
708B PNM 3.0 27.4 - - - +
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Residues in contact with SER 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B HIS* 3.7 9.8 + - - -
586B ASP* 3.3 21.9 - - - +
640B GLY* 3.2 18.7 + - - -
641B MET 3.2 0.6 - - - -
642B ALA* 1.3 77.2 - - - +
644B TYR* 1.3 63.6 + - - +
646B ALA* 3.2 6.3 + - - +
647B LYS* 2.8 33.6 + - - +
704B CD 2.6 20.5 - - - -
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Residues in contact with TYR 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ASP* 2.5 42.3 + - - -
633B VAL* 3.8 19.7 - - + -
636B VAL* 4.3 4.5 - - + -
639B LYS* 3.4 55.3 + - + +
641B MET 3.2 15.1 + - - +
643B SER* 1.3 77.7 - - - +
645B ASN* 1.3 63.2 + - - +
647B LYS* 3.1 18.5 + - + +
648B ILE* 3.0 43.0 + - + +
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Residues in contact with ASN 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B GLY* 3.1 31.3 + - - -
616B TRP 3.5 8.3 - - - -
617B PHE* 3.6 18.2 - - + +
631B ILE* 2.6 32.8 + - + +
633B VAL* 3.4 20.4 - - - +
636B VAL* 4.1 3.8 - - - +
641B MET 3.4 10.7 - - - +
642B ALA 3.1 6.2 + - - +
644B TYR* 1.3 76.7 - - - +
646B ALA* 1.3 58.2 + - - +
648B ILE* 3.2 11.2 + - - +
649B SER* 2.8 33.2 + - - -
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Residues in contact with ALA 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B HIS* 4.5 5.2 - - + -
586B ASP* 3.5 24.1 - - + +
587B ILE* 3.6 11.4 - - + +
617B PHE* 3.9 30.0 - - + +
642B ALA 3.0 12.5 + - - +
643B SER* 3.4 11.2 - - - +
645B ASN* 1.3 76.6 - - - +
647B LYS* 1.3 57.6 + - - +
649B SER* 3.2 7.4 + - - -
650B GLY 2.8 23.4 + - - -
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Residues in contact with LYS 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B GLU* 5.4 3.6 + - - +
586B ASP* 3.0 42.2 + - + +
589B ARG* 5.0 0.2 + - - -
639B LYS 5.6 2.9 - - - -
643B SER* 2.8 17.2 + - - +
644B TYR* 3.3 20.0 - - + +
646B ALA* 1.3 73.1 - - - +
648B ILE* 1.3 63.4 + - + +
650B GLY* 2.9 3.3 + - - -
651B LYS* 2.8 45.3 + - + +
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Residues in contact with ILE 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASN* 3.7 28.9 - - + +
340B MET* 4.3 7.9 - - + -
343B ASP* 4.6 2.7 - - - +
631B ILE* 3.6 31.2 - - + -
633B VAL* 4.1 15.5 - - + -
644B TYR* 3.0 49.3 + - + +
645B ASN* 3.4 6.3 - - - +
647B LYS* 1.3 74.9 - - + +
649B SER* 1.3 65.4 + - - +
651B LYS* 3.1 15.2 + - + +
652B VAL* 2.9 31.3 + - + +
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Residues in contact with SER 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B ILE* 3.4 20.6 - - - -
617B PHE* 3.9 13.5 + - - +
619B SER* 4.3 1.9 + - - -
629B MET* 3.9 21.3 - - - +
631B ILE* 3.7 14.1 - - - +
645B ASN 2.8 20.1 + - - -
646B ALA 3.3 8.1 - - - -
648B ILE* 1.3 77.2 - - - +
650B GLY* 1.3 64.5 + - - +
652B VAL* 3.1 3.4 + - - +
653B TYR* 2.9 29.5 + - - -
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Residues in contact with GLY 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ASP 4.2 4.0 - - - -
587B ILE* 4.0 9.1 - - - +
589B ARG* 3.3 28.0 + - - -
646B ALA 2.8 14.6 + - - -
647B LYS 2.9 4.4 + - - -
649B SER* 1.3 77.6 - - - +
651B LYS* 1.3 61.9 + - - +
653B TYR* 3.2 5.5 + - - +
654B ASP* 3.0 25.8 + - - +
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Residues in contact with LYS 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASN* 3.5 27.9 + - - +
589B ARG* 3.9 2.6 - - - +
647B LYS* 2.8 32.0 + - - +
648B ILE* 3.6 14.4 - - + +
650B GLY* 1.3 71.2 - - - +
652B VAL* 1.3 61.4 + - - +
654B ASP* 3.6 11.3 + - - +
655B GLU* 3.4 25.1 + - - +
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Residues in contact with VAL 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 5.6 0.4 - - + -
335B SER* 3.5 36.8 - - - +
336B ILE* 4.2 17.3 - - + -
339B ASN* 4.1 6.5 - - + +
627B MET* 5.0 0.2 - - + -
629B MET* 3.8 26.7 - - + -
631B ILE* 5.2 0.4 - - + -
648B ILE* 2.9 28.4 + - + +
649B SER 3.1 7.2 + - - +
651B LYS* 1.3 73.4 - - - +
653B TYR* 1.3 66.4 + - - +
654B ASP 3.1 1.3 - - - -
655B GLU* 3.0 14.0 + - - +
656B LEU* 3.0 29.5 + - + +
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Residues in contact with TYR 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B ILE* 4.2 5.8 - - + -
589B ARG* 5.3 0.7 - - + -
591B TYR* 3.4 10.8 - - + +
594B LEU* 3.7 45.5 - - + -
619B SER* 2.8 32.6 + - - -
620B TYR* 3.0 25.5 + - - -
621B ASP* 4.6 3.6 - - + -
627B MET* 4.0 24.4 + - + -
629B MET* 3.4 18.4 - - + +
649B SER 2.9 28.5 + - - +
650B GLY* 3.8 4.0 - - - +
652B VAL* 1.3 76.7 - - - +
654B ASP* 1.3 57.3 + - - +
656B LEU* 4.5 4.0 - - + +
657B TYR* 2.9 55.0 + + + +
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Residues in contact with ASP 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B ARG* 2.8 41.1 + - - -
591B TYR* 2.6 28.1 + - - -
650B GLY 3.0 10.1 + - - +
651B LYS* 3.6 12.3 - - - +
652B VAL 3.1 0.4 - - - -
653B TYR* 1.3 77.0 - - - +
655B GLU* 1.3 53.4 + - + +
658B GLU* 2.7 29.8 + - - -
659B ASN* 2.8 38.4 + - - +
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Residues in contact with GLU 655 (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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335B SER* 2.9 34.8 + - - +
338B ASN* 5.0 10.7 + - - +
339B ASN* 3.4 17.5 + - - -
651B LYS 3.4 11.9 + - - +
652B VAL 3.0 8.3 + - - +
654B ASP* 1.3 78.3 - - + +
656B LEU* 1.3 63.5 + - + +
657B TYR 3.3 0.5 + - - -
658B GLU* 3.5 16.3 + - - +
662B LYS* 5.3 0.3 - - - +
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Residues in contact with LEU 656 (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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331B LYS* 4.0 39.1 - - + +
332B VAL* 4.0 15.0 - - + +
335B SER* 4.3 6.5 - - - -
627B MET* 3.7 30.5 - - + -
652B VAL* 3.0 27.6 + - + +
653B TYR* 4.0 4.7 - - + +
655B GLU* 1.3 76.6 - - + +
657B TYR* 1.3 65.0 + - + +
658B GLU 3.6 0.2 - - - -
662B LYS* 3.5 17.2 - - - +
664B TYR* 3.3 47.2 - - + +
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Residues in contact with TYR 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B TYR* 3.6 36.6 - + + -
592B ALA* 4.1 10.5 - - + -
621B ASP* 2.5 39.9 + - + +
624B ASN* 3.2 17.0 + - - -
626B ASN* 5.0 1.0 + - - -
653B TYR* 2.9 39.4 + + - +
656B LEU* 1.3 87.5 - - + +
658B GLU* 1.3 67.6 + - - +
659B ASN 3.2 0.2 - - - -
660B GLY* 2.9 12.6 + - - +
662B LYS* 3.0 37.8 + - - -
663B LYS* 4.3 6.7 - - + -
664B TYR* 3.3 30.3 - + + -
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Residues in contact with GLU 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B ASP 2.7 14.4 + - - -
655B GLU* 3.5 11.9 + - - +
657B TYR* 1.3 72.5 - - - +
659B ASN* 1.3 69.1 + - - +
661B ASN* 2.8 36.3 + - + +
662B LYS* 3.4 36.0 + - + +
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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
------------------------------------------------------------
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