Contacts of the helix formed by residues 649 - 664 (chain B) in PDB entry 1MZC
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 HIS 649 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TYR* 3.5 41.9 - + + +
167A GLN* 4.8 8.7 + - - -
640B PHE 2.9 6.6 + - - +
648B PRO* 1.3 77.7 - - - +
650B LEU* 1.3 63.3 + - - +
651B ALA* 3.0 27.8 + - + -
652B PRO* 3.2 11.9 - - + +
653B THR* 2.7 32.2 + - - -
680B TYR* 3.3 6.3 + - - -
693B MET* 3.5 38.5 - - + +
694B HIS* 3.5 34.8 + + - -
698B GLU* 4.8 1.4 + - - -
702B ARG* 5.7 0.9 - - - -
1003B BNE 5.1 7.4 - - + +
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Residues in contact with LEU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B HIS* 1.3 72.3 + - - +
651B ALA* 1.3 61.6 + - - +
653B THR* 3.6 12.7 - - + -
654B TYR* 2.9 25.5 + - - +
680B TYR* 4.0 5.8 + - + -
681B LEU* 3.6 28.0 - - + -
684B LEU* 3.6 18.6 - - + -
691B PHE* 4.4 4.7 - - + -
692B LEU 3.4 23.6 - - - +
693B MET* 2.9 20.5 + - + +
703B SER* 3.6 27.1 - - - +
706B CYS* 3.5 15.3 - - + +
707B ALA* 4.1 19.1 - - + +
710B VAL* 5.1 0.2 - - + -
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Residues in contact with ALA 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B TRP* 3.2 30.7 - - + +
649B HIS* 3.0 20.3 + - + +
650B LEU* 1.3 78.8 - - - +
652B PRO* 1.3 72.4 - - + +
654B TYR* 3.2 1.4 + - - +
655B ALA 3.1 16.3 + - - -
693B MET* 4.1 8.6 - - + +
706B CYS* 4.1 8.5 - - - -
1002B FPP 5.2 2.2 - - + -
1003B BNE 3.6 18.6 - - + -
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Residues in contact with PRO 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 4.1 3.8 - - + +
598B ALA 4.9 3.8 - - - +
601B PRO* 3.7 14.0 - - + +
602B TRP* 3.5 15.9 - - + +
640B PHE* 3.5 12.5 - - - +
641B GLY 3.7 26.0 - - - +
642B GLY* 4.0 7.4 - - - +
649B HIS* 3.2 32.5 - - + +
651B ALA* 1.3 96.2 - - + +
653B THR* 1.3 54.7 + - - +
655B ALA* 3.7 2.9 - - + -
656B ALA* 2.8 32.2 + - - +
1003B BNE 5.4 0.7 - - + -
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Residues in contact with THR 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B GLY* 3.7 8.8 - - - -
640B PHE* 2.9 31.7 + - + -
649B HIS 2.7 25.1 + - - -
650B LEU* 3.6 15.2 - - + -
651B ALA 3.2 0.2 - - - -
652B PRO* 1.3 77.5 - - - +
654B TYR* 1.3 63.9 + - - +
656B ALA* 3.4 1.0 + - - +
657B VAL* 3.0 32.1 + - + +
677B LEU* 3.9 27.4 - - + -
680B TYR* 4.3 2.6 - - + -
710B VAL* 4.2 14.6 - - + -
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Residues in contact with TYR 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B TRP* 3.3 37.2 - + - -
605B TYR* 4.4 9.5 + + - -
650B LEU 2.9 17.7 + - - +
651B ALA 3.4 2.9 - - - +
653B THR* 1.3 78.9 - - - +
655B ALA* 1.3 60.6 + - - +
657B VAL* 3.5 2.4 + - - +
658B ASN* 3.0 44.2 + - - +
705B TYR* 2.9 40.8 + + - -
706B CYS* 3.8 21.5 - - + -
709B SER* 3.4 33.9 - - - -
710B VAL* 3.6 10.8 - - + -
753B PHE* 5.4 0.7 - - - -
802B PHE* 6.0 0.3 - - - -
803B TRP* 5.8 2.6 - + - -
865B TYR* 5.1 3.9 + - - -
901B TYR 3.2 14.0 + - - -
902B ASN* 4.5 3.1 - - - +
1002B FPP 4.6 3.3 - - + +
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Residues in contact with ALA 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B PRO 3.7 19.1 - - - +
602B TRP* 3.6 38.4 - - + +
605B TYR* 3.6 14.1 - - + +
651B ALA 3.1 4.4 + - - +
652B PRO* 3.7 6.7 - - + +
654B TYR* 1.3 87.2 - - - +
656B ALA* 1.3 57.2 + - - +
658B ASN* 3.4 1.7 + - - +
659B ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 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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601B PRO* 4.1 13.0 - - + +
630B LEU* 3.9 13.9 - - + +
640B PHE* 3.6 39.0 - - + -
652B PRO 2.8 21.7 + - - +
653B THR 3.8 0.9 - - - +
655B ALA* 1.3 72.0 - - - +
657B VAL* 1.3 59.2 + - - +
659B ALA* 3.2 2.4 + - - +
660B LEU* 2.9 37.1 + - - +
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Residues in contact with VAL 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B PHE* 4.3 16.8 - - + -
653B THR* 3.0 21.9 + - + +
654B TYR 3.8 0.7 - - - +
656B ALA* 1.3 75.4 - - - +
658B ASN* 1.3 63.3 + - - +
660B LEU* 3.3 8.6 + - - +
661B CYS* 3.0 29.0 + - - -
672B ILE* 4.4 12.1 - - + +
677B LEU* 4.8 7.4 - - + -
710B VAL* 3.7 28.7 - - + -
713B LEU* 4.1 21.8 - - + -
714B THR* 4.3 18.6 - - + -
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Residues in contact with ASN 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B TYR* 3.6 29.8 - - + -
654B TYR* 3.0 38.4 + - - +
655B ALA* 3.7 1.8 - - - +
657B VAL* 1.3 77.4 - - - +
659B ALA* 1.3 61.4 + - - +
661B CYS* 3.2 6.5 + - - +
662B ILE* 2.9 28.8 + - - +
709B SER* 4.3 5.0 + - - -
713B LEU* 3.6 21.7 - - - +
901B TYR* 2.9 27.3 + - - +
903B ILE* 3.5 13.7 - - + +
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Residues in contact with ALA 659 (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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604B CYS* 4.5 3.6 - - + -
605B TYR* 4.2 17.2 - - - +
608B LEU* 4.0 20.5 - - + +
630B LEU* 3.9 17.0 - - + -
655B ALA 2.9 18.1 + - - +
656B ALA* 3.6 4.7 - - - +
658B ASN* 1.3 75.8 - - - +
660B LEU* 1.3 64.0 + - - +
662B ILE* 3.2 11.7 + - - +
663B ILE* 3.2 26.8 + - - +
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Residues in contact with LEU 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B CYS* 4.2 8.1 - - - -
630B LEU* 3.7 19.7 - - + -
640B PHE* 4.1 18.4 - - + -
656B ALA 2.9 21.7 + - - +
657B VAL* 3.7 4.3 - - - +
659B ALA* 1.3 75.2 - - - +
661B CYS* 1.3 58.1 + - - +
663B ILE* 3.3 4.9 + - + -
664B GLY* 3.0 22.2 + - - -
668B ALA* 3.4 42.3 - - + +
669B TYR* 4.6 2.9 - - + +
671B ILE* 3.9 25.8 - - + -
672B ILE* 3.6 35.2 - - + -
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Residues in contact with CYS 661 (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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657B VAL* 3.0 33.8 + - - +
658B ASN* 3.6 4.7 - - - +
660B LEU* 1.3 76.2 - - - +
662B ILE* 1.3 66.3 + - - +
664B GLY* 3.1 12.9 + - - +
669B TYR* 4.3 11.8 + - - -
672B ILE* 5.5 1.6 - - - -
713B LEU* 4.3 12.6 - - - -
903B ILE* 3.9 18.8 - - + -
907B LYS* 3.6 18.5 - - - +
911B ALA* 3.6 27.8 - - + -
915B PHE* 4.7 10.1 - - - -
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Residues in contact with ILE 662 (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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605B TYR* 3.9 11.0 - - + -
608B LEU* 4.0 26.0 - - + +
609B HIS* 3.8 26.2 - - + +
612B GLU* 3.7 34.5 - - + +
618B ILE* 4.7 10.4 - - + +
658B ASN 2.9 20.4 + - - +
659B ALA* 3.2 10.5 + - - +
661B CYS* 1.3 72.9 - - - +
663B ILE* 1.3 67.1 + - - +
903B ILE* 3.8 21.8 - - + -
907B LYS* 3.0 31.4 + - - -
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Residues in contact with ILE 663 (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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608B LEU* 4.2 8.3 - - + -
618B ILE* 4.0 23.3 - - + +
623B ALA* 3.5 41.3 - - + +
626B VAL* 3.9 24.7 - - + -
627B CYS* 3.9 12.8 - - - -
659B ALA 3.2 13.9 + - - +
660B LEU* 3.6 11.2 - - + +
662B ILE* 1.3 76.2 - - - +
664B GLY* 1.3 64.1 + - - +
665B THR* 3.3 32.5 + - + +
668B ALA* 3.9 5.2 - - + -
907B LYS* 4.1 6.2 + - - -
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Residues in contact with GLY 664 (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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660B LEU 3.0 13.2 + - - -
661B CYS 3.1 15.1 + - - -
662B ILE 4.4 0.2 - - - -
663B ILE* 1.3 77.5 - - - +
665B THR* 1.3 62.0 + - - +
669B TYR* 3.4 21.2 + - - -
907B LYS* 5.1 2.7 - - - -
910B GLN* 2.7 28.4 + - - -
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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