Contacts of the helix formed by residues 542 - 561 (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 THR 542 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLU 4.2 7.9 - - - +
230A ASP* 2.8 43.2 + - - +
231A VAL* 4.4 8.7 - - + +
232A ARG* 2.9 26.5 + - - +
540B VAL* 4.5 10.3 - - + +
541B GLU* 1.3 79.9 - - - +
543B VAL* 1.3 67.5 + - - +
544B THR 3.0 5.4 + - - -
545B SER* 3.1 7.2 + - - -
546B ILE* 3.1 25.9 + - - +
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 6.5 0.4 - - - -
229A GLU 5.3 2.0 + - - +
230A ASP* 3.8 12.4 + - + +
542B THR* 1.3 72.9 - - - +
544B THR* 1.3 63.7 + - - +
546B ILE* 3.8 10.4 - - + +
547B GLU* 3.1 37.3 + - + +
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Residues in contact with THR 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 2.9 22.8 + - - +
230A ASP* 2.7 25.2 + - - -
232A ARG* 3.7 23.2 + - + +
542B THR* 3.0 1.7 - - - -
543B VAL* 1.3 79.0 - - - +
545B SER* 1.3 63.2 + - - +
547B GLU* 3.4 4.2 + - - +
548B GLN* 3.1 24.7 + - + +
793B ASN* 3.5 41.3 - - - +
795B LEU* 5.4 0.9 - - - +
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Residues in contact with SER 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 3.4 29.5 + - - +
535B LEU* 3.5 22.1 - - - +
537B ASP* 4.1 8.4 - - - +
540B VAL 3.9 0.2 + - - -
541B GLU* 3.6 9.7 - - - +
542B THR* 3.1 27.0 + - - -
544B THR* 1.3 77.3 - - - +
546B ILE* 1.3 60.3 + - - +
548B GLN* 4.3 1.3 - - - -
549B ALA* 2.9 31.7 + - - +
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Residues in contact with ILE 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B GLU* 4.4 29.6 - - + +
542B THR* 3.1 22.7 + - - +
543B VAL* 3.8 9.6 - - + +
545B SER* 1.3 77.8 + - - +
547B GLU* 1.3 67.9 + - - +
549B ALA* 3.4 6.3 + - - +
550B LYS* 3.1 47.7 + - + +
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Residues in contact with GLU 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B VAL* 3.1 31.3 + - + +
544B THR* 3.9 4.5 - - - +
546B ILE* 1.3 77.0 - - - +
548B GLN* 1.3 66.3 + - - +
550B LYS* 3.3 36.8 + - - +
551B VAL* 3.1 25.8 + - - +
795B LEU* 4.1 22.9 - - + +
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Residues in contact with GLN 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B LEU* 3.8 21.1 - - + -
544B THR* 3.1 21.0 + - + +
545B SER* 3.7 4.9 - - - +
547B GLU* 1.3 76.7 - - - +
549B ALA* 1.3 60.5 + - - +
551B VAL* 3.3 3.9 + - - +
552B GLU* 2.7 52.9 + - - +
782B MET* 3.6 21.6 - - - +
785B GLU* 3.0 27.8 + - - +
794B LYS 4.1 3.5 - - - +
795B LEU* 3.6 21.6 - - + +
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Residues in contact with ALA 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ARG* 4.7 3.0 + - - +
535B LEU* 4.2 10.7 - - + +
545B SER 2.9 18.5 + - - +
546B ILE* 3.7 6.5 - - - +
547B GLU 3.3 0.2 - - - -
548B GLN* 1.3 76.2 - - - +
550B LYS* 1.3 64.1 + - - +
552B GLU* 3.3 8.7 + - - +
553B GLU* 2.9 24.9 + - - +
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Residues in contact with LYS 550 (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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546B ILE* 3.1 34.6 + - + +
547B GLU* 3.3 36.6 + - - +
549B ALA* 1.3 77.6 - - + +
551B VAL* 1.3 64.3 + - + +
553B GLU* 3.4 6.6 + - - +
554B LYS* 3.3 20.3 + - - +
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Residues in contact with VAL 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B GLU 3.1 12.8 + - - +
548B GLN* 3.7 8.5 - - - +
550B LYS* 1.3 76.4 - - + +
552B GLU* 1.3 59.3 + - - +
554B LYS* 3.2 7.3 + - - +
555B ILE* 2.9 48.6 + - + +
785B GLU* 4.3 9.6 - - - +
795B LEU* 4.1 28.7 - - + -
796B VAL* 4.0 23.1 - - + -
853B LYS* 4.1 20.2 - - + -
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Residues in contact with GLU 552 (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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533B GLU 4.9 1.0 - - - +
534B ARG* 3.4 23.8 + - - +
535B LEU* 2.8 45.2 + - - +
548B GLN* 2.7 45.2 + - - +
549B ALA* 3.3 6.6 + - - +
551B VAL* 1.3 78.8 - - - +
553B GLU* 1.3 61.5 + - - +
555B ILE* 3.3 2.4 + - - -
556B GLN* 3.0 22.3 + - - +
784B PHE* 3.5 35.7 - - + +
785B GLU* 4.0 6.9 - - - +
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Residues in contact with GLU 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ARG* 3.6 22.2 + - - +
549B ALA 2.9 17.6 + - - +
550B LYS* 3.7 7.2 - - - +
551B VAL 3.3 0.2 - - - -
552B GLU* 1.3 77.9 - - - +
554B LYS* 1.3 63.5 + - - +
556B GLN* 3.4 7.3 + - - +
557B GLU* 3.3 37.7 + - - +
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Residues in contact with LYS 554 (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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550B LYS 3.3 9.4 + - - +
551B VAL* 3.2 10.4 + - - +
553B GLU* 1.3 79.6 - - - +
555B ILE* 1.3 63.7 + - + +
557B GLU* 3.1 34.6 + - + +
558B VAL* 3.1 21.4 + - - +
854B PRO* 3.8 40.6 - - + +
855B GLY* 5.1 2.0 - - - +
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Residues in contact with ILE 555 (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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551B VAL* 2.9 37.4 + - + +
552B GLU* 3.8 4.5 - - - +
554B LYS* 1.3 76.2 - - + +
556B GLN* 1.3 57.5 + - - +
558B VAL* 3.2 5.6 + - - +
559B PHE* 2.9 62.0 + - + -
784B PHE* 4.1 8.3 - - + -
785B GLU* 4.1 16.2 - - + -
838B TYR* 4.1 10.3 - - + +
842B CYS* 3.9 11.4 - - - -
854B PRO* 3.6 37.0 - - + -
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Residues in contact with GLN 556 (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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525B SER 5.3 2.5 + - - +
526B LEU* 5.6 1.2 - - - +
530B HIS* 5.2 1.8 + - - -
531B ALA* 5.0 11.5 - - - +
534B ARG* 3.9 19.9 - - - +
552B GLU 3.0 18.0 + - - +
553B GLU* 3.7 9.9 - - - +
554B LYS 3.2 0.2 - - - -
555B ILE* 1.3 76.5 - - - +
557B GLU* 1.3 58.7 + - - +
559B PHE* 3.3 12.9 + - - +
560B SER* 2.9 42.1 + - - +
784B PHE* 3.2 34.4 - - + -
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Residues in contact with GLU 557 (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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553B GLU* 3.5 35.0 - - - +
554B LYS* 3.1 29.0 + - + +
556B GLN* 1.3 79.9 - - + +
558B VAL* 1.3 62.5 + - + +
560B SER* 3.4 6.8 + - - -
561B SER* 3.2 21.0 + - - -
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Residues in contact with VAL 558 (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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554B LYS* 3.1 29.5 + - - +
555B ILE* 3.5 6.1 - - - +
557B GLU* 1.3 74.2 - - - +
559B PHE* 1.3 65.8 + - - +
561B SER* 2.6 26.6 + - - +
562B TYR* 3.2 18.3 - - + -
841B MET* 3.2 32.3 - - + +
842B CYS* 4.0 11.2 - - - -
854B PRO* 4.2 22.2 - - + -
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Residues in contact with PHE 559 (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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525B SER* 3.6 29.2 - - - +
526B LEU* 3.2 27.0 - - + +
530B HIS* 4.0 3.8 - + - -
555B ILE* 2.9 41.6 + - + +
556B GLN* 3.5 11.9 - - - +
558B VAL* 1.3 71.9 - - - +
560B SER* 1.3 63.4 + - - +
562B TYR* 3.1 16.8 + - - +
563B LYS 3.8 0.2 + - - -
784B PHE* 3.6 32.8 - + - -
785B GLU 3.5 20.4 - - - -
837B GLU 4.7 4.0 - - - -
838B TYR* 4.9 0.9 - - - -
841B MET* 3.8 33.9 - - + -
842B CYS* 3.8 21.1 - - - -
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Residues in contact with SER 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B LEU* 4.7 2.0 - - - -
556B GLN* 2.9 31.9 + - - +
557B GLU* 3.6 7.6 - - - -
558B VAL 3.2 0.2 - - - -
559B PHE* 1.3 77.5 - - - +
561B SER* 1.3 61.9 + - - +
562B TYR 3.1 1.1 + - - -
563B LYS* 3.2 27.9 + - - +
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Residues in contact with SER 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B GLU 3.2 10.9 + - - -
558B VAL* 2.6 25.8 + - - +
560B SER* 1.3 75.4 - - - +
562B TYR* 1.3 70.1 + - - +
563B LYS 3.4 0.9 - - - -
564B PHE* 3.6 20.8 - - - -
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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
------------------------------------------------------------
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