Contacts of the helix formed by residues 541 - 552 (chain E) in PDB entry 4CYM
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 541 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504E CYS 3.9 6.7 + - - +
505E GLN 3.0 27.0 + - - -
506E LYS 3.4 7.4 + - - -
507E GLY* 2.8 31.4 - - - -
536E ALA* 3.0 10.2 + - + +
539E TYR* 3.1 32.0 + + + +
540E GLY* 1.3 71.2 - - - -
542E GLU* 1.3 63.0 + - - +
543E ASP* 3.1 15.5 - - - +
544E CYS* 2.9 14.7 + - + +
545E VAL* 2.9 25.1 + - - +
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Residues in contact with GLU 542 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540E GLY 3.2 7.9 + - - +
541E HIS* 1.3 72.2 - - - +
543E ASP* 1.3 64.2 + - - +
545E VAL* 3.3 2.7 + - + +
546E LYS* 3.0 56.8 + - - +
579E GLY* 3.6 29.0 - - - +
580E VAL* 3.6 30.9 + - + +
583E THR* 4.2 2.6 + - - +
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Residues in contact with ASP 543 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 5.4 13.5 - - + +
60B VAL 5.3 1.3 - - - +
507E GLY 3.9 11.8 - - - +
509E GLN* 3.0 51.2 + - - +
541E HIS* 3.6 18.9 - - - +
542E GLU* 1.3 75.9 + - - +
544E CYS* 1.3 61.3 + - - -
546E LYS* 3.8 8.6 + - - +
547E ALA 3.3 16.6 + - - -
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Residues in contact with CYS 544 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E CYS* 4.4 12.1 - - - -
507E GLY* 3.5 25.8 - - - -
509E GLN* 3.5 30.1 - - - -
512E THR* 3.6 17.8 - - - +
536E ALA* 4.2 10.5 - - + -
541E HIS* 2.9 13.9 + - + +
543E ASP* 1.3 79.7 + - - +
545E VAL* 1.3 67.4 + - - +
546E LYS 3.2 1.1 - - - -
547E ALA* 3.1 8.9 + - - +
548E LEU* 2.9 27.4 + - - +
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Residues in contact with VAL 545 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E LEU* 4.1 18.4 - - + -
536E ALA* 3.8 25.1 - - + +
537E CYS* 4.0 15.0 - - - -
541E HIS 2.9 16.1 + - - +
542E GLU* 3.5 9.4 - - - +
544E CYS* 1.3 75.1 - - - +
546E LYS* 1.3 58.7 + - - +
548E LEU* 2.9 5.9 + - - +
549E VAL* 2.9 37.2 + - + +
580E VAL* 4.1 26.5 - - + -
583E THR* 4.4 14.6 - - + -
584E LEU* 4.5 7.0 - - + -
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Residues in contact with LYS 546 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL 5.5 0.7 - - - +
61B ASP* 2.7 33.8 + - - +
62B PHE* 3.4 33.6 + - + +
542E GLU* 3.0 45.2 + - + +
543E ASP* 3.8 7.5 - - - +
545E VAL* 1.3 77.1 - - - +
547E ALA* 1.3 66.8 + - - +
549E VAL* 3.1 3.6 + - - +
550E TYR* 2.8 36.1 + - + +
583E THR* 3.7 28.9 - - + +
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Residues in contact with ALA 547 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.7 14.9 - - + -
509E GLN* 4.1 9.4 - - + -
512E THR* 4.3 11.7 - - + -
513E LEU* 3.6 31.9 - - + -
516E LEU* 4.5 1.1 - - - -
543E ASP 3.3 10.8 + - - +
544E CYS 3.1 9.3 + - - +
546E LYS* 1.3 77.2 - - - +
548E LEU* 1.3 58.2 + - - +
551E TYR* 2.8 36.8 + - - +
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Residues in contact with LEU 548 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500E LEU* 4.3 7.4 - - + -
504E CYS* 3.6 28.9 - - - -
512E THR* 4.4 2.2 - - + -
516E LEU* 4.2 28.9 - - + -
522E ALA* 4.2 17.7 - - + -
532E PRO* 4.0 2.9 - - + +
533E LEU* 3.5 48.7 - - + +
536E ALA* 4.3 4.9 - - + -
544E CYS 2.9 17.9 + - - +
545E VAL 3.4 5.4 - - - +
547E ALA* 1.3 78.1 - - - +
549E VAL* 1.3 64.6 + - - +
551E TYR 3.8 0.2 + - - -
552E ASP* 3.4 23.3 - - - +
556E CYS* 4.0 7.2 - - - -
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Residues in contact with VAL 549 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLN* 4.6 2.4 - - - +
533E LEU* 4.7 5.6 - - + -
545E VAL* 2.9 33.2 + - + +
546E LYS* 3.8 4.0 - - - +
548E LEU* 1.3 79.2 - - - +
550E TYR* 1.3 66.7 + - + +
552E ASP* 4.2 4.2 + - - +
554E GLU* 5.0 4.5 + - - -
556E CYS* 3.9 21.4 - - + +
558E LEU* 4.4 22.0 - - + -
583E THR* 4.8 5.2 - - + +
584E LEU* 4.4 9.6 - - + -
587E ASN* 3.6 41.7 - - + +
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Residues in contact with TYR 550 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.4 49.5 + + + -
63B ALA* 3.6 24.5 - - - -
64B LEU* 3.5 25.8 + - + +
78B GLN* 3.2 50.4 + - + +
79B LEU 5.3 0.4 - - - -
80B TRP* 3.5 6.2 - - - +
546E LYS* 2.8 30.4 + - + +
549E VAL* 1.3 76.6 - - + +
551E TYR* 1.3 68.8 + - - +
552E ASP 3.1 3.1 + - - -
553E VAL 3.8 0.3 + - - -
583E THR* 4.2 17.8 - - + +
586E GLN* 4.7 8.0 + - - -
587E ASN* 3.6 30.4 + - - -
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Residues in contact with TYR 551 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TRP* 4.1 19.8 - + - -
94B VAL* 4.8 13.9 + - + -
97B LYS* 4.4 13.0 + - + +
98B GLU* 3.9 23.5 + - - +
513E LEU* 3.9 23.1 - - + -
516E LEU* 3.5 47.1 + - + -
517E HIS* 3.2 29.8 + - - +
547E ALA 2.8 20.2 + - - +
549E VAL 3.5 0.6 - - - -
550E TYR* 1.3 79.5 - - - +
552E ASP* 1.3 70.3 + - - +
553E VAL* 2.7 25.1 + - - +
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Residues in contact with ASP 552 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 5.0 1.9 - - - +
516E LEU* 4.5 10.4 - - - +
522E ALA* 4.5 16.0 - - - +
523E GLU* 5.4 2.8 - - - +
548E LEU 3.4 17.5 - - - +
549E VAL 4.5 0.7 - - - +
550E TYR 3.1 2.0 - - - -
551E TYR* 1.3 95.1 - - - +
553E VAL* 1.4 66.8 - - - +
554E GLU 4.3 1.6 - - - +
555E SER* 3.0 47.8 + - - +
556E CYS* 3.7 15.5 - - + +
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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