Contacts of the helix formed by residues 541 - 552 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504D CYS 3.9 8.1 - - - +
505D GLN 3.0 15.9 + - - -
506D LYS 3.3 12.8 - - - -
507D GLY* 2.7 34.3 + - - -
536D ALA* 3.0 10.1 + - - +
539D TYR* 3.0 33.1 + - + +
540D GLY* 1.3 69.4 - - - -
542D GLU* 1.3 64.0 + - - +
543D ASP* 3.2 13.8 + - - +
544D CYS* 3.0 13.5 + - + +
545D VAL* 2.9 25.4 + - - +
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Residues in contact with GLU 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D GLY 3.2 7.1 + - - +
541D HIS* 1.3 74.7 - - - +
543D ASP* 1.3 64.6 + - - +
545D VAL* 3.5 3.2 - - + +
546D LYS* 3.0 56.7 + - - +
579D GLY* 3.6 30.2 - - - +
580D VAL* 3.7 28.8 + - + +
583D THR* 4.2 3.4 - - - +
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Residues in contact with ASP 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 5.4 13.3 - - + +
60A VAL 5.2 1.6 - - - +
507D GLY 3.9 11.3 - - - +
509D GLN* 3.0 52.1 + - - +
541D HIS* 3.7 17.7 + - - +
542D GLU* 1.3 75.2 - - - +
544D CYS* 1.3 63.4 + - - -
546D LYS* 3.7 8.7 + - - +
547D ALA 3.2 16.5 + - - -
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Residues in contact with CYS 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D CYS* 4.5 12.1 - - - -
507D GLY* 3.6 25.1 - - - -
508D TYR 3.7 0.2 - - - -
509D GLN* 3.5 30.5 - - - -
512D THR* 3.6 17.8 - - + +
536D ALA* 4.2 10.1 - - + -
541D HIS* 3.0 14.0 + - + +
543D ASP* 1.3 80.3 + - - +
545D VAL* 1.3 66.4 + - - +
546D LYS 3.2 0.7 - - - -
547D ALA* 3.1 8.9 + - - +
548D LEU* 2.9 28.6 + - - +
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Residues in contact with VAL 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D LEU* 4.1 18.8 - - + -
536D ALA* 3.8 28.7 - - + +
537D CYS* 4.0 12.1 - - - -
541D HIS 2.9 19.9 + - - +
542D GLU* 3.5 8.7 - - - +
544D CYS* 1.3 74.5 - - - +
546D LYS* 1.3 58.3 + - + +
548D LEU* 2.9 7.0 + - - +
549D VAL* 2.9 37.3 + - + +
580D VAL* 4.1 24.5 - - + -
583D THR* 4.4 13.7 - - + -
584D LEU* 4.5 7.0 - - + -
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Residues in contact with LYS 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL 5.6 1.1 - - - +
61A ASP* 2.8 32.9 + - - +
62A PHE* 3.4 32.9 + - + +
542D GLU* 3.0 45.4 + - + +
543D ASP* 3.8 7.5 - - - +
545D VAL* 1.3 76.4 - - - +
547D ALA* 1.3 69.5 + - - +
549D VAL* 3.1 3.0 + - - +
550D TYR* 2.8 37.0 + - + +
583D THR* 3.7 28.0 - - + +
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Residues in contact with ALA 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.7 13.8 - - + -
509D GLN* 4.2 9.6 - - + -
512D THR* 4.3 10.1 - - + -
513D LEU* 3.6 31.4 - - + -
516D LEU* 4.5 1.6 - - - -
543D ASP 3.2 10.6 + - - +
544D CYS 3.1 9.9 + - - +
546D LYS* 1.3 75.7 - - - +
548D LEU* 1.3 58.9 + - - +
551D TYR* 2.9 36.3 + - - +
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Residues in contact with LEU 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D LEU* 4.3 7.9 - - + -
504D CYS* 3.7 29.4 - - - -
512D THR* 4.4 2.9 - - + -
516D LEU* 4.2 29.6 - - + -
522D ALA* 4.2 18.3 - - + +
532D PRO* 3.9 3.1 - - + +
533D LEU* 3.5 49.6 - - + +
536D ALA* 4.3 4.5 - - + -
544D CYS 2.9 14.7 + - - +
545D VAL 2.9 7.2 + - - +
547D ALA* 1.3 78.2 - - - +
549D VAL* 1.3 65.0 + - + +
550D TYR 3.5 0.2 + - - -
551D TYR* 3.8 4.2 + - - +
552D ASP* 4.2 14.7 - - - +
556D CYS* 4.1 10.4 - - - -
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Residues in contact with VAL 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLN* 4.6 1.9 - - - +
533D LEU* 4.7 6.5 - - + -
545D VAL* 2.9 32.7 + - + +
546D LYS* 3.8 4.5 - - - +
548D LEU* 1.3 80.0 - - - +
550D TYR* 1.3 66.9 + - + +
551D TYR 3.8 0.2 + - - -
552D ASP* 4.1 3.8 + - - +
554D GLU* 4.9 4.9 + - - -
556D CYS* 3.9 21.3 - - + +
558D LEU* 4.4 21.8 - - + -
583D THR* 4.8 5.4 - - + +
584D LEU* 4.4 9.2 - - + -
587D ASN* 3.6 42.1 + - + +
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Residues in contact with TYR 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.5 47.0 + + + -
63A ALA* 3.8 23.1 - - - -
64A LEU* 3.7 21.2 + - + +
78A GLN* 3.1 51.1 + - + +
79A LEU 5.4 0.4 - - - -
80A TRP* 3.7 4.7 - - - +
546D LYS* 2.8 31.9 + - + +
549D VAL* 1.3 73.5 - - + +
551D TYR* 1.3 70.5 + - - +
552D ASP 3.1 2.4 + - - -
553D VAL 3.8 0.4 + - - -
583D THR* 4.2 19.8 - - + +
586D GLN* 4.7 8.8 + - - -
587D ASN* 3.3 33.7 + - - -
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Residues in contact with TYR 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 5.5 3.4 + - - -
62A PHE* 5.3 0.2 - - - -
78A GLN* 4.8 0.3 + - - -
80A TRP* 4.1 22.0 - + - -
94A VAL* 4.9 12.8 - - + -
97A LYS* 4.3 14.6 + - + +
513D LEU* 3.9 22.7 - - + -
516D LEU* 3.5 44.4 + - + -
517D HIS* 3.2 31.2 + - + +
519D LYS* 5.9 0.7 + - - -
547D ALA 2.9 19.5 + - - +
548D LEU 4.4 2.7 - - - +
549D VAL 3.5 0.6 - - - -
550D TYR* 1.3 79.3 - - - +
552D ASP* 1.3 70.3 + - - +
553D VAL* 2.8 20.7 + - - +
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Residues in contact with ASP 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D LEU* 4.4 12.0 - - - +
522D ALA* 4.5 16.5 - - - +
523D GLU* 5.2 3.8 - - - +
548D LEU 4.2 12.5 - - - +
549D VAL 4.1 1.3 + - - +
550D TYR 3.1 1.8 - - - -
551D TYR* 1.3 93.5 - - - +
553D VAL* 1.3 71.2 + - - +
554D GLU 4.5 0.9 - - - +
555D SER* 2.8 42.9 + - - +
556D CYS* 3.8 17.1 - - + +
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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