Contacts of the strand formed by residues 541 - 545 (chain D) in PDB entry 1ZM9
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 ALA 541 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510D GLY 2.7 8.2 + - - +
511D PHE* 3.8 17.9 - - + -
512D TYR* 2.9 28.9 + - - -
537D LEU* 4.1 6.5 - - - +
540D ASP* 1.3 76.0 - - - +
542D ILE* 1.3 62.3 + - - +
543D THR* 5.6 0.2 - - - -
554D THR* 4.4 5.4 - - + -
555D ILE 3.7 5.8 - - - +
556D LEU* 3.5 37.7 - - + -
560D LEU* 3.7 3.6 - - + -
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Residues in contact with ILE 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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466D TRP* 4.9 1.6 - - + -
512D TYR* 3.4 13.9 - - + +
513D ARG* 4.6 1.8 - - - -
514D THR* 3.6 16.4 - - + -
518D LEU* 3.5 27.6 - - + -
527D VAL* 3.2 45.3 - - + -
530D LEU* 5.2 2.5 - - + -
531D ILE* 5.7 1.1 - - + -
537D LEU* 4.1 17.7 - - + +
541D ALA* 1.3 75.5 - - - +
543D THR* 1.3 69.8 + - - +
553D GLU 3.9 1.7 - - - +
554D THR* 3.6 1.2 - - - -
555D ILE* 3.0 38.2 + - + +
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Residues in contact with THR 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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511D PHE* 5.6 0.5 - - - -
512D TYR 2.8 13.9 + - - -
513D ARG* 3.2 6.5 - - + +
514D THR* 2.8 31.0 + - - +
518D LEU* 4.3 1.8 - - - -
542D ILE* 1.3 78.0 - - - +
544D GLY* 1.3 62.5 + - - +
552D LEU* 4.1 29.4 - - + -
553D GLU 3.7 6.7 - - - +
554D THR* 3.4 22.5 + - - +
600D TYR* 3.0 36.5 - - + -
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Residues in contact with GLY 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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514D THR* 3.5 5.4 - - - -
516D LEU 4.1 0.9 - - - -
518D LEU* 3.2 21.2 - - - +
543D THR* 1.3 79.6 - - - +
545D PRO* 1.3 80.0 - - - +
546D GLU 3.2 0.2 + - - -
552D LEU* 4.2 6.1 - - - -
553D GLU* 3.1 25.5 + - - +
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Residues in contact with PRO 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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514D THR 3.4 11.9 - - - +
515D SER* 3.4 17.3 - - - +
516D LEU 3.3 14.6 - - - +
517D THR* 3.5 26.2 - - + -
518D LEU* 3.7 5.2 + - - +
544D GLY* 1.3 83.0 - - - +
546D GLU* 1.3 67.5 + - - +
547D GLU 3.1 15.3 + - - +
549D GLY 5.0 4.7 - - - +
550D GLY 4.3 6.5 - - - +
551D ARG 3.6 8.3 - - - +
552D LEU* 4.2 11.2 - - + -
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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