Contacts of the strand formed by residues 542 - 547 (chain D) in PDB entry 5ED1
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 PHE 542 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355D VAL* 4.0 34.5 - - + -
400D ARG* 5.3 6.5 - - + -
403D LEU* 4.4 4.9 - - + -
442D PHE* 3.4 23.8 - - + +
444D LEU* 3.8 50.3 - - + -
520D ILE* 5.9 1.3 - - + -
523D TRP* 4.1 17.9 + + + -
524D ASN* 4.9 6.0 + - - +
528D ILE* 3.5 37.3 - - + +
541D TYR* 1.3 73.4 - - - +
543D SER* 1.3 59.2 + - - +
544D SER 3.4 9.0 - - - +
545D ILE* 4.8 10.8 - - + -
577D ASN* 2.8 34.1 + - - +
579D PRO* 3.3 4.4 - - + +
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Residues in contact with SER 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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312D SER* 3.9 8.0 + - - -
314D GLY* 6.5 1.1 - - - -
315D LEU 5.4 1.8 - - - -
441D GLN* 3.2 51.1 + - - +
442D PHE 2.8 12.7 + - - -
443D HIS* 4.0 5.6 - - - -
541D TYR 3.5 3.9 + - - -
542D PHE* 1.3 73.1 - - - +
544D SER* 1.3 61.7 + - - +
577D ASN* 5.3 1.8 - - - -
579D PRO* 3.2 6.1 - - - +
580D LEU* 2.9 21.7 + - - +
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Residues in contact with SER 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D LEU* 3.3 15.3 - - - +
442D PHE 3.8 2.2 + - - -
443D HIS* 2.8 29.7 + - - -
444D LEU* 2.8 31.7 + - - +
542D PHE* 3.4 4.2 - - - +
543D SER* 1.3 83.6 + - - +
545D ILE* 1.3 63.8 + - - +
546D ILE* 4.1 8.3 - - - -
579D PRO* 4.0 0.7 - - - -
580D LEU* 3.5 26.5 - - - +
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Residues in contact with ILE 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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444D LEU* 3.4 17.5 - - + +
446D ILE* 4.6 12.6 - - + -
450D PRO* 5.8 0.4 - - + -
520D ILE* 3.8 27.6 - - + -
524D ASN* 4.1 6.7 - - - +
542D PHE* 4.8 7.4 - - + -
544D SER* 1.3 78.5 - - - +
546D ILE* 1.3 63.2 + - - +
547D LEU* 4.1 21.9 - - + +
556D LEU* 5.0 4.1 - - + +
560D MET* 3.9 20.4 - - + -
579D PRO* 3.9 24.5 - - + -
580D LEU 2.9 9.7 + - - +
581D LEU* 3.7 12.6 - - + +
582D SER 3.3 23.2 + - - +
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Residues in contact with ILE 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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323D LEU* 5.0 1.6 - - + -
324D ALA* 3.6 36.1 - - + +
327D VAL* 4.0 18.4 - - + -
443D HIS* 5.5 1.1 - - + -
444D LEU 2.8 16.5 + - - +
445D TYR* 3.4 14.2 - - + -
446D ILE 3.0 26.5 + - - +
544D SER* 4.5 8.7 - - - -
545D ILE* 1.3 79.0 - - - +
547D LEU* 1.3 66.6 + - - +
580D LEU* 4.3 15.9 - - + -
582D SER* 3.4 20.0 - - - +
584D ILE* 3.5 28.5 - - + -
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Residues in contact with LEU 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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445D TYR* 4.3 2.9 - - - -
446D ILE* 3.3 31.4 - - + +
448D THR 4.1 5.2 - - - +
449D SER* 3.6 30.1 - - - +
450D PRO* 4.2 2.5 - - + -
545D ILE* 4.1 11.2 - - + +
546D ILE* 1.3 87.4 - - - +
548D GLY* 1.3 62.5 + - - +
549D SER 3.4 10.9 + - - +
550D LEU 4.5 0.2 - - - +
551D TYR* 4.0 19.0 - - + +
556D LEU* 3.5 33.2 - - + -
582D SER 2.9 12.9 + - - +
583D GLY* 3.5 3.5 - - - -
584D ILE* 3.5 23.2 + - - +
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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