Contacts of the strand formed by residues 542 - 547 (chain B) in PDB entry 1ZY7
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B VAL* 3.9 31.6 - - + -
400B ARG* 5.2 6.1 - - + -
403B LEU* 4.2 4.5 - - + -
442B PHE* 3.5 25.6 - - + -
444B LEU* 3.8 35.7 - - + -
520B ILE* 5.4 2.9 - - + -
523B TRP* 3.7 30.3 - + + -
524B ASN* 5.0 6.1 + - - +
528B ILE* 3.5 43.1 - - + +
541B TYR* 1.3 72.6 - - - +
543B SER* 1.3 61.2 + - - +
544B SER 3.8 12.6 - - - +
545B ILE* 4.7 8.1 - - + -
577B ASN* 2.9 29.1 + - - +
579B PRO* 3.5 3.3 - - - +
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Residues in contact with SER 543 (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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312B SER* 4.5 5.0 + - - -
441B GLN* 3.3 43.6 + - - +
442B PHE 2.8 13.6 + - - -
443B HIS* 3.9 10.1 - - - -
541B TYR 3.5 4.7 + - - -
542B PHE* 1.3 74.1 - - - +
544B SER* 1.3 61.2 + - - +
577B ASN* 5.6 0.4 - - - -
579B PRO* 3.4 5.8 - - - +
580B LEU* 2.9 22.3 + - - +
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Residues in contact with SER 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 3.5 10.9 - - - +
442B PHE 3.8 1.8 + - - -
443B HIS* 2.7 32.0 + - - -
444B LEU* 3.0 24.2 + - - +
542B PHE* 3.4 4.4 - - - +
543B SER* 1.3 80.6 + - - +
545B ILE* 1.3 68.9 + - - +
546B ILE* 4.0 20.6 - - - -
579B PRO* 3.9 0.7 - - - -
580B LEU* 3.3 22.4 - - - +
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Residues in contact with ILE 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU* 3.5 23.6 - - + +
446B ILE* 4.8 4.3 - - + -
450B PRO* 5.7 0.7 - - + -
520B ILE* 3.5 30.5 - - + -
524B ASN* 4.0 7.0 - - - +
542B PHE* 4.7 6.5 - - + -
544B SER* 1.3 77.7 - - - +
546B ILE* 1.3 61.6 + - - +
547B LEU* 4.1 20.4 + - + -
556B LEU* 4.7 6.6 - - + +
560B MET* 3.6 23.1 - - + -
579B PRO* 3.8 23.1 - - + -
580B LEU 2.7 9.7 + - - +
581B LEU* 3.4 15.6 - - + +
582B SER 3.2 22.7 + - - +
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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
----------------------------------------------------------
323B LEU* 4.5 3.8 - - + +
324B ALA* 3.7 44.0 - - + +
327B VAL* 3.6 37.5 - - + -
443B HIS* 4.3 2.5 - - + -
444B LEU 2.8 15.4 + - - +
445B TYR* 3.3 13.2 - - + -
446B ILE* 3.0 25.3 + - - +
544B SER* 4.0 22.4 - - - -
545B ILE* 1.3 77.8 - - - +
547B LEU* 1.3 65.6 + - - +
580B LEU* 5.4 2.2 - - + -
582B SER* 3.3 9.9 - - - +
584B ILE* 3.8 15.3 - - + -
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Residues in contact with LEU 547 (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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445B TYR* 4.2 2.7 - - - -
446B ILE* 3.2 9.9 - - + +
448B THR 3.7 16.8 - - - +
449B SER* 3.5 30.5 - - - +
450B PRO* 4.0 12.6 - - + -
545B ILE* 4.1 15.5 - - + -
546B ILE* 1.3 80.4 - - - +
548B GLY* 1.3 62.7 + - - +
549B SER 3.3 10.3 + - - +
551B TYR* 4.1 19.9 - - + +
556B LEU* 3.6 32.5 - - + -
582B SER 2.8 14.1 + - - +
583B GLY* 3.3 20.8 - - - -
584B ILE* 3.4 6.3 + - - +
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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