Contacts of the strand formed by residues 537 - 541 (chain A) in PDB entry 3ZRH
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 ILE 537 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A VAL* 4.9 5.2 - - + -
526A ILE* 3.6 29.4 - - + +
529A LEU* 3.9 11.2 - - + -
530A ALA* 3.4 35.0 - - + +
533A LEU* 4.2 9.4 - - + -
535A ARG 4.2 1.3 - - - +
536A PRO* 1.3 78.7 - - - +
538A ILE* 1.3 63.6 + - - +
539A VAL* 4.2 6.3 - - + -
561A VAL* 3.7 0.7 - - - -
562A TYR* 2.8 42.4 + - + +
577A ILE* 3.5 21.8 - - + +
579A LEU* 3.9 27.4 - - + -
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Residues in contact with ILE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PRO* 5.3 0.7 - - + -
537A ILE* 1.3 77.3 - - - +
539A VAL* 1.3 64.6 + - - +
540A TYR* 3.6 34.4 - - + +
560A GLY 3.5 4.7 - - - +
561A VAL* 4.4 16.2 - - + -
576A PRO* 4.0 31.2 - - + -
577A ILE 2.9 9.1 + - - +
578A ALA* 3.2 5.2 - - - +
579A LEU* 2.8 26.2 + - - +
617A LEU* 4.1 14.1 - - + -
618A PRO 4.6 0.2 - - - +
619A LEU* 3.8 22.7 - - + -
627A LEU* 3.8 22.4 - - + -
651A LEU* 4.9 2.0 - - + -
663A ALA* 4.3 6.5 - - + -
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Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ILE* 4.3 15.0 - - + -
537A ILE* 4.2 8.5 - - + -
538A ILE* 1.3 76.8 - - - +
540A TYR* 1.3 76.1 + - - +
558A PHE* 3.7 26.5 - - + +
559A GLN* 3.3 5.0 - - - +
560A GLY* 2.7 37.7 + - - +
562A TYR* 3.7 21.3 - - + -
579A LEU* 3.3 20.9 - - + +
581A TYR* 3.9 20.4 - - + +
586A PHE* 4.5 6.3 - - + -
627A LEU* 4.7 0.3 - - - +
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Residues in contact with TYR 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A LEU* 4.7 1.0 - - - +
417A ILE* 3.6 26.0 - - + +
418A ILE* 4.0 15.5 - - + -
420A TRP* 6.2 0.2 - - - -
432A LEU* 4.2 12.3 - - + -
538A ILE* 3.6 23.1 - - + +
539A VAL* 1.3 77.4 - - - +
541A GLY* 1.3 58.3 + - - +
559A GLN* 3.2 13.2 - - - -
578A ALA* 4.1 18.8 - - + -
579A LEU 2.9 9.3 + - - +
580A GLY* 3.3 4.7 - - - -
581A TYR* 2.9 23.4 + - - -
589A LEU* 3.9 19.1 - - + -
617A LEU* 3.4 12.1 - - + +
618A PRO* 2.8 55.3 + - + +
620A VAL 5.2 2.0 - - - -
627A LEU* 3.9 11.4 - - + -
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Residues in contact with GLY 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 4.7 0.2 - - - -
417A ILE* 3.4 17.1 - - - +
540A TYR* 1.3 73.5 - - - +
542A VAL* 1.3 71.5 + - - +
543A LYS 3.5 0.2 + - - -
556A THR* 6.0 0.2 - - - -
559A GLN* 3.1 31.3 + - - +
581A TYR* 3.4 23.3 - - - -
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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