Contacts of the strand formed by residues 538 - 545 (chain A) in PDB entry 3CTZ
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 ASN 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A ASP 4.7 0.2 - - - -
429A ARG* 2.8 33.6 + - - +
451A HIS* 3.5 28.0 + - + +
455A SER* 5.7 0.2 + - - -
521A THR* 3.2 4.2 - - - -
522A ASP* 2.8 33.3 + - - +
537A GLU* 1.3 74.9 - - - +
539A VAL* 1.3 66.9 + - - +
540A VAL* 3.9 8.4 + - + +
561A PRO* 3.9 9.7 - - + +
563A THR* 3.3 17.7 - - - +
567A ILE* 5.2 1.0 - - - +
584A TRP* 4.6 3.2 - - - -
588A TYR* 3.4 29.3 + - - -
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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
----------------------------------------------------------
330A MET* 4.6 2.9 - - + -
334A HIS* 3.4 36.3 - - + +
425A THR 4.8 0.2 - - - -
426A ASP* 3.5 28.6 + - + +
491A VAL* 4.2 9.2 - - + -
519A ILE* 3.3 28.5 - - + -
520A VAL 3.5 4.3 - - - +
521A THR* 3.9 16.6 - - + +
538A ASN* 1.3 72.2 - - - +
540A VAL* 1.3 64.8 + - - +
561A PRO* 3.6 1.0 - - - +
562A LEU* 2.8 31.3 + - + -
563A THR* 2.8 11.2 + - - -
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A HIS* 5.7 0.2 - - - +
455A SER* 4.0 18.2 - - - +
518A MET 4.1 0.2 - - - +
519A ILE* 3.4 8.1 - - - +
520A VAL* 2.8 62.3 + - + +
522A ASP* 4.4 16.2 - - + +
538A ASN* 4.3 15.5 - - + +
539A VAL* 1.3 79.2 - - - +
541A LEU* 1.3 59.5 + - - +
542A VAL 4.1 0.2 + - - -
559A LEU* 4.0 29.8 - - + -
560A GLU 3.3 7.0 - - - +
561A PRO* 3.8 14.6 - - + -
562A LEU* 4.2 0.9 - - - +
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Residues in contact with LEU 541 (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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327A SER* 4.3 19.5 - - - +
331A ARG* 3.5 32.1 - - - +
517A GLY* 4.0 19.3 - - - +
518A MET 3.6 15.0 - - - +
519A ILE* 3.7 21.1 - - + -
540A VAL* 1.3 73.2 - - - +
542A VAL* 1.3 63.8 + - - +
543A VAL* 3.4 20.9 + - + +
559A LEU* 3.4 2.7 - - - -
560A GLU* 2.8 36.2 + - + +
562A LEU* 4.0 16.9 - - + +
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Residues in contact with VAL 542 (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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459A PHE* 4.7 1.8 - - + -
514A LEU* 4.3 19.7 - - + -
515A GLU 3.3 31.4 - - - +
516A ALA* 3.5 2.3 - - - +
517A GLY 2.9 24.1 + - - -
518A MET* 2.8 34.8 + - + +
520A VAL* 5.0 7.0 - - + -
541A LEU* 1.3 73.0 - - - +
543A VAL* 1.3 63.5 - - - +
557A LEU* 3.7 26.7 - - + -
558A THR 3.5 6.7 - - - +
559A LEU* 3.6 18.8 - - + -
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ARG* 5.0 0.4 - - - +
541A LEU* 3.7 29.4 - - + +
542A VAL* 1.3 79.8 - - - +
544A PRO* 1.3 77.2 - - + +
557A LEU* 3.1 8.6 - - - -
558A THR* 2.8 59.5 + - + +
560A GLU* 3.8 28.9 - - + +
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Residues in contact with PRO 544 (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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516A ALA* 4.1 20.4 - - + -
543A VAL* 1.3 98.8 - - + +
545A VAL* 1.3 62.2 + - - +
556A SER 3.5 10.8 - - - +
557A LEU* 3.9 4.7 - - + -
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Residues in contact with VAL 545 (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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458A VAL* 4.0 22.9 - - + -
544A PRO* 1.3 77.1 - - - +
546A LYS* 1.3 78.6 + - - +
547A THR* 3.8 2.2 + - + -
556A SER* 3.1 20.9 + - - +
557A LEU 3.7 30.5 - - - +
558A THR* 3.8 22.2 - - + +
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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