Contacts of the strand formed by residues 345 - 351 (chain A) in PDB entry 3AR2
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 THR 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A THR 3.5 3.2 + - - -
342A LEU* 3.1 39.6 + - + +
343A GLY 3.2 1.8 - - - +
344A CYS* 1.3 77.2 - - - +
346A SER* 1.3 62.3 + - - +
347A VAL 3.4 28.3 - - - +
348A ILE* 3.9 17.3 - - + -
619A ILE* 3.3 25.9 - - + +
697A ILE* 3.5 17.2 - - - +
699A ALA* 4.1 8.3 - - + +
716A ILE* 4.2 4.0 - - - +
747A VAL* 5.2 0.2 - - - -
821A PRO* 3.5 8.2 - - - +
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Residues in contact with SER 346 (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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344A CYS 3.3 3.0 + - - -
345A THR* 1.3 74.7 - - - +
347A VAL* 1.3 63.5 + - - +
618A GLY 3.8 4.1 - - - +
619A ILE* 3.4 7.6 - - - -
620A ARG* 3.0 21.5 + - - +
696A GLU* 3.2 44.2 - - - +
697A ILE 3.1 8.2 + - - -
821A PRO* 3.8 22.2 - - - -
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Residues in contact with VAL 347 (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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345A THR* 3.4 4.1 - - - +
346A SER* 1.3 90.5 + - - +
348A ILE* 1.3 68.2 + - - +
349A CYS* 3.7 5.4 + - - +
620A ARG* 3.6 24.2 - - + +
622A ILE* 3.7 29.8 - - + -
691A LEU* 4.2 20.2 - - + -
696A GLU* 3.5 27.8 - - + +
697A ILE 3.7 2.1 + - - +
698A THR* 3.7 10.1 - - + -
699A ALA 3.1 24.6 + - - +
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Residues in contact with ILE 348 (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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342A LEU* 5.2 0.9 - - + -
345A THR* 3.9 13.2 - - + -
347A VAL* 1.3 73.9 - - - +
349A CYS* 1.3 68.2 + - - +
350A SER* 3.7 6.6 + - - -
614A CYS* 3.8 20.9 - - - -
619A ILE* 3.7 23.6 - - + -
620A ARG 2.7 13.6 + - - +
621A VAL* 3.3 13.5 - - + +
622A ILE 3.2 21.5 + - - +
699A ALA* 4.1 11.9 - - + -
701A THR* 4.1 13.7 - - - +
740A PHE* 4.8 12.3 - - + -
743A ILE* 3.8 25.8 - - + -
747A VAL* 4.8 10.3 - - + -
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Residues in contact with CYS 349 (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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347A VAL* 3.7 3.3 + - - -
348A ILE* 1.3 74.9 - - - +
350A SER* 1.3 59.9 + - - +
622A ILE* 3.7 26.7 - - - -
624A ILE* 4.6 6.5 - - + -
687A ILE* 4.5 15.0 - - - -
688A VAL* 3.8 20.6 - - + -
691A LEU* 4.5 3.8 - - - -
698A THR* 4.2 13.0 - - - -
699A ALA 3.0 16.6 + - - +
700A MET* 3.3 19.9 - - - -
701A THR* 2.8 26.0 + - - -
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Residues in contact with SER 350 (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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348A ILE* 4.5 4.9 - - - -
349A CYS* 1.3 76.5 - - - +
351A ASP* 1.3 69.6 + - - +
355A THR* 3.4 15.1 - - - +
356A LEU* 3.4 21.9 - - - +
621A VAL* 4.9 4.0 - - - -
622A ILE 2.8 13.4 + - - -
623A MET* 3.4 6.9 - - - -
624A ILE* 2.8 28.6 + - - +
700A MET* 4.3 3.5 - - - +
701A THR* 3.5 11.3 - - - -
740A PHE* 3.7 11.3 - - - -
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Residues in contact with ASP 351 (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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350A SER* 1.3 85.6 + - - +
352A LYS* 1.3 66.1 + - - +
353A THR 2.5 30.3 - - - +
355A THR* 3.2 18.9 + - - +
356A LEU* 3.2 6.6 - - - +
624A ILE 3.3 8.3 - - - -
684A LYS* 2.7 21.7 + - - -
700A MET* 3.8 3.9 - - - +
701A THR 2.7 17.7 + - - +
703A ASP* 3.0 3.2 - - - +
707A ASP* 3.1 28.8 - - - +
1001A CA 2.9 3.1 - - - -
1002A ACP 2.3 24.8 + - - -
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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