Contacts of the strand formed by residues 343 - 348 (chain A) in PDB entry 5IVK
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 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A MET* 3.6 24.4 - - + +
240A GLY 3.2 11.7 - - - +
242A LEU* 4.8 3.4 - - + -
338A GLY 4.3 2.3 + - - -
341A ILE 2.9 15.3 + - - -
342A PRO* 1.3 73.2 + - - +
344A MET* 1.3 66.1 + - - +
345A MET* 3.6 36.3 - - + -
432A ARG* 4.6 8.7 + - - +
440A PRO 3.1 6.7 + - - +
441A VAL* 3.1 16.2 - - + -
442A TYR* 2.9 26.0 + - - -
507A PHE* 3.6 4.0 - - - -
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Residues in contact with MET 344 (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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240A GLY 3.0 6.7 + - - +
241A ILE* 3.1 23.3 - - + +
242A LEU 2.8 24.9 + - - -
343A THR* 1.3 74.7 - - - +
345A MET* 1.3 65.6 + - - +
442A TYR* 3.3 16.2 - - + +
444A TYR* 3.8 22.9 - - + -
503A ILE* 4.3 8.3 - - + -
504A TRP* 4.2 18.2 - - + -
507A PHE* 3.5 45.7 - - + -
513A PRO* 4.7 4.0 - - - -
526A TRP* 3.9 28.5 - - - -
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Residues in contact with MET 345 (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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225A HIS* 5.9 0.4 - - + -
228A MET* 6.1 0.4 - - + -
242A LEU* 3.3 34.8 - - + +
246A ASN* 5.4 1.6 - - - -
343A THR* 3.6 23.6 - - + -
344A MET* 1.3 79.3 - - - +
346A GLY* 1.3 58.5 + - - +
425A MET* 4.4 27.6 - - + -
428A LEU* 3.5 32.3 - - + -
429A LEU* 4.5 11.7 - - + -
432A ARG* 4.9 10.5 - - - -
441A VAL* 4.5 11.2 - - + -
442A TYR 2.9 7.5 + - - +
443A LEU* 3.3 13.7 - - + +
444A TYR* 3.0 28.9 + - - -
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Residues in contact with GLY 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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242A LEU 3.2 6.0 + - - +
244A SER 2.8 30.7 + - - -
245A GLY 4.8 0.3 + - - -
345A MET* 1.3 78.8 - - - +
347A ASN* 1.3 65.6 + - - +
422A TRP* 6.0 0.4 - - - -
425A MET* 4.8 4.2 - - - -
444A TYR* 3.0 34.0 + - - -
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Residues in contact with ASN 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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244A SER* 3.4 20.2 - - - -
245A GLY 4.3 1.4 + - - -
346A GLY* 1.3 78.4 - - - +
348A THR* 1.3 63.4 + - - +
351A GLU* 3.2 13.5 - - + +
421A PHE* 3.5 19.8 - - - +
422A TRP* 3.6 39.7 - - + +
425A MET* 3.6 32.5 - - - +
444A TYR* 3.5 7.7 + - - -
445A ARG* 3.3 6.8 - - - +
446A PHE* 2.8 24.2 + - - +
474A GLU* 6.3 0.2 - - - -
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Residues in contact with THR 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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244A SER* 4.4 1.1 - - - +
347A ASN* 1.3 79.9 - - - +
349A SER* 1.3 63.2 + - - +
350A TYR 3.5 0.3 + - - -
351A GLU* 2.8 39.8 + - - +
422A TRP* 3.7 16.6 + - - -
445A ARG* 4.6 1.3 - - - -
446A PHE* 3.2 18.4 - - + +
469A VAL* 2.9 28.4 + - + -
470A SER 3.4 18.4 - - - +
471A HIS* 4.4 1.3 - - - +
473A ASP 4.8 0.2 - - - +
474A GLU* 3.3 27.4 - - - +
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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