Contacts of the strand formed by residues 342 - 346 (chain A) in PDB entry 6DSU
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 GLY 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A VAL* 3.4 2.8 - - - -
339A ASN* 3.0 34.7 + - - +
340A GLU 3.6 0.4 - - - -
341A HIS* 1.3 80.4 - - - +
343A ARG* 1.3 66.8 + - - +
344A PHE* 3.7 11.6 - - - -
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Residues in contact with ARG 343 (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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300A ALA* 3.1 25.5 + - - +
301A PHE* 3.7 8.0 - - + +
302A THR* 3.0 27.5 + - - -
337A VAL 3.3 4.0 - - - -
338A VAL* 3.9 20.6 - - + +
342A GLY* 1.3 78.8 - - - +
344A PHE* 1.3 66.6 + - - +
448A VAL* 3.8 28.9 - - + -
452A ALA* 4.4 14.8 - - - +
903A SO4 3.3 43.5 + - - -
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Residues in contact with PHE 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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302A THR* 3.5 24.7 - - + +
308A THR* 4.8 0.2 - - - -
310A GLU* 3.4 39.3 - - + -
311A MET* 3.8 45.1 - - + -
336A ALA* 3.1 8.3 - - - +
337A VAL* 2.7 57.4 + - + +
338A VAL* 5.1 0.2 - - - +
339A ASN* 3.8 19.3 - - - -
341A HIS 4.4 1.3 - - - -
342A GLY* 3.7 26.9 - - - -
343A ARG* 1.3 80.5 - - - +
345A PHE* 1.3 62.7 + - - +
346A LEU* 4.9 2.7 - - + -
448A VAL* 4.0 6.3 - - - +
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Residues in contact with PHE 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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301A PHE* 4.1 11.0 - - + -
302A THR 2.8 12.0 + - - +
303A LEU* 3.9 13.5 - - + -
304A ALA* 2.9 30.8 + - - +
333A VAL 4.6 1.3 - - - -
334A GLY* 4.1 10.1 - - - -
335A ILE 3.3 12.6 - - - -
344A PHE* 1.3 73.2 - - - +
346A LEU* 1.3 77.0 + - - +
347A ARG* 4.0 9.4 - - + -
348A PRO* 5.4 0.2 - - + -
440A GLU* 4.0 28.0 - - + -
443A LEU* 4.4 12.1 - - + -
444A ALA* 3.4 43.7 - - + -
447A LEU* 3.7 28.3 - - + -
448A VAL* 4.1 5.1 - - + +
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Residues in contact with LEU 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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304A ALA* 3.7 20.4 - - + +
306A ARG 4.2 6.5 - - - +
307A VAL* 4.0 15.5 - - + -
311A MET* 3.6 34.5 - - + -
334A GLY* 4.0 0.5 - - - -
335A ILE* 2.8 47.3 + - + +
337A VAL* 4.4 10.3 - - + -
344A PHE* 4.9 3.6 - - + -
345A PHE* 1.3 80.4 - - - +
347A ARG* 1.3 65.1 + - - +
350A THR* 5.3 3.8 - - + -
351A ALA* 4.0 14.8 - - + -
357A PHE* 3.7 32.5 - - + -
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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