Contacts of the strand formed by residues 353 - 357 (chain A) in PDB entry 3S3J
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 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A SER 3.3 2.6 - - - +
341A TRP* 3.4 32.6 - - - -
342A MET 2.9 27.8 + - - -
352A GLU* 1.3 75.9 - - - +
354A TRP* 1.3 61.9 + - - -
355A GLN* 2.9 13.4 + - - +
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Residues in contact with TRP 354 (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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150A LEU* 5.7 1.1 - - + -
155A GLU* 5.3 2.9 - - - -
159A TYR* 3.5 50.0 - + + -
294A PRO* 3.7 22.4 - - + -
295A THR* 4.4 0.2 - - - -
296A ARG* 3.2 37.8 - - + +
339A GLU* 3.7 29.2 - - + +
340A SER 3.6 18.4 - - - -
341A TRP* 3.5 35.2 - + + -
353A GLY* 1.3 72.4 - - - -
355A GLN* 1.3 63.0 + - - +
375A PRO* 3.8 1.2 - - - +
376A VAL* 3.1 34.5 + - + +
377A ARG 4.7 0.9 + - - -
442A THR* 6.2 2.5 - - + -
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Residues in contact with GLN 355 (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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339A GLU* 3.0 5.8 - - - -
340A SER* 2.7 47.2 + - - +
342A MET* 3.4 32.3 + - + -
344A ARG* 2.9 35.1 + - - +
351A TYR 3.1 23.6 + - - -
353A GLY 2.9 22.5 + - - +
354A TRP* 1.3 76.5 + - - +
356A ALA* 1.3 61.9 + - - +
357A LEU* 3.7 2.1 + - - +
373A PRO* 3.7 18.2 - - + -
374A VAL 3.2 8.3 - - - +
375A PRO* 3.4 12.7 - - - +
376A VAL* 4.5 0.2 - - - -
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Residues in contact with ALA 356 (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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337A TRP* 3.7 24.2 - - + +
338A VAL 3.3 5.6 - - - -
339A GLU* 4.3 2.0 - - - +
355A GLN* 1.3 71.4 - - - +
357A LEU* 1.3 59.3 + - - +
372A GLY* 3.9 2.1 - - - -
373A PRO* 3.3 5.5 - - - +
374A VAL* 2.8 42.0 + - + +
376A VAL* 4.1 7.6 - - + +
393A VAL* 4.1 24.0 - - + +
443A TYR* 3.8 10.1 - - + +
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Residues in contact with LEU 357 (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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221A GLY* 3.8 35.9 - - - +
225A SER* 4.2 10.1 - - - -
288A LEU* 4.1 7.4 - - + -
337A TRP* 3.3 2.9 - - - +
338A VAL* 2.8 48.7 + - + +
340A SER* 4.0 28.5 - - - +
342A MET* 5.4 1.6 - - + -
355A GLN 4.5 1.1 - - - +
356A ALA* 1.3 74.6 - - - +
358A ASP* 1.3 60.4 + - - +
359A PRO* 3.4 4.9 - - + +
371A CYS 3.5 6.1 - - - +
372A GLY 3.5 6.1 - - - +
373A PRO* 3.2 43.3 - - + -
393A VAL* 6.1 0.4 - - - -
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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