Contacts of the strand formed by residues 352 - 356 (chain A) in PDB entry 3CL0
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 PHE 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A SER* 3.8 10.3 - - - -
290A VAL* 4.2 8.7 - - - -
300A ARG* 4.1 5.4 - - - +
351A GLY* 1.3 74.8 - - - +
353A SER* 1.3 74.6 + - - +
354A PHE* 3.8 27.4 - + - -
363A GLY* 3.6 23.8 + - - +
374A PHE* 3.7 14.1 - + - -
376A MET* 3.7 29.6 - - + -
407A SER* 3.4 23.8 - - - -
408A GLY 3.7 14.4 - - - -
409A SER* 3.7 20.2 - - - +
422A PHE* 3.3 41.1 - + + -
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Residues in contact with SER 353 (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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279A SER 5.6 0.2 - - - +
281A TYR* 3.3 20.1 + - - -
290A VAL* 3.5 20.7 - - - +
300A ARG* 5.0 2.8 - - - -
317A ILE* 3.8 22.3 - - - +
352A PHE* 1.3 85.5 + - - +
354A PHE* 1.3 65.2 + - - +
355A LYS 4.0 0.8 + - - -
360A VAL* 3.7 14.8 - - - -
361A TRP 3.2 15.3 + - - -
362A ILE* 3.7 16.8 - - - +
383A TRP* 4.6 0.4 - - - -
409A SER* 5.7 0.5 - - - -
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Residues in contact with PHE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.3 7.2 - - + -
97A TRP* 3.7 29.6 - + - -
281A TYR* 3.7 39.7 - + + -
352A PHE* 3.8 27.1 - + - -
353A SER* 1.3 71.4 - - - +
355A LYS* 1.3 63.8 + - - +
356A TYR* 3.5 21.2 + - + -
360A VAL* 3.4 5.9 - - - -
361A TRP* 3.0 37.2 + - + -
409A SER* 3.5 15.5 - - - -
410A PHE 4.2 2.9 - - - -
411A VAL* 4.8 2.0 - - + -
420A PRO* 3.7 24.2 - - + -
421A CYS 3.4 26.7 - - - -
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Residues in contact with LYS 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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91A LEU* 3.9 13.2 - - - +
281A TYR* 2.8 19.1 + - - +
283A ASN* 4.5 6.6 - - - +
286A GLU* 5.8 5.2 - - - -
288A THR* 4.8 8.1 - - + +
304A SER* 5.7 3.6 - - - +
353A SER 4.0 1.6 - - - -
354A PHE* 1.3 71.9 - - - +
356A TYR* 1.3 64.0 + - - +
357A GLY* 2.5 44.0 + - - +
358A ASN* 4.3 7.7 + - - -
359A GLY 3.7 4.7 - - - +
383A TRP* 3.3 55.6 - - + +
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Residues in contact with TYR 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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91A LEU* 3.6 33.1 - - + +
92A CYS 2.5 31.0 + - - -
93A PRO* 4.5 7.0 - - + -
94A ILE* 3.8 12.2 - - + +
354A PHE* 3.5 19.9 + - + -
355A LYS* 1.3 76.8 - - - +
357A GLY* 1.3 58.3 + - - +
358A ASN 3.4 0.2 + - - -
359A GLY* 2.9 28.2 + - - -
361A TRP* 3.9 22.7 - + - -
378A TRP* 3.9 24.7 - + + -
420A PRO* 3.4 21.7 - - + +
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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