Contacts of the strand formed by residues 353 - 360 (chain A) in PDB entry 4N20
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 ILE 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A ARG* 4.4 2.2 - - - +
348A TRP* 3.4 36.0 + - + +
349A ILE* 3.7 15.7 - - + +
350A GLN 3.5 11.6 - - - +
351A ASP 3.5 0.4 - - - -
352A GLU* 1.3 81.4 - - - +
354A GLU* 1.3 64.0 + - - +
355A PHE* 3.8 28.5 - - + -
368A VAL* 3.6 23.6 - - + -
369A LEU 3.3 1.6 - - - -
370A ASP* 3.4 36.8 - - + +
384A GLU 4.8 7.4 - - - +
392A TYR* 6.4 0.2 - - + -
408A PHE* 3.5 3.7 - - - +
650A ASN* 3.1 15.9 + - - -
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Residues in contact with GLU 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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297A TRP* 3.7 27.9 - - + -
299A MET* 3.3 24.3 - - + +
353A ILE* 1.3 77.6 - - - +
355A PHE* 1.3 71.2 + - - +
356A GLY 3.8 0.2 + - - -
367A VAL 3.9 0.3 - - - +
368A VAL* 3.3 4.9 - - - -
369A LEU* 2.9 35.4 + - + -
408A PHE* 3.2 35.5 - - + +
411A LEU* 3.6 7.0 - - + +
650A ASN* 4.2 11.1 + - - +
706A CA 2.5 30.1 - - - -
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Residues in contact with PHE 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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297A TRP* 4.0 5.7 - - - -
299A MET* 4.1 7.1 - - - +
300A THR* 3.7 22.6 + - - +
310A PHE* 3.6 35.7 - + + -
349A ILE* 5.0 3.4 - - + -
353A ILE* 3.8 17.0 - - + -
354A GLU* 1.3 79.9 + - - +
356A GLY* 1.3 59.4 + - - +
366A PRO* 5.6 1.1 - - + -
367A VAL 4.2 1.1 - - - -
368A VAL* 3.6 20.2 - - + -
390A PHE* 3.4 34.8 - + - -
650A ASN* 3.5 40.8 - - + +
651A VAL 4.1 17.0 - - - +
652A ARG* 3.7 14.4 - - + -
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Residues in contact with GLY 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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297A TRP* 3.6 11.2 - - - -
298A ILE 3.0 15.5 - - - -
299A MET* 4.3 0.7 - - - -
300A THR* 4.7 5.4 - - - -
354A GLU 3.8 0.2 + - - -
355A PHE* 1.3 76.4 - - - +
357A TYR* 1.3 65.0 + - - +
366A PRO* 3.3 7.4 - - - +
367A VAL 2.8 32.3 + - - -
652A ARG* 5.3 1.0 + - - +
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Residues in contact with TYR 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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296A PRO 3.8 0.5 - - - +
297A TRP* 3.8 1.8 - - - +
298A ILE* 2.8 76.4 + - + +
300A THR* 3.8 20.0 - - + -
356A GLY* 1.3 76.5 - - - +
358A ILE* 1.3 78.7 + - - +
359A GLU* 4.2 20.6 + - + -
365A PHE 3.4 14.8 - - - +
366A PRO* 4.0 4.9 - - + -
367A VAL* 3.8 3.6 - - - +
426A LEU* 4.3 3.1 - - - +
652A ARG* 5.6 2.9 - - - +
653A ARG 5.8 0.4 - - - +
655A PRO* 3.6 42.4 - - + -
656A PHE* 3.3 32.8 + + - +
658A PHE 4.6 2.9 + - - -
660A TRP* 5.4 0.9 - + - +
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Residues in contact with ILE 358 (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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152A LEU* 3.9 22.2 - - + -
153A VAL 3.9 19.1 - - - +
155A CYS* 4.4 3.6 - - - -
257A PHE* 3.6 31.4 - - + -
295A ALA* 4.5 4.0 - - + +
296A PRO 3.6 12.8 - - - +
297A TRP* 4.1 2.7 - - - -
298A ILE* 5.5 0.2 - - - -
357A TYR* 1.3 87.2 - - - +
359A GLU* 1.3 63.1 + - - +
364A GLY* 3.3 1.6 - - - -
365A PHE* 3.1 62.9 + - + +
367A VAL* 3.7 17.9 - - + +
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Residues in contact with GLU 359 (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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152A LEU* 3.8 4.0 - - - -
295A ALA* 3.5 10.9 - - - +
296A PRO 5.1 0.2 + - - -
357A TYR* 4.2 22.0 - - + -
358A ILE* 1.3 77.4 - - - +
360A ALA* 1.3 73.2 + - - +
362A HIS 5.5 1.9 + - - -
363A LYS 3.4 9.6 - - - +
364A GLY* 4.1 2.5 - - - -
655A PRO* 5.2 5.3 - - - +
656A PHE 4.6 7.8 - - - +
658A PHE 4.8 1.2 - - - +
659A LYS* 2.6 51.9 + - - +
660A TRP* 2.8 37.1 + - + +
661A TRP* 3.9 9.9 - - + -
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Residues in contact with ALA 360 (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 ILE* 3.8 17.0 - - + +
152A LEU* 3.7 27.5 - - + +
182A SER* 5.6 0.4 - - - +
359A GLU* 1.3 82.1 - - - +
361A PRO* 1.3 78.0 - - + +
362A HIS 3.0 1.2 + - - -
363A LYS* 2.6 37.6 + - + +
661A TRP* 3.8 6.1 - - - -
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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