Contacts of the strand formed by residues 363 - 370 (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 LYS 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ASP* 5.4 3.4 + - - -
128A GLY* 5.4 4.5 - - - -
150A ILE 5.2 1.6 + - - -
152A LEU* 4.2 16.2 - - + -
179A LYS 4.7 6.5 - - - +
180A ASP* 4.2 21.8 - - - +
181A MET 4.0 18.2 - - - +
182A SER* 4.6 12.1 + - - +
183A GLN* 5.7 1.1 - - - +
359A GLU* 3.4 5.6 + - - +
360A ALA* 2.6 47.7 + - + +
361A PRO* 3.0 26.1 + - - +
362A HIS* 1.3 84.0 - - + +
364A GLY* 1.3 58.4 + - - +
365A PHE* 6.1 0.2 - - + -
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Residues in contact with GLY 364 (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* 4.8 2.7 - - - -
358A ILE 3.3 15.5 - - - -
359A GLU* 4.1 4.7 - - - -
363A LYS* 1.3 77.1 - - - +
365A PHE* 1.3 73.3 + - - +
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Residues in contact with PHE 365 (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 20.2 - - + -
153A VAL 4.3 8.7 - - - -
154A ASN* 5.8 0.4 - - - -
155A CYS* 4.2 16.6 - - + -
180A ASP* 3.3 37.2 - - + -
357A TYR* 3.4 4.7 - - - -
358A ILE* 3.1 53.5 + - + -
363A LYS* 6.1 0.7 - - + -
364A GLY* 1.3 81.2 - - - +
366A PRO* 1.3 87.4 - - + +
367A VAL* 3.7 8.0 - - + +
389A ASP 3.8 9.9 - - - +
390A PHE 4.9 0.2 - - - -
391A GLY* 4.1 8.1 - - - -
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Residues in contact with PRO 366 (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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355A PHE* 5.6 0.7 - - + -
356A GLY 3.3 11.4 - - - +
357A TYR* 4.0 4.0 - - + -
365A PHE* 1.3 92.9 - - + +
367A VAL* 1.3 61.8 + - - +
389A ASP* 3.6 18.6 - - + +
390A PHE* 3.4 29.4 - - + -
391A GLY 2.9 21.9 + - - -
652A ARG* 3.2 37.2 - - + +
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Residues in contact with VAL 367 (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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155A CYS* 4.0 10.8 - - - -
257A PHE* 4.5 1.6 - - + -
297A TRP* 3.0 39.1 + - + -
356A GLY 2.8 23.3 + - - +
357A TYR* 4.5 0.9 - - - -
358A ILE* 3.7 38.1 - - + +
365A PHE* 3.7 13.2 - - + +
366A PRO* 1.3 79.9 - - - +
368A VAL* 1.3 64.5 + - - +
390A PHE* 5.2 0.2 - - - -
391A GLY* 3.3 10.5 - - - +
393A VAL* 3.9 26.5 - - + -
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Residues in contact with VAL 368 (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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353A ILE* 3.6 30.3 - - + -
354A GLU 3.3 3.8 - - - +
355A PHE* 3.6 37.7 - - + -
366A PRO 4.3 0.2 - - - -
367A VAL* 1.3 72.9 - - - +
369A LEU* 1.3 78.5 + - - +
370A ASP* 3.8 2.4 + - + +
390A PHE* 3.9 14.8 - - + -
391A GLY 2.8 10.4 + - - +
392A TYR* 3.5 23.0 - - + +
393A VAL* 2.9 26.5 + - - +
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Residues in contact with LEU 369 (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* 3.5 63.0 - - + +
352A GLU 3.5 0.7 - - - +
353A ILE* 3.3 6.9 - - - -
354A GLU* 2.9 32.8 + - + +
367A VAL 3.9 0.2 + - - -
368A VAL* 1.3 74.8 - - - +
370A ASP* 1.3 59.3 + - - +
393A VAL* 3.4 30.1 - - + +
408A PHE* 3.6 26.7 - - + -
411A LEU* 5.7 0.4 - - + -
447A VAL* 6.4 0.2 - - + -
450A PHE* 4.0 14.4 - - + -
451A LEU* 5.1 3.4 - - + -
703A MPD 3.9 20.9 - - + -
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Residues in contact with ASP 370 (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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344A ARG* 3.1 34.4 + - - -
352A GLU 3.3 5.9 - - - +
353A ILE* 3.4 13.0 - - + +
368A VAL* 3.8 6.3 + - + +
369A LEU* 1.3 73.4 - - - +
371A SER* 1.3 66.9 + - - +
372A PRO* 3.4 9.1 - - - +
376A ASN* 3.1 25.0 + - - -
384A GLU 4.8 3.0 - - - +
392A TYR* 5.5 6.3 - - + -
393A VAL 2.8 14.0 + - - +
394A THR* 3.4 11.0 + - - +
395A ARG 3.0 27.0 + - - -
703A MPD 5.1 0.6 + - - -
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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