Contacts of the strand formed by residues 396 - 402 (chain A) in PDB entry 4J2X
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 MET 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LEU* 3.4 13.2 - - - +
389A ASN* 3.2 53.1 + - + +
390A GLY 3.4 3.4 + - - -
393A ASP* 5.7 3.8 - - + +
394A VAL* 3.3 33.7 + - + +
395A ALA* 1.3 74.8 - - - +
397A LEU* 1.3 59.3 + - - +
428A LEU* 4.5 11.9 - - + -
429A CYS 3.3 12.8 - - - +
430A VAL* 3.8 26.5 - - + -
431A VAL* 4.4 1.1 - - - -
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 4.1 36.6 - - + -
387A GLN 3.4 13.7 - - - +
388A LEU* 4.0 13.7 - - + -
396A MET* 1.3 72.1 - - - +
398A GLU* 1.4 60.9 + - - +
399A LEU* 4.0 3.0 - - + +
412A PHE* 3.7 29.6 - - + -
427A MET 3.9 0.5 - - - +
428A LEU* 3.4 7.2 - - - +
429A CYS* 2.8 48.5 + - - -
431A VAL* 4.4 3.1 - - + +
452A VAL* 4.3 12.8 - - + -
468A PHE* 3.8 28.5 - - + -
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER 3.8 0.7 - - - +
386A LEU* 3.2 9.2 - - - +
387A GLN* 2.6 53.4 + - + +
389A ASN* 3.9 9.5 + - - +
397A LEU* 1.4 71.9 - - - +
399A LEU* 1.3 63.6 + - - +
400A THR* 3.9 16.1 + - - -
422A ARG* 4.1 17.9 + - - +
426A SER* 3.3 18.5 + - - +
427A MET 3.6 5.2 - - - +
428A LEU* 3.8 19.3 - - + +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 3.8 21.5 - - + -
385A SER 3.8 3.4 - - - -
386A LEU* 3.7 26.2 - - + -
397A LEU* 4.0 12.3 - - + +
398A GLU* 1.3 75.5 - - - +
400A THR* 1.3 61.3 + - - +
404A PHE* 3.4 13.0 - - + -
410A VAL* 3.9 31.4 - - + -
426A SER* 3.3 11.6 + - - -
427A MET* 2.8 48.1 + - + +
429A CYS* 4.1 9.6 - - - -
452A VAL* 4.4 10.5 - - + -
454A LEU* 4.5 10.3 - - + -
464A THR* 5.6 0.4 - - + -
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Residues in contact with THR 400 (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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383A VAL* 3.5 4.3 - - - -
384A GLU* 2.6 46.2 + - + +
385A SER* 3.2 29.7 + - - +
398A GLU* 3.9 17.7 + - - +
399A LEU* 1.3 74.2 + - - +
401A GLY* 1.3 55.8 + - - +
404A PHE* 3.8 2.5 - - - -
425A GLU* 3.6 8.8 + - + +
426A SER* 5.3 0.3 + - - -
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Residues in contact with GLY 401 (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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382A VAL 3.1 14.4 - - - -
384A GLU* 3.7 24.8 - - - +
400A THR* 1.3 77.9 - - - +
402A GLN* 1.3 63.1 + - - +
404A PHE* 3.5 5.3 - - - -
425A GLU* 3.3 29.9 + - - +
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Residues in contact with GLN 402 (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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381A PRO* 3.3 0.9 - - - +
382A VAL* 2.9 37.0 + - + +
384A GLU* 4.8 5.8 - - - +
401A GLY* 1.3 73.6 + - - +
403A ASN* 1.4 101.1 + - - +
404A PHE* 3.3 7.3 + - - -
424A GLY* 3.4 9.8 + - - +
425A GLU* 3.5 34.9 + - - +
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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