Contacts of the strand formed by residues 384 - 391 (chain A) in PDB entry 5JPM
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 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A THR* 4.8 5.8 - - - -
375A LYS* 4.2 18.4 - - + -
376A ARG* 4.2 15.3 - - - -
377A HIS 3.8 21.1 - - - -
378A LEU* 3.7 24.0 - - + -
379A VAL 5.5 0.9 - - - -
382A ALA 3.4 1.2 + - - -
383A PRO* 1.3 71.7 - - - +
385A LEU* 1.3 79.2 + - - +
386A LEU* 4.3 6.3 - - + -
433A ILE 3.5 1.9 - - - +
434A PRO 3.4 0.3 - - - -
435A ILE* 2.5 55.9 + - + +
437A ILE* 4.1 15.3 - - + -
444A LEU* 4.1 13.7 - - + -
446A LEU* 3.8 26.5 - - + -
460A LEU* 5.5 0.4 - - + -
462A VAL* 4.6 10.5 - - + -
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Residues in contact with LEU 385 (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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374A THR* 4.8 5.9 - - - +
375A LYS* 4.9 8.5 + - + +
383A PRO* 3.7 20.9 - - + +
384A PHE* 1.3 87.2 - - - +
386A LEU* 1.3 62.2 + - - +
387A GLN* 3.5 22.6 + - + +
432A SER* 5.5 7.9 - - - -
433A ILE 3.7 2.7 - - - +
434A PRO* 3.7 35.2 - - + -
475A ILE 5.4 7.2 - - - +
476A GLU* 5.9 7.0 - - + -
477A ARG 6.0 3.8 - - - +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.9 13.2 - - + -
374A THR* 3.6 22.4 - - + -
384A PHE* 3.6 5.6 + - + -
385A LEU* 1.3 68.8 - - - +
387A GLN* 1.3 59.9 + - - +
388A ALA* 4.5 15.9 - - + -
403A VAL* 5.5 0.7 - - + -
405A VAL* 4.3 16.8 - - + -
431A VAL* 3.7 3.5 - - + +
432A SER* 3.3 3.1 + - - -
433A ILE* 2.8 65.1 + - + +
435A ILE* 4.1 14.6 - - + -
446A LEU* 4.0 19.5 - - + -
448A VAL* 4.2 20.9 - - + -
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Residues in contact with GLN 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASP 4.2 0.2 - - - +
371A LEU* 3.7 9.3 - - - +
373A LYS* 3.3 55.5 - - + +
374A THR* 3.2 25.6 + - - +
375A LYS* 5.5 4.5 - - - +
385A LEU* 3.5 21.5 + - + +
386A LEU* 1.3 75.5 - - - +
388A ALA* 1.3 61.1 + - - +
431A VAL 3.3 9.1 + - - +
432A SER* 4.5 9.1 - - - -
477A ARG* 5.5 3.8 - - - +
480A SER* 3.6 21.3 + - - -
558A LEU* 5.0 11.3 - - - +
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Residues in contact with ALA 388 (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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369A LEU* 4.0 18.4 - - + -
370A ASP 3.2 10.3 - - - +
371A LEU* 3.8 15.7 - - + -
373A LYS* 4.5 2.6 - - - +
386A LEU* 4.5 6.7 - - + -
387A GLN* 1.3 75.4 - - - +
389A LEU* 1.3 62.1 + - - +
390A VAL* 4.3 0.9 - - + -
403A VAL* 5.3 0.4 - - + -
429A GLY 4.0 0.2 - - - +
430A GLN* 3.6 7.5 - - - +
431A VAL* 3.0 48.2 + - + +
448A VAL* 5.1 2.9 - - + -
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Residues in contact with LEU 389 (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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368A SER 3.5 2.4 - - - +
369A LEU* 3.5 1.5 - - - -
370A ASP* 2.7 51.0 + - + +
373A LYS* 4.0 8.1 - - - +
388A ALA* 1.3 75.5 - - - +
390A VAL* 1.3 67.3 + - - +
391A ARG* 3.5 41.2 + - + +
396A SER* 4.5 7.0 - - - +
428A SER 3.3 26.0 - - - +
429A GLY 3.3 13.2 - - - +
430A GLN* 3.3 28.7 - - - +
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Residues in contact with VAL 390 (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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367A PHE* 3.9 29.4 - - + -
368A SER 3.3 5.8 - - - +
369A LEU* 3.7 23.1 - - + -
388A ALA* 5.3 2.0 - - + -
389A LEU* 1.3 78.8 - - - +
391A ARG* 1.3 62.3 + - - +
396A SER 3.0 12.6 - - - +
398A ALA* 3.2 28.0 + - + +
401A ILE* 4.3 11.4 - - + -
403A VAL* 4.9 2.9 - - + -
425A THR* 3.8 25.6 - - + -
429A GLY 3.1 10.3 + - - +
431A VAL* 5.6 0.2 - - + -
450A ALA* 4.0 13.5 - - + -
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Residues in contact with ARG 391 (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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367A PHE* 3.2 8.1 - - - +
368A SER* 2.9 47.3 + - - +
370A ASP* 3.2 30.3 + - - +
389A LEU* 3.5 26.9 - - + +
390A VAL* 1.3 75.1 - - - +
392A GLU* 1.3 60.4 + - - +
393A MET* 3.5 5.2 - - - +
395A GLY 3.9 5.6 - - - +
396A SER* 2.9 44.8 + - - +
398A ALA* 4.2 2.9 - - - -
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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