Contacts of the strand formed by residues 387 - 394 (chain A) in PDB entry 1SLL
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 387 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU* 3.7 35.9 - - + -
306A ILE* 4.0 22.0 - - + -
327A PHE* 4.2 4.3 - - + -
378A LEU* 5.5 0.4 - - + -
379A LEU 3.2 7.4 - - - +
380A GLU* 4.2 6.7 - - + -
385A LYS 4.1 7.6 - - - +
386A ARG* 1.3 78.4 - - - +
388A PHE* 1.3 62.4 + - - +
512A TYR* 3.2 6.8 - - - +
513A SER* 2.9 46.4 + - - +
516A GLU* 4.1 12.1 - - + +
517A GLY 4.1 17.9 - - - +
520A TRP* 3.7 24.6 - - + -
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Residues in contact with PHE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL 3.6 0.3 - - - +
378A LEU* 3.5 10.5 - - - +
379A LEU* 2.7 50.1 + - + +
381A ASP* 3.9 16.2 - - + -
386A ARG* 3.7 40.4 - - + -
387A ILE* 1.3 75.9 - - - +
389A LEU* 1.3 61.1 + - - +
390A PHE* 3.5 26.4 - + + -
510A MET* 3.4 25.1 - - + -
511A ARG 3.5 5.6 - - - +
512A TYR* 3.8 12.6 - + + -
520A TRP* 4.3 3.1 - - - -
556A LEU* 4.0 13.0 - - + -
576A HIS 3.4 25.1 - - - -
577A GLY* 3.9 15.7 - - - -
580A TRP* 4.9 0.4 - + - -
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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
----------------------------------------------------------
308A ALA* 4.3 4.0 - - + -
325A ILE* 4.0 15.7 - - + -
327A PHE* 5.4 3.6 - - + -
343A PRO* 3.7 32.5 - - + -
344A LEU* 3.8 24.4 - - + +
376A PRO* 4.0 18.4 - - + -
377A VAL 3.5 12.3 - - - +
378A LEU* 3.8 15.3 - - + -
388A PHE* 1.3 74.4 - - - +
390A PHE* 1.3 70.2 + - - +
510A MET* 3.0 25.3 - - - +
511A ARG* 3.0 12.2 + - + +
520A TRP* 3.7 22.6 - - + -
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Residues in contact with PHE 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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344A LEU* 4.6 0.7 - - - -
375A ASP 4.3 0.2 - - - -
376A PRO* 3.2 5.2 - - - +
377A VAL* 2.9 52.7 + - + -
379A LEU* 4.2 13.0 - - + -
388A PHE* 3.5 27.6 - + + -
389A LEU* 1.3 77.7 - - - +
391A ALA* 1.3 62.6 + - - +
509A ALA 3.2 8.5 - - - +
510A MET* 3.4 30.3 - - + -
526A VAL* 5.3 1.1 - - + -
539A VAL* 4.6 11.9 - - + -
558A VAL* 3.6 18.8 - - + -
571A MET* 3.4 30.1 - - + -
580A TRP* 3.6 36.8 - + - -
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Residues in contact with ALA 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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325A ILE* 3.8 19.5 - - + -
344A LEU* 3.7 22.0 - - + +
373A TYR* 4.5 2.9 - - + -
374A ILE 3.8 4.7 - - - +
375A ASP 3.2 15.3 - - - +
376A PRO* 4.4 0.4 - - + -
390A PHE* 1.3 78.2 - - - +
392A ASP* 1.3 69.1 + - - +
508A LEU* 4.0 2.9 - - - +
509A ALA* 3.1 30.1 + - - +
539A VAL* 4.7 5.7 - - - +
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Residues in contact with ASP 392 (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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372A SER 3.9 0.2 - - - +
373A TYR* 3.1 8.7 - - - -
374A ILE* 2.8 57.1 + - + +
375A ASP* 3.8 16.5 + - - +
391A ALA* 1.3 73.1 - - - +
393A LEU* 1.3 60.2 + - - +
394A MET* 4.0 12.6 + - + +
506A ASN* 4.5 0.4 - - - +
507A TYR 3.6 7.6 - - - +
508A LEU* 3.9 5.1 - - - +
538A VAL* 3.2 27.8 - - + +
539A VAL* 3.0 29.6 + - - +
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Residues in contact with LEU 393 (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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346A PHE* 3.2 27.6 - - + -
372A SER 3.7 2.5 - - - -
373A TYR* 3.5 33.0 - - + +
391A ALA 3.7 0.4 + - - -
392A ASP* 1.3 72.5 - - - +
394A MET* 1.3 71.0 + - - +
395A PRO* 3.7 2.9 - - - +
494A PHE* 3.8 37.0 - - + -
506A ASN* 3.6 4.2 - - - -
507A TYR* 2.9 50.2 + - + +
509A ALA* 4.0 17.5 - - + -
523A LEU* 4.5 5.2 - - + -
525A ILE* 4.5 8.1 - - + -
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Residues in contact with MET 394 (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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319A SER* 3.7 17.7 - - - +
371A ALA* 3.3 3.6 - - - +
372A SER* 2.8 46.5 + - - +
374A ILE* 3.9 14.8 - - + -
392A ASP* 4.0 20.0 - - + +
393A LEU* 1.3 77.5 - - - +
395A PRO* 1.3 68.0 - - + +
398A ILE* 3.3 25.1 - - - +
399A GLY* 4.0 16.6 - - - -
400A SER* 3.9 20.4 - - - +
506A ASN* 3.6 29.8 - - + -
538A VAL* 4.4 10.8 - - + -
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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