Contacts of the strand formed by residues 387 - 397 (chain A) in PDB entry 3SY7
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 SER 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A LYS* 3.8 21.4 - - - -
376A TYR 3.4 4.3 - - - -
377A VAL* 4.3 13.8 - - - +
385A ASP 3.9 6.5 - - - -
386A LEU* 1.3 76.5 - - - +
388A PHE* 1.3 65.2 + - - +
389A ARG* 4.8 2.3 + - - +
412A ILE 3.5 1.6 + - - +
413A VAL* 3.2 8.5 - - - +
414A ASP* 2.9 53.7 + - - +
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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
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374A ALA 3.8 0.7 - - - +
375A LYS* 3.3 6.1 - - - +
376A TYR* 2.8 58.6 + + + +
378A VAL* 4.6 8.5 - - + -
386A LEU* 3.5 37.0 - - + -
387A SER* 1.3 75.1 + - - +
389A ARG* 1.3 60.2 + - - +
390A ILE* 4.3 2.0 - - + -
411A LEU* 4.9 10.3 - - + -
412A ILE 3.7 2.5 - - - -
413A VAL* 3.7 31.4 - - + -
429A C8E 5.2 3.6 - - - -
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Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY 6.0 0.2 - - - -
130A SER* 3.2 25.7 + - - +
373A GLU* 3.0 34.5 + - + +
374A ALA 3.5 8.5 - - - +
375A LYS* 4.4 26.0 - - + +
387A SER* 5.1 3.8 - - - +
388A PHE* 1.3 75.1 - - - +
390A ILE* 1.3 64.7 + - - +
391A ARG* 3.7 24.5 - - + +
410A ARG 3.6 0.5 - - - +
411A LEU* 3.2 6.9 - - - +
412A ILE* 2.9 56.9 + - + +
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Residues in contact with ILE 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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372A LEU 5.2 0.9 - - - +
373A GLU* 3.2 7.1 - - - +
374A ALA* 2.9 44.8 + - + +
388A PHE* 4.3 1.5 - - + -
389A ARG* 1.3 73.9 - - - +
391A ARG* 1.3 70.0 + - - +
392A GLN* 4.5 4.9 - - + +
409A PHE* 3.6 36.8 - - + -
410A ARG 3.3 3.4 - - - +
411A LEU* 3.5 25.6 - - + -
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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
----------------------------------------------------------
130A SER* 3.3 30.5 + - - -
303A VAL 5.0 0.6 - - - -
304A GLN* 3.1 52.8 + - - +
337A ARG* 4.1 7.3 - - - +
372A LEU 3.6 4.0 - - - -
373A GLU* 2.7 31.1 + - - +
389A ARG* 3.7 32.9 - - + +
390A ILE* 1.3 81.6 - - - +
392A GLN* 1.3 59.9 + - - +
409A PHE* 3.6 0.5 - - - -
410A ARG* 2.9 64.8 + - + +
412A ILE* 4.6 13.0 - - + -
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Residues in contact with GLN 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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304A GLN* 3.5 2.6 - - - +
370A THR 3.9 0.4 - - - +
371A ASN* 3.2 4.0 - - - -
372A LEU* 2.8 47.0 + - + +
390A ILE* 4.2 4.4 - - + -
391A ARG* 1.3 74.1 - - - +
393A ALA* 1.3 80.7 + - - +
394A TRP* 3.3 50.5 - - + +
407A ASN* 4.5 4.2 - - - +
408A GLU 3.3 13.0 + - - +
409A PHE* 3.3 35.0 - - + +
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Residues in contact with ALA 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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304A GLN* 3.5 24.2 + - + +
305A TYR* 4.6 8.1 - - + -
369A GLU* 4.0 6.5 - - - +
370A THR 3.3 4.7 - - - -
371A ASN* 3.4 18.8 - - - +
392A GLN* 1.3 80.2 + - - +
394A TRP* 1.3 63.5 + - - +
395A HIS 4.2 0.7 - - - +
406A GLN 3.8 0.7 - - - +
407A ASN* 3.4 2.3 - - - -
408A GLU* 2.8 41.1 + - + +
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Residues in contact with TRP 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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368A HIS* 3.9 1.9 + - - +
369A GLU* 3.2 5.1 - - - -
370A THR* 2.9 68.8 + - + +
372A LEU* 4.3 25.1 - - + -
392A GLN* 3.3 42.0 - - + +
393A ALA* 1.3 72.1 - - - +
395A HIS* 1.3 60.8 + - - +
396A ARG* 4.1 15.1 + - + +
406A GLN 3.4 4.5 - - - -
407A ASN* 3.1 32.8 - - - +
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Residues in contact with HIS 395 (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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305A TYR* 3.6 22.1 - + + -
306A SER* 3.8 10.7 - - - -
367A HIS* 2.8 30.1 + - + -
368A HIS 3.5 10.1 - - - -
369A GLU* 3.4 27.6 - - + +
393A ALA 4.2 0.8 - - - -
394A TRP* 1.3 74.1 - - - +
396A ARG* 1.3 77.7 + - - +
397A ALA* 3.7 8.7 - - + -
401A GLN* 3.5 21.3 - - - -
403A GLU* 4.1 9.6 - - + -
404A GLY 2.7 27.9 + - - -
405A ASP* 3.2 1.9 - - - -
406A GLN* 2.8 31.9 + - + +
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Residues in contact with ARG 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A HIS* 3.0 5.2 - - - +
368A HIS* 2.8 65.5 + - + +
394A TRP* 4.1 14.5 - - + +
395A HIS* 1.3 96.5 + - - +
397A ALA* 1.3 61.4 + - - +
405A ASP* 3.3 22.5 + - - +
406A GLN 3.2 11.3 + - - +
407A ASN* 2.9 38.6 + - - +
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Residues in contact with ALA 397 (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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366A LYS 3.4 6.3 - - - +
367A HIS* 3.6 9.2 - - + +
395A HIS* 3.7 7.0 - - + -
396A ARG* 1.3 76.9 - - - +
398A ASN* 1.3 68.0 + - - +
401A GLN* 3.2 27.4 - - + +
404A GLY* 4.0 12.7 - - - +
405A ASP* 3.0 17.6 + - - +
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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