Contacts of the strand formed by residues 388 - 395 (chain A) in PDB entry 5UMS
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 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A ARG* 4.4 3.5 - - - +
382A GLY* 3.2 21.4 + - - +
384A THR* 5.2 0.5 - - - -
385A THR* 2.9 37.1 + - - +
386A THR* 3.2 0.8 - - - -
387A ARG* 1.3 79.9 + - - +
389A PHE* 1.3 64.7 + - - +
405A SER* 3.9 23.2 + - - -
406A ILE 3.1 14.4 - - - -
407A GLU* 4.7 1.1 - - - -
408A ARG* 4.1 2.2 - - - +
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Residues in contact with PHE 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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379A PHE* 3.7 29.4 - + + -
380A ALA 3.2 16.2 - - - +
381A ARG* 4.7 1.8 - - - -
382A GLY 3.9 2.5 - - - +
388A SER* 1.3 74.9 - - - +
390A ASP* 1.3 78.2 + - - +
391A PHE* 4.3 2.9 - - + -
405A SER 3.4 0.6 + - - -
406A ILE* 2.9 67.8 + - + +
407A GLU 3.4 22.2 - - - -
408A ARG* 4.1 16.2 - - - +
410A GLU 4.3 0.4 - - - -
411A TYR* 3.7 40.2 - + + -
414A LEU* 4.2 11.9 - - + -
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Residues in contact with ASP 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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378A ASN 3.6 1.4 - - - +
379A PHE* 3.5 4.7 - - - -
380A ALA* 2.8 46.3 + - + +
381A ARG 4.4 3.0 - - - +
382A GLY* 4.1 18.5 - - - -
383A THR* 5.1 2.1 + - - -
389A PHE* 1.3 78.2 - - - +
391A PHE* 1.3 59.6 + - - +
392A GLU* 3.9 4.4 - - + +
402A THR* 4.0 18.7 - - + +
403A PHE 3.5 3.6 - - - -
404A SER* 3.1 28.1 - - - -
405A SER* 3.2 9.4 + - - -
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Residues in contact with PHE 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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352A LEU* 4.1 15.0 - - + -
359A PHE* 3.8 27.6 - + - -
377A VAL* 3.7 31.0 - - + -
378A ASN 3.6 5.2 - - - -
379A PHE* 3.7 34.1 - + - -
389A PHE* 4.3 2.6 + - + -
390A ASP* 1.3 71.6 - - - +
392A GLU* 1.3 63.2 + - - +
393A ILE* 3.8 18.2 - - + -
402A THR* 3.6 1.1 - - - -
403A PHE* 2.8 44.3 + + + +
406A ILE* 3.8 20.2 - - + -
414A LEU* 3.8 15.7 - - + -
418A VAL* 3.8 20.0 - - + -
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Residues in contact with GLU 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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376A PHE* 6.1 1.9 - - + -
377A VAL* 3.1 8.7 - - - +
378A ASN* 2.9 65.5 + - + +
380A ALA* 4.1 13.9 - - - +
390A ASP* 4.9 6.7 - - + +
391A PHE* 1.3 76.1 - - - +
393A ILE* 1.3 61.6 + - - +
400A GLN* 4.8 20.1 + - + +
401A TYR 3.4 5.2 - - - +
402A THR* 3.6 27.0 + - + +
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Residues in contact with ILE 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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352A LEU* 5.9 0.2 - - + -
359A PHE* 3.6 31.9 - - + -
369A ILE* 4.2 23.3 - - + -
374A ILE* 3.7 33.0 - - + -
376A PHE 3.8 2.7 - - - +
377A VAL* 4.0 5.4 - - + -
391A PHE* 3.8 22.7 - - + -
392A GLU* 1.3 79.2 - - - +
394A GLU* 1.3 65.3 + - - +
395A THR* 4.7 2.0 - - + -
399A THR 3.7 1.2 - - - +
400A GLN* 3.3 6.4 - - - +
401A TYR* 2.8 41.6 + - + +
403A PHE* 3.9 20.2 - - + -
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Residues in contact with GLU 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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374A ILE* 3.7 2.9 - - - +
375A SER* 2.8 26.3 + - - -
376A PHE* 2.9 57.2 + - + +
392A GLU 4.2 0.6 - - - -
393A ILE* 1.3 74.5 - - - +
395A THR* 1.3 72.0 + - - +
398A GLY* 4.0 13.6 - - - -
399A THR 3.4 12.7 + - - +
400A GLN* 4.0 19.0 - - + +
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Residues in contact with THR 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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369A ILE* 4.3 18.6 - - + -
373A GLU* 3.1 18.8 - - + +
375A SER* 4.0 4.0 - - - -
393A ILE* 4.7 2.7 - - + -
394A GLU* 1.3 88.4 - - - +
396A LYS* 1.3 65.6 + - - +
397A GLN* 3.6 8.0 + - - +
398A GLY* 3.2 14.7 + - - -
399A THR* 2.8 34.0 + - - +
401A TYR* 3.7 31.4 - - + -
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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