Contacts of the strand formed by residues 392 - 403 (chain B) in PDB entry 2HU4
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 VAL 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASN 5.1 6.7 - - - +
361B TRP* 4.5 13.5 - - + -
376B MET 4.4 0.2 - - - -
377B ILE* 3.3 8.9 - - - +
378B TRP* 2.8 46.3 + - + -
390B PHE* 3.6 2.9 - - - -
391B SER* 1.3 92.0 - - - +
394B LYS* 1.3 82.7 + - - +
395B GLN* 5.3 3.6 - - + +
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Residues in contact with LYS 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ARG* 4.9 3.6 - - - +
366B LYS* 3.8 11.9 - - - +
375B GLU* 2.9 39.8 + - + +
376B MET 3.1 5.6 - - - +
377B ILE* 3.8 18.8 - - + +
390B PHE* 3.8 23.3 - - + -
392B VAL* 1.3 85.0 - - - +
395B GLN* 1.3 63.4 + - - +
396B ASP* 4.1 10.1 - - - +
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Residues in contact with GLN 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY* 3.8 4.0 - - - -
97B TRP* 2.9 61.8 - - - +
361B TRP* 5.2 3.6 - - + -
375B GLU* 3.3 3.1 - - - -
376B MET* 2.8 42.1 + - + +
392B VAL* 5.3 4.7 - - + +
394B LYS* 1.3 75.6 - - - +
396B ASP* 1.3 69.4 + - - +
397B ILE* 3.3 12.3 - - + +
446B PHE* 5.5 2.4 - - - -
453B THR* 3.6 12.6 + - - -
454B VAL 3.0 17.4 - - - +
455B GLY* 3.7 17.7 - - - +
458B TRP* 5.7 0.2 - - - -
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Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 3.0 28.5 + - - +
374B PHE 4.2 4.0 - - - -
394B LYS* 4.1 13.9 - - - +
395B GLN* 1.3 75.2 - - - +
397B ILE* 1.3 65.1 + - - +
398B VAL 4.9 3.6 - - - +
399B ALA* 6.4 0.2 - - - -
455B GLY* 3.1 13.3 - - - -
456B TRP* 3.0 38.2 + - - +
458B TRP* 4.2 2.8 - - - -
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Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TRP* 5.5 0.9 - - + -
374B PHE* 3.1 31.2 + - + +
376B MET* 4.0 16.8 - - + +
395B GLN* 3.3 28.3 - - + +
396B ASP* 1.3 82.4 - - - +
398B VAL* 1.3 81.5 + - + +
422B PHE* 4.1 13.5 - - + -
424B VAL* 4.4 2.5 - - + -
444B ILE* 3.7 17.5 - - + -
446B PHE* 3.9 28.5 - - + -
456B TRP 3.4 7.1 - - - +
457B SER* 3.5 0.2 - - - -
458B TRP* 3.1 26.5 + - + +
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 3.0 14.7 - - - +
373B GLY* 4.0 3.1 - - - -
374B PHE* 3.0 35.8 + - + +
396B ASP* 5.6 1.8 - - - -
397B ILE* 1.3 99.2 - - + +
399B ALA* 1.3 71.9 + - - +
402B ASP* 3.9 26.2 - - + +
403B TRP 4.4 8.1 - - - +
404B SER* 5.0 2.0 - - - -
424B VAL* 5.3 0.4 - - + -
426B LEU* 4.5 8.5 - - + -
444B ILE* 3.8 15.7 - - + -
456B TRP 3.8 1.3 + - - -
457B SER* 3.8 8.7 - - - +
458B TRP 4.0 8.5 - - - +
459B PRO* 4.4 7.2 - - + -
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B LYS* 4.2 3.4 - - - +
373B GLY* 3.4 3.7 - - - -
396B ASP* 6.4 0.4 - - - -
398B VAL* 1.3 73.7 - - - +
400B ILE* 1.3 60.7 + - - +
401B THR* 3.0 16.8 - - - +
402B ASP* 2.8 35.0 + - - +
456B TRP 4.9 0.2 + - - -
457B SER* 3.1 25.3 + - - +
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Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 3.7 40.0 - - + +
367B SER* 4.4 20.0 - - - +
372B SER* 3.3 19.2 - - - -
373B GLY* 4.2 8.7 - - - +
399B ALA* 1.3 72.9 - - - +
401B THR* 1.3 62.3 + - + +
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Residues in contact with THR 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B SER* 5.5 0.2 - - - -
399B ALA* 3.9 13.0 - - - +
400B ILE* 1.3 81.2 - - + +
402B ASP* 1.3 67.9 + - - +
403B TRP* 4.4 2.6 + - - -
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Residues in contact with ASP 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B SER* 3.5 4.9 - - - -
373B GLY* 2.9 29.1 + - - -
398B VAL* 3.9 8.1 - - + +
399B ALA* 2.8 14.0 + - - +
400B ILE 3.2 0.2 - - - -
401B THR* 1.3 91.1 + - - +
403B TRP* 1.3 63.9 + - - +
457B SER* 4.0 6.8 + - - -
459B PRO* 3.4 40.7 - - + +
461B GLY 5.8 0.3 + - - -
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Residues in contact with TRP 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B SER* 4.2 9.4 - - - -
371B ARG* 3.7 10.3 - - + -
372B SER* 3.5 24.5 - - - -
398B VAL* 4.4 4.7 - - - +
401B THR 5.8 2.4 + - - -
402B ASP* 1.3 78.5 + - - +
404B SER* 1.3 60.6 + - - +
426B LEU* 3.9 18.9 - - - +
427B ILE 3.5 21.3 - - - +
428B ARG* 3.7 31.0 - - - -
432B LYS* 3.5 49.1 - - + -
433B GLU* 3.3 27.0 + - + +
460B ASP* 5.1 5.4 + - + +
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Residues in contact with SER 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B THR* 4.0 6.8 - - - +
371B ARG* 2.8 27.6 + - - +
373B GLY* 3.0 32.3 + - - -
374B PHE* 4.7 3.7 - - - -
398B VAL* 5.0 2.2 - - - -
402B ASP 3.6 0.4 + - - -
403B TRP* 1.3 73.7 - - - +
405B GLY* 1.3 69.7 + - - +
424B VAL* 4.6 13.0 - - - -
425B GLU 3.1 11.7 - - - -
426B LEU* 4.2 7.2 - - - +
427B ILE* 3.0 25.2 + - - +
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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