Contacts of the strand formed by residues 392 - 403 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C ASN 5.2 8.1 - - - +
361C TRP* 4.6 13.0 - - + -
376C MET 4.4 0.7 - - - -
377C ILE* 3.4 9.7 - - - +
378C TRP* 3.0 44.3 + - + -
390C PHE* 3.9 2.8 - - - -
391C SER* 1.3 89.1 - - - +
394C LYS* 1.3 79.2 + - - +
395C GLN* 5.4 3.4 - - + +
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Residues in contact with LYS 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C ARG* 4.7 4.2 - - - +
366C LYS* 4.4 1.1 - - - +
375C GLU* 2.8 42.3 + - + +
376C MET 3.3 7.2 - - - +
377C ILE* 3.8 15.5 - - + +
390C PHE* 4.2 24.1 - - + -
392C VAL* 1.3 83.9 - - - +
395C GLN* 1.3 62.5 + - - +
396C ASP* 4.1 18.5 + - - +
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Residues in contact with GLN 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C GLY* 3.7 4.6 - - - -
97C TRP* 2.9 64.9 - - - +
361C TRP* 5.0 4.4 - - + -
375C GLU* 3.3 1.4 - - - -
376C MET* 2.7 44.5 + - + +
392C VAL* 4.8 4.7 - - + +
394C LYS* 1.3 75.1 - - - +
396C ASP* 1.3 75.0 + - - +
397C ILE* 3.3 9.8 - - + +
446C PHE* 5.4 0.9 - - - -
453C THR* 3.6 13.4 + - - -
454C VAL* 3.3 15.0 - - - +
455C GLY* 3.9 12.8 - - - +
458C TRP* 5.9 0.2 - - - -
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Residues in contact with ASP 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C LYS* 2.6 32.5 + - - +
374C PHE 4.1 3.8 - - - -
375C GLU* 4.4 0.2 - - - +
394C LYS* 4.1 17.1 + - - +
395C GLN* 1.3 73.7 - - - +
397C ILE* 1.3 67.2 - - - +
398C VAL 5.1 1.3 - - - +
399C ALA* 6.0 0.7 - - - +
455C GLY* 3.3 11.9 - - - -
456C TRP* 3.3 34.2 + - - +
458C TRP* 4.3 2.1 - - - -
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Residues in contact with ILE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C TRP* 5.3 0.7 - - + -
374C PHE* 3.0 31.2 + - + +
376C MET* 4.0 17.7 - - + +
395C GLN* 3.3 28.0 - - + +
396C ASP* 1.3 96.0 - - - +
398C VAL* 1.3 75.6 + - + +
422C PHE* 4.1 11.2 - - + -
424C VAL* 4.5 1.1 - - + -
444C ILE* 3.9 17.0 - - + -
446C PHE* 3.7 30.5 - - + -
456C TRP 3.3 8.3 - - - +
458C TRP* 3.0 31.9 + - + +
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Residues in contact with VAL 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C LYS* 3.0 9.7 - - - +
373C GLY* 2.8 12.6 - - - -
374C PHE* 2.6 41.1 + - + +
396C ASP* 5.8 1.1 - - - -
397C ILE* 1.3 97.5 - - + +
399C ALA* 1.3 71.7 + - - +
402C ASP* 3.9 20.0 - - + +
403C TRP 4.3 9.6 - - - +
404C SER* 4.8 1.8 - - - -
424C VAL* 5.2 1.1 - - + -
426C LEU* 4.3 9.6 - - + -
444C ILE* 3.9 7.6 - - + -
456C TRP 5.0 0.7 - - - -
457C SER* 3.9 3.8 - - - +
458C TRP 3.7 20.0 - - - +
459C PRO* 4.6 6.3 - - + -
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Residues in contact with ALA 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C LYS* 4.1 6.3 - - - +
373C GLY* 3.1 12.2 - - - -
396C ASP* 6.4 0.4 - - - -
398C VAL* 1.3 75.2 - - - +
400C ILE* 1.3 63.5 + - + +
401C THR* 3.0 19.7 - - + +
402C ASP* 3.0 18.3 + - - +
456C TRP 5.0 0.4 + - - -
457C SER* 3.0 28.0 + - - +
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Residues in contact with ILE 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C LYS* 3.7 39.4 - - + +
367C SER* 4.2 20.4 - - - +
372C SER* 3.4 17.6 + - - -
373C GLY* 4.1 8.1 - - - -
399C ALA* 1.3 72.8 - - + +
401C THR* 1.3 62.5 + - + +
402C ASP 3.2 2.2 + - - -
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Residues in contact with THR 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C SER* 5.6 0.2 - - - -
399C ALA* 3.7 12.7 - - + +
400C ILE* 1.3 81.8 - - + +
402C ASP* 1.3 74.9 + - - +
403C TRP* 5.8 1.7 - - - -
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Residues in contact with ASP 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C SER* 3.4 5.2 - - - -
373C GLY* 2.8 29.1 + - - -
398C VAL* 3.9 5.9 - - + +
399C ALA* 3.0 14.1 + - - +
400C ILE 3.2 0.4 - - - -
401C THR* 1.3 95.0 + - - +
403C TRP* 1.3 66.2 + - - +
457C SER* 4.7 0.7 + - - -
459C PRO* 3.4 39.6 - - + +
460C ASP 5.3 0.3 + - - -
461C GLY* 5.4 2.9 + - - -
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Residues in contact with TRP 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C SER* 4.2 13.7 - - - -
371C ARG* 3.5 22.7 - - + +
372C SER* 3.7 17.0 - - - -
398C VAL* 4.3 4.4 - - - +
401C THR 5.8 2.0 + - - -
402C ASP* 1.3 80.4 + - - +
404C SER* 1.3 59.4 + - - +
426C LEU* 3.5 18.7 - - - +
427C ILE 3.3 23.3 - - - +
428C ARG* 3.5 30.7 - - - +
432C LYS* 3.5 48.0 - - + -
433C GLU* 3.4 26.5 + - + +
460C ASP* 5.0 5.2 + - - +
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Residues in contact with SER 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C THR* 3.7 8.1 - - - +
371C ARG* 2.9 27.1 + - - +
373C GLY* 3.0 31.7 + - - -
374C PHE* 4.7 2.7 - - - -
398C VAL* 4.8 2.2 - - - -
403C TRP* 1.3 75.3 - - - +
405C GLY* 1.3 68.0 + - - -
424C VAL* 4.5 10.5 - - - -
425C GLU 3.0 11.9 - - - -
426C LEU* 3.8 10.5 - - - +
427C ILE* 3.0 27.0 + - - +
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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