Contacts of the strand formed by residues 276 - 283 (chain H) 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 GLU 276 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224H ARG* 2.3 55.8 + - + +
242H THR* 4.2 9.6 - - - +
246H SER* 3.9 3.9 - - - -
274H HIS* 3.0 29.1 - - - -
275H TYR* 1.3 78.0 - - - +
277H GLU* 1.3 78.3 + - + +
278H CYS* 3.2 4.8 + - - -
291H CYS* 4.1 3.2 - - - +
292H ARG* 2.9 40.3 + - + +
294H ASN* 3.6 12.8 - - - +
807H G39 3.5 18.8 - - + +
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Residues in contact with GLU 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H THR 4.0 13.6 + - - +
226H GLN 3.3 19.5 - - - +
227H GLU* 4.1 11.5 - - + +
242H THR* 5.4 0.2 + - - -
276H GLU* 1.3 85.4 - - + +
278H CYS* 1.3 59.0 + - - +
279H SER* 3.5 1.6 + - - -
291H CYS* 4.6 1.9 - - - -
292H ARG* 2.7 30.6 + - - -
350H LYS* 2.8 47.5 + - + +
351H GLY 4.6 2.1 + - - +
406H TYR* 2.5 32.4 + - - -
807H G39 3.6 22.0 + - + +
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Residues in contact with CYS 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H THR 5.5 0.2 - - - -
226H GLN* 3.2 21.1 - - + +
228H SER* 3.0 15.2 + - - -
240H VAL* 4.1 31.4 - - + -
275H TYR* 4.2 13.0 - - - -
276H GLU* 3.2 4.1 + - - -
277H GLU* 1.3 77.3 - - - +
279H SER* 1.3 59.0 + - - +
280H CYS* 3.7 7.9 - - - -
289H CYS* 4.0 13.2 - - + -
291H CYS* 2.0 48.2 - - - -
303H VAL* 5.2 1.1 - - - -
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Residues in contact with SER 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228H SER* 3.7 6.2 + - - -
277H GLU 3.5 0.4 + - - -
278H CYS* 1.3 72.0 - - - +
280H CYS* 1.3 60.6 + - - +
281H TYR* 4.6 4.2 - - - -
288H THR 3.8 1.9 - - - +
289H CYS* 3.4 0.7 - - - -
290H VAL* 2.8 32.4 + - - +
350H LYS* 3.2 15.9 + - - -
351H GLY 2.9 26.2 + - - -
352H PHE* 3.6 16.9 - - - +
353H SER 5.4 0.2 - - - +
408H GLY* 3.4 13.5 - - - -
409H SER* 3.7 12.9 + - - -
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Residues in contact with CYS 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H GLN* 4.1 20.9 + - - +
229H GLU* 4.0 21.1 + - - +
231H ALA* 4.5 12.6 - - + +
238H PHE 5.6 1.3 - - - +
239H THR* 5.4 2.0 - - - -
240H VAL* 3.9 15.0 - - - -
278H CYS* 3.7 9.2 + - - -
279H SER* 1.3 75.6 - - - +
281H TYR* 1.3 63.9 + - - +
287H ILE* 3.8 11.2 - - + -
288H THR 3.3 4.9 - - - -
289H CYS* 2.0 46.0 - - - -
305H PHE* 5.3 0.7 - - - -
409H SER* 3.8 7.0 + - - -
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Residues in contact with TYR 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H LEU* 3.5 26.2 - - + -
231H ALA* 4.1 5.6 - - - -
279H SER 4.6 4.3 - - - -
280H CYS* 1.3 77.9 - - - +
282H PRO* 1.3 83.1 - - + +
283H ASN* 4.0 13.2 - - + -
287H ILE* 3.6 1.2 - - - -
288H THR* 3.0 62.5 + - + +
290H VAL* 5.0 1.6 - - + -
353H SER 3.4 22.2 - - - -
354H PHE* 3.8 25.6 - + + -
355H LYS* 2.9 36.1 + - - +
409H SER* 4.6 6.7 - - - +
411H VAL* 4.1 13.0 - - + -
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Residues in contact with PRO 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H GLY 5.2 0.7 - - - +
91H LEU* 4.3 0.3 - - - +
229H GLU* 5.5 1.3 - - - +
230H CYS 5.7 0.2 - - - +
231H ALA* 3.7 17.7 - - + -
232H CYS 3.9 6.5 - - - +
233H VAL* 3.9 24.9 - - + -
281H TYR* 1.3 92.2 - - + +
283H ASN* 1.3 65.8 + - - +
286H GLU 3.5 6.5 - - - +
287H ILE* 4.6 1.3 - - + -
411H VAL* 3.7 16.8 - - + -
412H HIS* 3.8 30.3 - - - +
418H ILE* 3.7 22.8 - - + +
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Residues in contact with ASN 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H GLY 4.7 0.2 + - - -
89H SER 4.2 4.0 - - - -
90H SER* 3.5 8.3 + - - +
91H LEU* 2.9 45.7 - - - +
281H TYR* 4.0 17.3 - - + +
282H PRO* 1.3 78.2 - - - +
284H ALA* 1.3 79.6 + - - +
285H GLY 3.1 2.3 - - - +
286H GLU* 2.7 30.6 + - - +
288H THR* 5.3 4.5 - - - +
355H LYS 5.7 1.1 + - - -
418H ILE* 4.3 1.1 - - - +
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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