Contacts of the strand formed by residues 276 - 283 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E ARG* 2.5 47.8 + - + +
242E THR* 4.3 9.4 - - + -
246E SER* 3.8 4.3 - - - -
274E HIS* 2.9 29.3 - - - -
275E TYR* 1.3 76.8 - - - +
277E GLU* 1.3 79.0 + - + +
278E CYS* 3.4 3.3 + - - -
291E CYS* 3.5 2.7 - - - +
292E ARG* 3.0 35.4 + - - +
294E ASN* 3.4 13.9 - - - +
804E G39 3.3 26.0 - - + +
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Residues in contact with GLU 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E ARG* 6.4 1.3 - - + -
225E THR 3.7 13.7 + - - +
226E GLN 3.3 19.7 - - - +
227E GLU* 3.8 16.7 - - + +
276E GLU* 1.3 82.5 - - + +
278E CYS* 1.3 62.9 + - - +
279E SER* 3.7 1.7 + - - -
291E CYS* 4.2 5.5 - - - -
292E ARG* 2.8 23.4 + - - -
350E LYS* 3.4 28.9 + - + +
351E GLY 4.7 0.9 - - - +
406E TYR* 2.4 44.8 + - - -
804E G39 3.7 22.9 + - + +
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Residues in contact with CYS 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E GLN* 3.1 24.8 - - + +
228E SER* 3.1 14.7 + - - -
240E VAL* 3.9 33.8 + - + +
275E TYR* 4.3 10.1 - - - -
276E GLU 3.4 3.1 + - - -
277E GLU* 1.3 75.0 - - - +
279E SER* 1.3 59.8 + - - +
280E CYS* 3.7 8.3 - - - -
289E CYS* 3.9 11.2 - - + -
291E CYS* 2.0 49.4 - - - -
303E VAL* 5.7 1.3 - - - -
350E LYS* 3.9 0.7 - - - -
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Residues in contact with SER 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E SER* 3.7 6.5 - - - -
277E GLU 3.7 0.2 + - - -
278E CYS* 1.3 72.4 - - - +
280E CYS* 1.3 60.5 + - - +
281E TYR* 4.2 3.5 + - - -
288E THR 3.8 0.9 - - - +
289E CYS* 3.2 1.9 - - - -
290E VAL* 3.1 28.3 + - - +
350E LYS* 3.3 15.0 + - - -
351E GLY 2.5 29.3 + - - -
352E PHE* 3.6 19.3 - - - +
408E GLY* 3.7 6.4 - - - -
409E SER* 3.7 18.2 + - - -
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Residues in contact with CYS 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E GLN* 3.5 24.9 + - - +
228E SER* 4.6 0.2 + - - -
229E GLU* 3.9 23.2 + - - +
231E ALA* 4.2 13.7 - - + +
238E PHE 5.2 3.1 - - - +
239E THR* 5.5 0.4 - - - -
240E VAL* 3.9 15.7 - - - -
278E CYS* 3.9 4.3 - - - -
279E SER* 1.3 74.6 - - - +
281E TYR* 1.3 60.9 + - - +
287E ILE* 3.7 12.3 - - + -
288E THR 3.3 3.6 - - - -
289E CYS* 2.0 46.0 - - - -
305E PHE* 5.5 0.9 - - - -
409E SER* 4.1 6.4 + - - +
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Residues in contact with TYR 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E LEU* 3.7 24.2 - - + -
231E ALA* 4.2 4.5 - - - -
279E SER 4.7 3.6 - - - -
280E CYS* 1.3 74.5 - - - +
282E PRO* 1.3 79.7 - - + +
283E ASN* 4.0 12.6 - - + -
286E GLU 4.0 0.2 - - - +
287E ILE* 3.6 1.6 - - - -
288E THR* 2.9 68.5 + - + +
290E VAL* 5.1 2.2 - - + -
353E SER 3.4 23.1 + - - -
354E PHE* 3.5 27.6 - + + -
355E LYS* 3.1 30.8 + - - +
383E TRP* 5.6 0.2 - - - -
409E SER* 4.3 9.4 - - - +
411E VAL* 3.8 15.7 - - + -
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Residues in contact with PRO 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E GLY 5.1 0.7 - - - +
91E LEU* 4.4 0.3 - - - +
229E GLU* 5.4 1.3 - - - +
231E ALA* 3.8 16.2 - - + -
232E CYS 3.9 5.8 - - - +
233E VAL* 3.8 26.2 - - + -
280E CYS 4.6 0.4 - - - +
281E TYR* 1.3 91.5 - - - +
283E ASN* 1.3 65.4 + - - +
286E GLU 3.7 6.3 - - - +
287E ILE* 4.6 1.8 - - - -
411E VAL* 3.5 19.3 - - + -
412E HIS* 3.8 28.7 - - - +
418E ILE* 3.9 24.9 - - + +
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Residues in contact with ASN 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E GLY 4.7 0.4 + - - -
89E SER 4.0 2.9 - - - -
90E SER* 3.3 9.5 + - - +
91E LEU* 2.6 49.7 - - - +
281E TYR* 4.0 16.2 - - + -
282E PRO* 1.3 78.4 - - - +
284E ALA* 1.3 77.3 + - - +
285E GLY 3.1 1.5 - - - +
286E GLU* 2.9 28.6 + - - +
288E THR* 5.3 3.6 - - - +
355E LYS 5.7 0.8 - - - +
418E ILE* 4.6 2.4 - - - +
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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