Contacts of the strand formed by residues 276 - 283 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G ARG* 2.4 52.3 + - + +
242G THR* 4.2 10.3 - - - +
246G SER* 3.5 5.2 - - - -
274G HIS* 3.0 26.6 - - - -
275G TYR* 1.3 76.4 - - - +
277G GLU* 1.3 74.3 + - + +
278G CYS* 3.3 4.1 + - - -
291G CYS* 3.5 2.3 - - - +
292G ARG* 3.0 40.0 + - + +
294G ASN* 3.4 13.9 - - - +
806G G39 3.4 21.6 - - + +
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Residues in contact with GLU 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G THR 4.0 12.9 + - - +
226G GLN 3.2 19.5 - - - +
227G GLU* 4.0 15.0 - - + +
276G GLU* 1.3 81.9 - - + +
278G CYS* 1.3 60.2 + - - +
279G SER* 3.7 1.2 + - - -
291G CYS* 4.6 3.9 - - - -
292G ARG* 2.6 35.1 + - - -
350G LYS* 2.9 34.2 + - + +
351G GLY 4.6 1.2 - - - +
406G TYR* 2.5 36.8 + - - -
806G G39 3.7 23.5 + - + +
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Residues in contact with CYS 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G GLN* 3.1 22.5 + - + +
228G SER* 2.9 17.0 + - - -
240G VAL* 3.9 34.3 - - + -
275G TYR* 4.3 10.5 - - - -
276G GLU* 4.6 2.9 - - - -
277G GLU* 1.3 75.7 - - - +
279G SER* 1.3 59.6 + - - +
280G CYS* 3.9 18.2 - - - -
289G CYS* 4.4 0.9 - - - -
290G VAL 3.9 0.2 - - - -
291G CYS* 2.0 49.6 - - - -
303G VAL* 5.1 0.4 - - - -
350G LYS* 3.4 0.2 + - - -
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Residues in contact with SER 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G SER* 3.8 5.6 + - - -
278G CYS* 1.3 70.3 - - - +
280G CYS* 1.3 62.0 + - - +
281G TYR* 4.2 3.3 + - - -
288G THR 3.6 1.9 - - - +
289G CYS* 3.4 0.9 - - - -
290G VAL* 3.0 31.4 + - - +
350G LYS* 3.2 16.3 + - - -
351G GLY 2.7 27.0 + - - -
352G PHE* 3.7 16.6 - - - -
353G SER 5.6 0.2 - - - +
408G GLY* 3.7 9.7 - - - -
409G SER* 3.8 15.7 + - - -
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Residues in contact with CYS 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G GLN* 3.7 23.1 + - - +
229G GLU* 3.9 19.9 + - - +
230G CYS 4.3 1.9 - - - +
231G ALA* 3.9 14.9 - - + +
238G PHE 5.7 1.3 - - - +
239G THR* 5.5 2.5 - - - -
240G VAL* 4.0 8.1 - - - -
278G CYS* 4.0 9.9 - - - -
279G SER* 1.3 73.5 - - - +
281G TYR* 1.3 61.0 + - - +
287G ILE* 3.7 13.0 - - + -
288G THR 3.2 3.4 - - - -
289G CYS* 2.0 47.1 - - - -
305G PHE* 5.6 0.2 - - - -
409G SER* 4.2 5.8 + - - -
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Residues in contact with TYR 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LEU* 3.6 29.2 - - + -
229G GLU* 5.7 0.2 - - - +
231G ALA* 4.1 3.6 - - - -
279G SER 4.6 2.9 - - - -
280G CYS* 1.3 75.7 - - - +
282G PRO* 1.3 81.6 - - + +
283G ASN* 4.2 9.2 - - + -
286G GLU 4.0 0.2 - - - +
287G ILE* 3.5 1.7 - - - -
288G THR* 2.9 67.5 + - + +
290G VAL* 5.0 1.8 - - + -
353G SER 3.4 20.8 + - - -
354G PHE* 3.7 25.3 - + + -
355G LYS* 3.0 30.9 + - - +
383G TRP* 5.6 0.2 - - - -
409G SER* 4.4 9.2 - - - +
411G VAL* 3.9 16.2 - - + -
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Residues in contact with PRO 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G GLY 5.0 0.4 - - - +
91G LEU* 4.2 0.2 - - - +
229G GLU* 5.7 0.7 - - - +
231G ALA* 3.9 15.7 - - + -
232G CYS 3.9 4.0 - - - +
233G VAL* 3.7 28.7 - - + -
280G CYS 4.7 0.2 - - - +
281G TYR* 1.3 91.6 - - + +
283G ASN* 1.3 62.9 + - - +
286G GLU 3.5 5.4 - - - +
287G ILE* 4.5 2.5 - - + -
411G VAL* 3.8 15.5 - - + -
412G HIS* 3.6 31.2 - - - +
418G ILE* 3.3 25.6 - - + +
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Residues in contact with ASN 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G SER 4.0 3.4 - - - -
90G SER* 3.5 8.4 + - - +
91G LEU* 2.8 48.3 - - + +
281G TYR* 4.2 16.4 - - + -
282G PRO* 1.3 74.3 - - - +
284G ALA* 1.3 79.3 + - - +
285G GLY 3.2 1.7 - - - +
286G GLU* 2.7 29.3 + - - +
288G THR* 5.2 4.5 - - - +
355G LYS 5.6 1.7 + - - -
418G ILE* 4.7 0.2 - - - -
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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