Contacts of the strand formed by residues 251 - 258 (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 SER 251 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218G TRP* 3.1 28.5 + - - -
219G ARG* 3.9 17.1 + - - -
241G MET 3.9 0.3 - - - +
242G THR* 3.4 1.2 - - - +
243G ASP 3.1 36.4 + - - -
250G ALA* 1.3 74.9 - - - +
252G TYR* 1.3 68.2 + - - +
267G GLU* 2.9 29.1 + - - +
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Residues in contact with TYR 252 (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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240G VAL* 5.4 4.0 - - + -
241G MET 3.5 5.2 - - - +
242G THR* 3.7 14.1 - - + +
249G GLN* 3.9 1.9 + - - -
250G ALA* 3.0 52.1 + - + +
251G SER* 1.3 81.7 + - - +
253G LYS* 1.3 59.1 + - - +
267G GLU* 3.2 8.0 - - - +
268G LEU* 2.7 55.3 + - + -
270G ALA* 4.1 20.4 - - + -
273G TYR 2.6 29.6 + - - -
274G HIS* 3.3 7.7 - + - -
275G TYR* 3.4 48.9 - + + -
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Residues in contact with LYS 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G TRP* 3.4 60.3 - - + +
240G VAL* 3.5 7.7 - - - +
241G MET 2.9 31.6 + - - -
252G TYR* 1.3 79.8 - - - +
254G ILE* 1.3 64.0 - - - +
255G PHE* 3.8 23.7 - - + -
265G SER* 5.2 8.6 + - - +
266G VAL 3.2 7.0 - - - +
267G GLU* 3.7 32.5 - - + +
268G LEU* 4.5 0.7 - - - +
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Residues in contact with ILE 254 (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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239G THR 3.6 8.1 - - - +
240G VAL* 5.1 5.4 - - + -
253G LYS* 1.3 76.7 - - - +
255G PHE* 1.3 67.0 + - - +
265G SER* 3.1 7.4 - - - -
266G VAL* 2.7 38.7 + - + +
268G LEU* 3.5 34.8 - - + -
303G VAL* 4.4 2.2 - - + -
305G PHE* 3.7 52.0 - - + -
310G LEU* 3.7 28.0 - - + +
312G TYR* 4.2 14.6 - - + -
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Residues in contact with PHE 255 (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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215G ILE* 3.6 35.0 - - + -
218G TRP* 4.0 22.2 - + - -
237G CYS 3.8 0.3 - - - +
238G PHE* 3.2 9.7 - - - +
239G THR* 3.1 47.9 + - + +
241G MET* 3.6 36.3 - - + -
253G LYS* 3.8 26.0 - - + -
254G ILE* 1.3 80.1 - - - +
256G LYS* 1.3 59.7 + - - +
257G MET* 4.2 10.9 - - - +
262G VAL* 4.0 15.0 - - + -
264G LYS 3.6 2.0 - - - +
265G SER* 3.7 20.9 - - - -
310G LEU* 4.7 0.2 - - - -
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Residues in contact with LYS 256 (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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236G SER* 3.7 13.5 - - - -
237G CYS 3.5 3.4 - - - -
238G PHE* 3.8 13.5 - - + -
255G PHE* 1.3 74.3 - - - +
257G MET* 1.3 63.7 + - - +
258G GLU* 3.6 21.8 + - - -
262G VAL* 3.6 3.8 - - - -
263G VAL* 2.9 40.3 + - + +
264G LYS* 2.8 30.7 + - + +
308G GLN* 2.8 31.7 + - - +
309G ASN* 3.9 11.3 + - - +
310G LEU* 4.0 17.5 - - + +
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Residues in contact with MET 257 (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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190G LEU* 4.0 23.1 - - + -
192G ILE* 3.5 19.5 - - + -
205G LEU* 3.9 23.8 - - - -
215G ILE* 5.8 1.1 - - - -
230G CYS* 5.2 1.3 - - - -
236G SER* 3.4 3.8 - - - -
237G CYS* 2.7 53.2 + - - +
238G PHE 4.4 1.8 - - - -
239G THR* 3.2 42.8 - - + +
255G PHE* 4.4 11.9 - - - +
256G LYS* 1.3 74.0 - - - +
258G GLU* 1.3 65.0 + - - +
260G GLY* 4.4 2.9 - - - +
261G LYS 3.2 25.1 - - - +
262G VAL* 4.2 2.7 - - - +
263G VAL* 4.4 1.1 - - - +
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Residues in contact with GLU 258 (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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235G GLY 3.7 15.3 - - - +
236G SER* 2.5 30.4 + - - +
256G LYS* 3.6 13.3 + - - -
257G MET* 1.3 76.2 - - - +
259G LYS* 1.3 75.3 + - + +
261G LYS* 3.1 20.7 + - - +
263G VAL* 3.9 27.8 - - + +
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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