Contacts of the strand formed by residues 244 - 258 (chain C) in PDB entry 3HB8
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 LYS 244 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C ASN 3.5 22.2 + - - -
206C SER* 3.1 17.8 + - - +
207C GLU* 3.1 26.8 + - + +
208C LEU 3.0 16.9 + - - -
238C ALA* 4.3 0.9 - - - -
243C LEU* 1.3 75.5 - - - +
245C PRO* 1.3 76.1 - - + +
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Residues in contact with PRO 245 (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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67C LEU* 3.4 33.7 - - + +
68C ARG* 3.8 14.9 - - - +
207C GLU* 4.1 3.6 - - - +
208C LEU 3.7 7.9 - - - +
234C THR* 4.8 2.2 - - + -
235C TYR* 3.9 37.0 - - + +
238C ALA* 3.7 23.1 - - + -
243C LEU 3.9 0.9 - - - +
244C LYS* 1.3 89.7 - - + +
246C GLY* 1.3 62.8 + - - +
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Residues in contact with GLY 246 (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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67C LEU* 2.8 26.5 + - - +
68C ARG* 3.0 17.0 + - - +
207C GLU* 3.3 24.0 - - - -
208C LEU 2.8 18.2 + - - -
209C SER* 3.9 5.6 - - - -
244C LYS 3.4 1.6 + - - -
245C PRO* 1.3 72.1 - - - +
247C ASP* 1.3 58.1 + - - -
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Residues in contact with ASP 247 (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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64C ARG* 3.5 41.0 + - + -
65C TYR 3.2 18.6 - - - +
66C SER* 4.1 0.7 - - - -
67C LEU* 3.9 7.7 - - - +
68C ARG* 3.3 25.2 + - - +
209C SER* 3.0 22.8 + - - -
210C CYS 3.1 23.6 + - - +
246C GLY* 1.3 75.0 - - - +
248C PHE* 1.3 61.8 + - - +
249C ILE* 4.0 3.4 - - - +
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Residues in contact with PHE 248 (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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64C ARG* 3.7 1.0 - - - -
65C TYR* 2.8 46.1 + + + +
67C LEU* 3.9 24.9 - - + +
210C CYS* 3.2 20.2 - - + +
212C LEU* 3.8 31.4 - - + -
227C ILE* 3.7 37.0 - - + -
230C TYR* 3.4 40.2 - - + -
231C ALA* 4.7 1.8 - - + -
234C THR* 5.2 0.4 - - - +
247C ASP* 1.3 73.1 - - - +
249C ILE* 1.3 64.1 + - - +
250C HIS* 3.7 27.1 - + + -
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Residues in contact with ILE 249 (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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62C GLN* 3.6 39.7 - - + +
63C ALA 3.5 4.5 - - - +
64C ARG* 3.9 42.4 - - + +
209C SER* 4.9 3.8 - - - -
210C CYS 2.7 23.9 + - - +
211C GLN* 3.3 21.9 - - + +
212C LEU 2.9 27.5 + - - -
247C ASP* 4.0 13.9 - - - +
248C PHE* 1.3 81.2 - - - +
250C HIS* 1.3 62.8 + - - +
251C THR* 3.7 1.4 + - - +
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Residues in contact with HIS 250 (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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36C GLN* 4.9 6.6 + - - -
61C MET 4.5 0.2 - - - -
62C GLN* 3.3 3.6 - - - -
63C ALA* 2.8 38.5 + - + +
65C TYR* 4.1 11.1 + - + -
212C LEU* 3.9 22.1 - - + +
214C GLN* 3.0 31.1 + - - +
223C VAL* 3.6 36.1 - - + +
226C ASN* 4.5 1.7 - - + +
227C ILE* 3.9 10.2 - - + +
248C PHE* 3.7 21.4 + + + -
249C ILE* 1.3 72.1 - - - +
251C THR* 1.3 67.0 + - - +
252C LEU* 3.9 20.9 + - + +
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Residues in contact with THR 251 (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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61C MET 3.6 10.3 - - - +
62C GLN* 3.0 16.3 + - + +
211C GLN* 2.6 31.7 + - - +
212C LEU 2.9 15.1 + - - +
213C TYR* 3.8 28.0 - - + -
214C GLN* 2.9 29.6 + - - +
249C ILE* 3.9 0.5 - - - +
250C HIS* 1.3 75.2 - - - +
252C LEU* 1.3 67.1 + - - +
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Residues in contact with LEU 252 (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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36C GLN* 4.7 6.7 - - - +
60C GLY* 3.4 5.7 - - - -
61C MET* 2.8 46.1 + - + +
213C TYR* 4.9 4.1 - - - -
214C GLN* 3.4 27.4 - - + +
217C GLY* 3.5 30.5 - - - +
219C MET* 4.0 18.4 - - - -
223C VAL* 4.1 3.8 - - + -
250C HIS* 3.9 27.8 + - + +
251C THR* 1.3 79.6 - - - +
253C GLY* 1.3 60.0 + - - +
255C ALA* 3.6 30.7 - - + -
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Residues in contact with GLY 253 (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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58C VAL 3.2 0.2 - - - +
59C PHE* 3.2 25.2 - - - -
60C GLY* 2.9 24.4 + - - -
213C TYR* 4.0 14.1 + - - -
214C GLN 3.0 13.7 + - - -
215C ARG 3.5 6.3 - - - -
252C LEU* 1.3 71.7 - - - +
254C ASP* 1.3 59.6 + - - +
255C ALA* 3.1 7.3 + - - +
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Residues in contact with ASP 254 (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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47C LYS* 3.4 30.1 + - - +
57C SER* 2.7 25.8 + - - -
58C VAL 3.9 3.1 - - - -
59C PHE* 3.7 11.4 - - + -
215C ARG 2.7 16.3 + - - +
216C SER* 3.7 9.1 - - - +
217C GLY 3.2 13.4 + - - -
253C GLY* 1.3 69.6 - - - -
255C ALA* 1.3 50.0 + - - +
256C HIS* 2.7 35.0 + - - -
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Residues in contact with ALA 255 (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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40C ILE* 4.3 4.9 - - + +
56C LEU 4.0 0.5 - - - +
57C SER* 3.5 0.2 - - - -
58C VAL* 2.9 39.0 + - - +
61C MET* 3.4 37.0 - - + -
217C GLY 3.7 6.7 - - - +
219C MET* 4.4 1.1 - - - -
252C LEU* 3.6 25.4 - - + -
253C GLY 3.1 3.8 + - - +
254C ASP* 1.3 70.7 - - - +
256C HIS* 1.3 60.1 + - - +
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Residues in contact with HIS 256 (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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40C ILE* 4.5 1.3 - - - -
49C ASP* 6.3 1.3 - - + -
55C THR* 3.8 21.1 - - + +
56C LEU 3.1 13.5 - - - +
57C SER* 3.8 3.4 - - - -
216C SER* 3.4 17.6 + - - -
217C GLY 2.9 27.0 + - - +
218C ASP* 3.8 8.6 - - + +
219C MET* 3.0 30.6 + - - +
254C ASP* 2.7 30.8 + - - +
255C ALA* 1.3 74.0 - - - +
257C ILE* 1.3 64.8 + - - +
258C TYR* 3.8 32.0 + + - -
365C UMP 4.7 8.8 - - - -
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Residues in contact with ILE 257 (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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37C ILE* 3.5 45.3 - - + +
40C ILE* 3.8 18.2 - - + -
41C LEU* 4.0 12.8 - - + -
55C THR* 3.0 5.2 - - - -
56C LEU* 2.7 38.2 + - + +
218C ASP* 5.2 1.8 - - - -
219C MET* 3.8 14.6 - - + +
220C GLY 5.3 0.9 - - - +
256C HIS* 1.3 79.6 - - - +
258C TYR* 1.3 75.4 + - - +
259C LEU 3.6 0.2 + - - -
261C HIS* 4.0 6.1 - - + +
262C ILE* 4.5 12.3 - - + -
265C LEU* 3.4 21.3 - - + -
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Residues in contact with TYR 258 (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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49C ASP* 3.1 27.2 + - + +
53C THR* 3.7 36.1 - - + -
54C GLY 4.1 0.9 - - - -
55C THR* 3.5 26.2 - - + -
218C ASP* 4.4 17.0 + - - -
256C HIS* 3.8 23.6 + + - -
257C ILE* 1.3 80.6 - - - +
259C LEU* 1.3 60.0 + - - +
260C ASN* 3.4 16.2 - - - +
261C HIS* 2.8 44.7 + + + +
262C ILE* 3.6 1.4 + - - +
365C UMP 3.9 23.7 + - - -
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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