Contacts of the strand formed by residues 244 - 258 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ARG* 4.0 23.0 - - - +
69A ASP* 4.6 13.9 - - - +
206A SER 3.4 16.8 + - - +
207A GLU* 3.1 12.5 + - + +
208A LEU 2.7 31.3 + - - -
238A ALA* 4.5 1.3 - - - -
243A LEU* 1.3 76.7 - - - +
245A PRO* 1.3 97.7 + - + +
114D SER* 5.9 2.9 - - - +
116D ASP* 4.4 26.7 - - + +
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Residues in contact with PRO 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.4 33.2 - - + +
68A ARG* 3.4 12.8 + - - +
207A GLU* 4.2 1.0 - - - +
208A LEU* 3.7 5.4 - - + +
234A THR* 4.9 1.8 - - + -
235A TYR* 3.9 35.0 - - + -
238A ALA* 4.2 16.4 - - + -
243A LEU 3.9 6.1 - - - +
244A LYS* 1.3 109.5 + - + +
246A GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 2.9 27.7 + - - +
68A ARG* 3.5 29.9 + - - -
207A GLU* 3.9 11.7 - - - -
208A LEU 2.5 18.3 + - - -
209A SER* 3.8 3.6 - - - -
244A LYS 3.2 1.4 + - - -
245A PRO* 1.3 72.9 - - - +
247A ASP* 1.3 59.8 + - - -
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Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 3.4 43.2 + - + +
65A TYR 3.5 3.6 - - - +
66A SER* 3.7 12.6 - - - -
67A LEU* 4.1 6.3 - - - +
68A ARG* 3.1 33.8 + - - -
209A SER* 2.7 21.1 + - - +
210A CYS 2.8 31.9 + - - +
246A GLY* 1.3 72.7 - - - +
248A PHE* 1.3 55.3 + - - +
249A ILE* 3.9 5.1 + - + +
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Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA 3.7 0.9 - - - +
64A ARG* 3.6 0.7 - - - -
65A TYR* 2.7 53.5 + + + +
67A LEU* 3.8 20.8 - - + +
72A PRO* 5.3 0.2 - - + -
210A CYS* 3.2 23.8 - - + +
212A LEU* 3.8 16.4 - - + -
227A ILE* 3.8 36.1 - - + -
230A TYR* 3.4 36.3 - - + -
231A ALA* 4.8 4.9 - - + -
247A ASP* 1.3 72.9 - - - +
249A ILE* 1.3 72.2 + - - +
250A HIS* 3.9 30.7 - - + -
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 3.6 38.1 - - + +
63A ALA 3.3 3.4 - - - +
64A ARG* 3.2 55.6 - - + +
210A CYS 2.7 10.6 + - - +
211A GLN* 3.2 26.9 - - + -
212A LEU 3.0 23.4 + - - -
247A ASP* 4.2 6.3 - - + +
248A PHE* 1.3 79.3 - - - +
250A HIS* 1.3 60.6 + - - +
251A THR* 4.2 0.7 - - - +
59B PHE* 3.7 20.6 - - + +
60B GLY* 4.1 5.2 - - - -
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Residues in contact with HIS 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 4.8 7.0 + - - -
61A MET 3.8 0.7 - - - +
62A GLN* 3.2 4.7 - - - -
63A ALA* 2.7 37.0 + - + +
65A TYR* 4.2 12.6 - + + -
212A LEU* 3.6 24.5 - - + +
214A GLN* 2.9 34.4 + - + -
223A VAL* 3.8 23.0 - - + +
226A ASN* 4.6 5.8 - - + -
227A ILE* 4.7 6.5 - - + +
248A PHE* 3.7 19.0 + + + -
249A ILE* 1.3 73.8 - - - +
251A THR* 1.3 60.3 + - - +
252A LEU* 3.5 31.7 + - + +
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Residues in contact with THR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MET 3.4 3.4 - - - -
62A GLN* 2.8 19.4 + - - +
211A GLN* 2.7 25.7 + - - +
212A LEU 3.0 16.5 + - - +
213A TYR* 3.8 21.3 - - + -
214A GLN* 3.0 27.9 + - - +
249A ILE 3.9 0.6 + - - -
250A HIS* 1.3 73.1 + - - +
252A LEU* 1.3 63.6 + - - +
62B GLN* 3.7 7.2 - - - +
211B GLN* 3.6 26.0 - - - +
213B TYR* 5.2 0.2 - - - -
251B THR* 3.8 6.1 - - + -
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Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 4.8 4.5 - - - +
60A GLY* 3.2 16.3 - - - -
61A MET* 2.9 27.6 + - + +
213A TYR* 5.0 0.4 - - - -
214A GLN* 3.4 36.3 - - + +
217A GLY* 3.9 20.2 - - - +
219A MET* 3.7 31.6 - - + -
223A VAL* 4.5 2.7 - - + -
250A HIS* 3.5 28.7 + - + +
251A THR* 1.3 74.1 - - - +
253A GLY* 1.3 60.9 + - - +
255A ALA* 3.9 17.5 - - + -
211B GLN* 3.0 17.1 + - - +
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 2.9 14.5 - - - -
60A GLY 2.7 26.7 + - - -
213A TYR* 3.9 1.1 - - - -
214A GLN 2.7 13.9 + - - -
215A ARG 3.4 8.7 - - - -
252A LEU* 1.3 72.9 - - - +
254A ASP* 1.3 58.9 + - - +
255A ALA 3.4 2.9 + - - -
200B GLN* 3.6 12.3 - - - -
211B GLN* 3.5 13.2 - - - -
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Residues in contact with ASP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.1 19.1 + - - +
57A SER* 3.0 28.0 + - - -
58A VAL 3.8 4.0 - - - +
59A PHE* 3.8 3.8 - - + -
215A ARG 2.7 18.7 + - - +
216A SER* 4.3 0.9 - - - -
217A GLY 3.2 13.5 + - - -
252A LEU* 5.1 0.7 - - - -
253A GLY* 1.3 71.4 - - - +
255A ALA* 1.3 55.6 + - - +
256A HIS* 2.8 22.0 + - - +
175B ARG* 2.9 38.4 + - + -
200B GLN* 5.2 1.3 - - - +
202B TYR* 3.8 17.4 - - + -
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 3.1 14.4 - - + +
57A SER* 3.2 0.5 - - - -
58A VAL* 2.9 34.6 + - + +
61A MET* 3.5 35.2 - - + -
217A GLY 3.9 6.1 - - - +
219A MET* 4.1 5.4 - - - -
252A LEU* 3.9 23.1 - - + +
253A GLY 3.4 2.6 + - - -
254A ASP* 1.3 70.0 - - - +
256A HIS* 1.3 58.5 + - - +
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Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 4.9 0.4 - - - -
55A THR* 3.9 18.2 - - + +
56A LEU 3.2 5.8 - - - +
57A SER* 3.5 18.2 - - - -
216A SER* 4.2 2.0 - - - -
217A GLY* 3.2 33.2 + - - +
218A ASP* 3.5 13.9 + - + -
219A MET* 2.9 28.2 + - - +
254A ASP* 2.8 21.3 + - - +
255A ALA* 1.3 74.8 - - - +
257A ILE* 1.3 67.9 + - - +
258A TYR* 5.3 4.0 - + - -
314A UMP 3.5 25.4 + - - -
175B ARG* 3.4 38.3 + - - +
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.7 26.0 - - + +
40A ILE* 4.4 19.3 - - + -
41A LEU* 5.0 8.3 - - + -
55A THR* 3.2 5.3 - - - -
56A LEU* 2.8 38.5 + - + +
218A ASP* 5.1 3.8 - - - -
219A MET* 3.9 18.4 - - + +
220A GLY 4.8 1.8 - - - +
256A HIS* 1.3 81.6 - - - +
258A TYR* 1.3 75.4 + - - +
262A ILE* 4.2 15.9 - - + -
265A LEU* 3.5 36.3 - - + -
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Residues in contact with TYR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 3.4 26.8 + - + -
51A THR* 5.5 0.5 + - - +
53A THR* 3.7 25.1 - - + -
54A GLY 4.0 1.6 - - - -
55A THR* 3.9 14.6 - - + -
218A ASP* 3.8 26.1 + - - -
221A LEU* 4.8 3.1 - - + -
256A HIS* 5.3 4.0 - + - -
257A ILE* 1.3 84.1 - - - +
259A LEU* 1.3 66.0 + - - +
260A ASN* 4.3 4.3 - - + +
261A HIS* 2.8 51.8 + + + +
262A ILE 3.5 0.5 + - - -
314A UMP 4.9 8.6 + - - -
175B ARG* 5.9 1.0 + - - -
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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