Contacts of the strand formed by residues 229 - 238 (chain H) in PDB entry 5U07
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 GLY 229 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G TYR* 5.1 6.2 - - - -
11H THR* 3.5 1.5 - - - -
12H LEU* 2.9 32.7 + - - +
193H THR* 4.4 7.0 - - - -
195H HIS* 3.5 16.4 - - - -
228H ALA* 1.3 77.2 - - - +
230H THR* 1.3 65.6 + - - -
231H PHE* 3.5 12.6 + - - -
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Residues in contact with THR 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G TYR* 6.4 1.1 - - + -
31G GLY* 6.3 0.9 - - - -
301G GLU* 5.5 4.0 - - + +
9H ILE* 4.6 11.8 - - - +
11H THR* 3.6 32.5 - - + +
193H THR* 4.7 0.6 - - - +
194H VAL* 3.0 40.4 + - - +
195H HIS* 3.5 14.4 + - + -
229H GLY* 1.3 70.5 - - - -
231H PHE* 1.3 65.4 + - - +
310H TYR* 4.1 25.1 - - + +
311H THR* 4.2 9.2 - - + +
314H ALA* 5.1 1.6 - - - +
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Residues in contact with PHE 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ALA 3.9 0.5 - - - +
9H ILE* 3.6 4.9 - - - +
10H GLN* 2.9 35.7 + - + +
12H LEU* 3.3 35.7 - - + -
15H SER* 4.6 9.6 - - - -
17H ILE* 4.2 2.5 - - + -
36H THR* 3.8 15.7 - - - -
37H ARG 5.2 0.4 - - - -
38H VAL* 3.3 33.7 - - + -
43H TRP* 5.8 3.6 - + - -
191H ALA* 4.4 17.0 - - + -
192H PHE 3.3 6.1 - - - +
193H THR* 3.2 39.3 - - + -
194H VAL* 4.8 1.3 - - - -
227H SER* 6.0 1.3 - - - -
228H ALA 5.3 1.1 - - - -
229H GLY* 3.5 12.1 + - - -
230H THR* 1.3 73.9 - - - +
232H TYR* 1.3 60.3 + - - +
233H ARG* 4.1 7.9 + - + +
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Residues in contact with TYR 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H HIS* 3.1 19.9 + - + -
8H ALA 3.6 3.4 - - - -
9H ILE* 3.6 19.5 - - + -
190H HIS 4.5 0.7 - - - +
191H ALA* 3.2 23.6 - - - -
192H PHE* 2.7 41.6 + + + +
194H VAL* 4.2 15.7 - - + -
230H THR 3.6 1.6 + - - -
231H PHE* 1.3 72.6 - - - +
233H ARG* 1.3 73.1 + - - +
234H TYR* 4.0 17.4 - + + +
295H SER* 5.4 0.4 - - - -
296H PHE* 3.0 31.1 + - + +
297H ALA* 3.8 20.4 - - + -
300H PHE* 3.7 14.6 - + + -
318H LEU* 3.8 20.9 - - + -
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Residues in contact with ARG 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H HIS* 3.4 4.2 - - - -
8H ALA* 2.9 44.2 + - + +
10H GLN* 2.7 45.7 + - - -
43H TRP* 3.0 34.7 - - - -
188H PHE* 5.2 3.6 - - + -
189H ALA 5.8 0.2 - - - -
191H ALA* 3.7 20.6 - - + +
231H PHE* 4.4 9.0 - - + +
232H TYR* 1.3 84.6 - - - +
234H TYR* 1.3 62.3 + - - +
263H PHE* 2.7 64.8 + - + -
264H LEU* 4.6 1.0 + - - +
281H PRO* 3.9 13.1 - - - +
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Residues in contact with TYR 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D ALA* 3.5 32.3 - - + -
278D MET* 4.6 2.7 - - + +
5H ASP* 3.7 12.6 - - + +
6H ILE 3.3 7.2 - - - -
7H HIS* 3.5 35.9 - + - -
188H PHE* 4.2 3.8 - - - -
189H ALA* 3.2 38.0 + - + +
232H TYR* 4.0 15.0 - - + +
233H ARG* 1.3 76.8 - - - +
235H ALA* 1.3 67.8 + - - +
236H ASN* 2.3 39.6 + - - -
263H PHE* 4.4 3.8 - - - -
293H PRO* 3.4 11.3 - - - +
294H ILE 3.6 8.8 + - - -
295H SER* 3.5 27.6 + - - -
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Residues in contact with ALA 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H ASP* 3.3 4.0 - - - +
6H ILE* 2.9 44.2 + - + +
187H GLN 3.2 12.8 - - - +
188H PHE* 4.2 8.1 - - + -
234H TYR* 1.3 81.4 - - - +
236H ASN* 1.3 66.5 + - - +
237H VAL* 5.6 0.2 - - - -
259H PHE* 4.7 9.4 - - + -
263H PHE* 3.6 25.8 - - + -
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Residues in contact with ASN 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D ALA* 4.6 0.4 - - - +
278D MET* 4.1 4.2 - - - +
3H PHE* 5.5 3.8 - - + -
4H VAL 3.5 3.1 - - - +
5H ASP* 3.1 13.7 - - - +
186H VAL* 3.2 9.0 - - - +
187H GLN* 2.6 63.8 + - + +
234H TYR* 2.3 42.8 + - - -
235H ALA* 1.3 71.4 - - - +
237H VAL* 1.3 70.9 + - - +
238H ASN 4.2 0.9 - - - +
293H PRO* 3.2 24.0 - - + +
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Residues in contact with VAL 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H PHE* 3.5 2.7 - - - -
4H VAL* 2.8 42.9 + - + +
6H ILE* 6.3 1.1 - - + -
169H LEU* 4.9 0.9 - - + -
185H ALA 3.4 9.0 - - - +
186H VAL* 3.7 9.2 - - + -
235H ALA 5.6 0.4 - - - -
236H ASN* 1.3 80.9 - - - +
238H ASN* 1.3 61.0 + - - +
239H LEU* 3.1 27.7 + - + +
242H LEU* 4.1 11.9 - - + -
256H VAL* 4.1 15.0 - - + -
259H PHE* 3.6 33.0 - - + -
260H LEU* 4.5 9.4 - - + -
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Residues in contact with ASN 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H THR* 3.8 4.5 + - - +
3H PHE* 3.2 41.4 - - + -
185H ALA* 2.9 17.7 + - - +
187H GLN* 6.1 3.6 - - + +
236H ASN* 4.2 1.6 - - + +
237H VAL* 1.3 69.0 - - - +
239H LEU* 1.3 66.5 + - - +
240H ASP* 2.5 29.7 + - - +
241H ARG* 3.2 34.8 + - + +
242H LEU* 3.1 18.5 + - - +
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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