Contacts of the strand formed by residues 186 - 193 (chain D) 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 VAL 186 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LYS* 3.9 15.2 + - - +
169D LEU* 3.3 45.8 - - + +
170D PHE* 4.5 14.1 - - + -
184D GLY* 3.1 2.1 - - - -
185D ALA* 1.3 84.5 - - - +
187D GLN* 1.3 62.9 + - - +
188D PHE* 3.7 31.4 - - + -
236D ASN* 3.4 5.6 - - - +
237D VAL* 3.7 14.8 - - + -
259D PHE* 4.3 7.6 - - + -
141N ARG* 3.5 20.0 + - - +
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Residues in contact with GLN 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D VAL* 1.3 72.8 - - - +
188D PHE* 1.3 61.7 + - - +
189D ALA 3.6 0.5 + - - -
234D TYR* 4.8 2.4 - - - -
235D ALA* 3.3 4.5 - - - -
236D ASN* 2.8 63.6 + - - +
293D PRO* 5.0 0.5 - - - +
135N GLN* 3.2 19.0 - - - +
136N PRO 3.7 9.5 + - - +
137N TYR* 3.6 13.1 - - - +
141N ARG* 3.1 43.5 + - - +
143N PHE 3.5 7.7 + - - -
144N VAL* 3.3 27.6 - - + +
145N PRO* 4.3 1.1 - - - +
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Residues in contact with PHE 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D SER* 3.0 30.4 + - - +
43D TRP* 3.0 46.0 - + + -
44D LYS* 3.5 41.8 - - + +
47D VAL* 3.9 5.4 - - + -
170D PHE* 4.7 0.2 - + - -
186D VAL* 3.7 17.1 + - + -
187D GLN* 1.3 71.1 - - - +
189D ALA* 1.3 63.5 - - - +
234D TYR 4.0 2.5 - - - +
235D ALA* 3.5 20.0 - - + -
259D PHE* 3.4 39.3 - + - -
263D PHE* 3.9 1.6 - + - -
141N ARG* 5.2 3.2 - - - +
142N ALA* 3.3 17.3 - - - +
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D SER* 4.2 5.3 - - - -
187D GLN 3.6 2.8 + - - -
188D PHE* 1.3 76.4 - - - +
190D HIS* 1.3 67.0 + - - +
191D ALA* 3.2 4.3 + - - +
233D ARG* 6.0 0.2 - - - +
234D TYR* 2.9 50.3 + - + +
142N ALA 3.5 8.3 - - - +
144N VAL* 3.6 21.9 - - + +
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Residues in contact with HIS 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 3.5 18.4 + - - -
38D VAL 4.5 1.1 - - - +
39D SER* 3.2 25.9 + - - -
40D SER* 3.0 28.3 + - - +
41D GLN* 4.0 3.6 - - - -
189D ALA* 1.3 74.4 - - - +
191D ALA* 1.3 63.8 + - - +
192D PHE* 3.5 16.3 + - + +
232D TYR 4.7 0.7 - - - +
234D TYR 6.0 0.2 - - - -
11N PRO* 5.9 1.6 - - - +
12N MET* 3.4 37.2 - - + +
72N ASP* 4.5 7.4 - - - -
142N ALA* 3.2 33.7 + - + +
143N PHE* 3.5 17.2 - + - -
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Residues in contact with ALA 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 3.0 28.9 - - - +
38D VAL* 3.2 30.7 + - + +
40D SER* 5.5 0.2 - - - +
43D TRP* 6.5 0.4 - - + -
189D ALA 3.2 6.7 + - - +
190D HIS* 1.3 71.3 - - - +
192D PHE* 1.3 58.5 + - - +
231D PHE* 4.2 6.7 - - + -
232D TYR 3.8 8.7 - - - -
233D ARG* 3.4 34.5 - - + +
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Residues in contact with PHE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 5.2 7.6 - - + -
30D TYR* 4.0 18.2 - + + -
35D ARG* 3.4 43.7 - - + +
36D THR 3.4 9.9 - - - +
37D ARG* 4.2 6.5 - - + +
190D HIS 3.6 14.1 - - - +
191D ALA* 1.3 74.5 - - - +
193D THR* 1.3 64.8 + - - +
231D PHE* 4.2 3.8 - - - -
232D TYR* 3.0 51.5 + + + +
297D ALA* 3.9 36.3 - - + -
300D PHE* 4.5 10.1 - + + -
11N PRO* 4.7 13.2 - - + -
12N MET* 6.2 1.3 - - + -
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Residues in contact with THR 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ARG* 2.9 50.1 + - - +
36D THR* 3.0 16.7 + - - +
192D PHE* 1.3 75.6 - - - +
194D VAL* 1.3 63.8 + - - +
195D HIS* 3.2 16.0 + - + -
197D THR* 3.8 11.8 - - + +
228D ALA 4.9 0.7 - - - +
229D GLY* 3.9 20.9 - - - -
230D THR 3.8 6.5 - - - +
231D PHE* 3.3 31.6 - - + -
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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