Contacts of the strand formed by residues 194 - 199 (chain D) in PDB entry 1UU1
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 LEU 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D ILE* 5.3 1.8 - - + -
164D LEU* 3.9 19.3 - - + -
169D PHE* 3.6 8.0 - - - -
170D VAL* 3.4 30.7 - - + +
172D LEU* 3.9 21.8 - - + -
184D TYR* 3.9 14.1 - - + +
187D PHE* 3.9 29.2 - - + +
188D LEU* 3.7 35.3 - - + +
191D TYR* 4.6 7.6 - - + +
192D GLU 3.3 3.6 + - - +
193D ASN* 1.3 79.5 - - - +
195D ALA* 1.3 72.1 + - - +
196D VAL* 4.7 2.5 - - + -
216D ALA* 3.7 8.0 - - - +
217D SER 4.4 1.4 + - - -
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Residues in contact with ALA 195 (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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92D MET* 4.1 10.5 - - + -
169D PHE* 3.4 22.9 - - + -
170D VAL 2.8 10.0 + - - +
171D ALA* 3.6 2.6 - - - -
172D LEU* 2.9 25.6 + - - +
194D LEU* 1.3 79.6 - - - +
196D VAL* 1.3 64.0 + - - +
197D ILE* 3.9 1.6 + - - +
214D VAL* 4.1 14.1 - - + -
215D VAL 3.5 5.6 - - - +
216D ALA* 3.9 12.8 - - + -
220D PHE* 4.4 1.6 - - + -
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Residues in contact with VAL 196 (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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172D LEU* 3.5 14.8 - - + -
174D GLU* 3.5 41.5 - - + +
184D TYR 4.2 5.2 - - - +
185D VAL* 3.9 38.4 - - + +
188D LEU* 4.8 1.8 - - + -
194D LEU* 4.7 9.2 - - + -
195D ALA* 1.3 75.7 - - - +
197D ILE* 1.3 63.4 + - - +
198D ARG* 3.9 11.2 - - + +
213D TYR 3.9 0.5 - - - +
214D VAL* 3.2 5.6 - - - -
215D VAL* 2.9 41.0 + - + +
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Residues in contact with ILE 197 (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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85D ALA* 3.6 31.6 - - + +
88D ILE* 3.8 25.8 - - + -
89D ILE* 4.3 15.9 - - + -
92D MET* 3.9 24.7 - - + -
143D PHE* 5.0 1.1 - - + -
171D ALA* 4.2 20.9 - - + -
172D LEU 3.1 6.1 + - - -
173D ASP* 4.2 24.2 - - + +
174D GLU* 2.8 34.8 + - - +
175D ALA 3.6 1.1 + - - -
195D ALA 4.5 1.8 - - - +
196D VAL* 1.3 76.8 - - - +
198D ARG* 1.3 63.2 + - - +
213D TYR 3.6 7.9 - - - +
214D VAL* 4.1 1.3 - - + -
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Residues in contact with ARG 198 (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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68D TYR* 4.4 2.4 - - - -
69D LEU* 3.7 19.1 - - - +
85D ALA* 4.1 7.3 - - - +
174D GLU* 2.8 44.0 + - - +
175D ALA* 5.2 0.4 - - - -
177D TYR* 3.5 36.5 + - - +
178D GLU* 4.3 4.5 + - - +
183D SER* 3.2 28.7 + - - -
185D VAL* 4.0 9.7 - - - +
196D VAL* 3.9 9.4 - - + +
197D ILE* 1.3 74.3 - - - +
199D THR* 1.3 64.3 + - - +
212D GLY* 3.1 4.3 - - - -
213D TYR* 2.8 79.4 + - + +
215D VAL* 5.1 2.7 - - + -
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Residues in contact with THR 199 (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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85D ALA* 4.2 4.9 - - - -
174D GLU 5.1 0.2 + - - -
175D ALA* 3.5 37.2 - - + +
178D GLU* 4.6 10.3 + - - +
198D ARG* 1.3 78.3 - - - +
200D PHE* 1.3 72.7 + - - +
201D SER* 2.8 14.1 + - - +
202D LYS* 4.1 19.3 + - + +
203D ALA* 5.5 1.4 + - - +
204D PHE* 4.2 11.4 - - - -
211D VAL 3.6 7.9 + - - -
212D GLY* 4.0 0.4 - - - -
213D TYR* 4.7 3.8 + - - -
1335D PMP 2.8 31.2 + - - +
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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