Contacts of the strand formed by residues 194 - 199 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ILE* 5.4 2.0 - - + -
164B LEU* 4.3 15.7 - - + -
169B PHE* 3.4 8.4 - - - -
170B VAL* 3.2 24.7 - - + +
172B LEU* 3.9 28.5 - - + -
184B TYR* 4.0 10.1 - - + +
187B PHE* 3.6 37.2 - - + +
188B LEU* 3.6 30.3 - - + +
191B TYR* 4.5 5.6 - - + -
192B GLU 2.9 6.9 + - - +
193B ASN* 1.3 78.5 - - - +
195B ALA* 1.3 72.7 + - - +
196B VAL* 4.7 4.7 - - + -
216B ALA* 3.5 13.3 - - - +
217B SER 4.5 0.2 + - - -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B MET* 4.2 8.1 - - + -
169B PHE* 3.6 21.3 - - + -
170B VAL 2.9 6.3 + - - -
171B ALA* 3.4 2.5 - - - +
172B LEU* 2.7 33.6 + - - +
188B LEU* 5.2 0.2 - - - -
194B LEU* 1.3 79.4 - - - +
196B VAL* 1.3 61.4 + - - +
197B ILE* 3.9 1.5 + - + +
214B VAL* 4.1 14.8 - - + -
215B VAL 3.5 5.6 - - - -
216B ALA* 3.9 11.9 - - + -
220B PHE* 4.1 6.1 - - + -
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B LEU* 3.4 13.2 - - + -
174B GLU* 3.2 32.1 - - + +
184B TYR 4.2 7.0 - - - +
185B VAL* 3.8 39.9 - - + +
188B LEU* 4.6 6.5 - - + -
194B LEU* 4.7 5.6 - - + -
195B ALA* 1.3 75.6 - - - +
197B ILE* 1.3 63.0 + - - +
198B ARG* 3.8 17.5 - - + +
213B TYR 3.7 0.7 - - - +
214B VAL* 3.4 4.9 - - - -
215B VAL* 3.0 38.4 + - + +
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA* 3.5 35.4 - - + +
88B ILE* 4.0 20.9 - - + -
89B ILE* 4.0 19.7 - - + -
92B MET* 3.9 24.2 - - - -
143B PHE* 4.8 1.1 - - + -
171B ALA* 4.2 14.6 - - + -
172B LEU 3.0 10.6 + - - +
173B ASP* 4.1 20.6 - - + +
174B GLU* 2.7 34.3 + - - +
175B ALA 3.6 0.7 + - - -
195B ALA 4.6 4.0 - - - +
196B VAL* 1.3 74.9 - - - +
198B ARG* 1.3 63.2 + - - +
213B TYR 3.6 3.1 - - - -
214B VAL* 4.2 6.7 - - + -
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Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B TYR* 4.2 4.2 - - - -
69B LEU* 3.7 19.0 - - - +
85B ALA* 3.6 8.6 - - - +
174B GLU* 3.0 41.9 + - - +
175B ALA* 5.2 0.4 - - - -
177B TYR* 3.6 31.3 - - - +
178B GLU* 4.4 3.5 + - - +
183B SER* 3.1 28.7 + - - -
185B VAL* 3.6 13.1 - - - +
196B VAL* 3.8 9.4 - - + +
197B ILE* 1.3 74.8 - - - +
199B THR* 1.3 66.5 + - - +
212B GLY* 3.3 4.2 - - - -
213B TYR* 2.9 82.4 + - + +
215B VAL* 5.1 1.1 - - + -
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Residues in contact with THR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA* 4.1 2.5 - - - -
174B GLU 5.0 0.4 + - - -
175B ALA* 3.8 20.8 - - - +
178B GLU* 4.6 13.5 + - - +
198B ARG* 1.3 78.1 - - - +
200B PHE* 1.3 71.3 + - - +
201B SER* 2.9 15.6 + - - +
202B LYS* 3.7 32.0 + - + +
203B ALA 5.6 1.4 + - - -
204B PHE* 4.5 6.6 - - - -
211B VAL 3.5 8.3 + - - -
212B GLY* 4.1 0.7 - - - -
213B TYR* 4.4 5.7 - - - -
1335B PMP 2.6 34.7 + - - +
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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