Contacts of the strand formed by residues 186 - 195 (chain H) in PDB entry 3UAJ
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 TYR 186 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120H ILE* 3.7 24.3 - - - +
154H ASP 3.1 23.2 + - - -
155H TYR* 2.8 52.7 + + + +
156H PHE* 3.6 27.4 - + - -
157H PRO* 4.3 1.1 - - + -
158H GLU* 3.8 43.3 - - + +
178H ALA* 4.0 14.4 - - + -
179H VAL 3.5 2.0 - - - -
180H LEU* 3.6 39.7 - - + +
181H GLN* 3.8 1.1 - - - -
185H LEU* 1.3 73.5 - - - +
187H SER* 1.3 59.3 + - - +
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Residues in contact with SER 187 (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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151H LEU* 5.1 7.8 - - - +
152H VAL 3.5 4.5 + - - -
153H LYS* 4.0 15.0 - - - +
155H TYR* 4.5 0.2 - - - -
177H PRO 4.5 0.7 - - - +
178H ALA* 3.5 3.7 - - - -
179H VAL* 3.0 46.0 + - - +
181H GLN* 3.7 27.2 + - - -
186H TYR* 1.3 73.6 - - - +
188H LEU* 1.3 62.5 + - - +
161L GLN* 5.2 1.1 - - - -
179L THR* 5.2 9.4 + - - +
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Residues in contact with LEU 188 (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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151H LEU* 3.6 6.0 - - - +
152H VAL* 2.7 53.0 + - + +
155H TYR* 3.4 24.2 - - - +
158H GLU* 4.8 1.8 - - - +
160H VAL* 3.8 12.3 - - + +
162H VAL* 3.9 21.5 - - + -
175H THR* 3.9 26.0 - - + -
176H PHE 3.4 20.2 - - - +
177H PRO* 4.7 1.8 - - + -
178H ALA* 3.7 16.6 - - + +
187H SER* 1.3 75.5 + - - +
189H SER* 1.3 71.6 + - - +
190H SER 4.7 0.2 - - - +
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Residues in contact with SER 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H LEU* 4.8 8.7 - - - -
150H CYS 3.5 9.6 - - - -
151H LEU* 4.7 13.5 - - - -
175H THR* 3.9 0.5 - - - -
176H PHE* 3.0 38.6 + - - +
188H LEU* 1.3 80.2 - - - +
190H SER* 1.3 60.3 + - - +
191H VAL* 4.9 4.3 - - - -
134L ALA* 5.8 3.4 - - - -
177L SER* 3.2 27.4 + - - -
179L THR* 5.4 4.8 + - - -
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Residues in contact with SER 190 (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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149H GLY* 3.2 3.3 - - - -
150H CYS* 3.1 30.4 + - - -
152H VAL* 5.9 0.7 - - - -
162H VAL* 3.8 25.0 + - - +
164H TRP* 3.2 26.9 + - - -
173H VAL* 4.0 3.3 - - - +
174H HIS 3.4 4.5 - - - -
175H THR* 2.9 30.5 + - - +
188H LEU* 4.7 1.5 - - - +
189H SER* 1.3 72.7 - - - +
191H VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 191 (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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134H LEU* 4.7 10.8 - - + -
147H ALA* 4.1 1.8 - - + -
148H LEU 3.4 24.0 - - - +
149H GLY* 4.0 4.3 - - - -
164H TRP* 5.0 0.9 - - - -
172H GLY 3.4 3.0 - - - +
173H VAL* 3.7 0.6 - - - -
174H HIS* 2.8 40.5 + - + +
176H PHE* 3.9 12.8 - - + -
189H SER* 4.9 3.8 - - - -
190H SER* 1.3 78.5 - - - +
192H VAL* 1.3 61.6 + - - +
119L PHE* 3.9 14.6 - - + -
136L LEU* 3.7 48.9 - - + -
177L SER* 5.7 1.8 - - - -
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Residues in contact with VAL 192 (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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146H ALA 4.0 0.3 - - - +
147H ALA* 3.5 4.5 - - - -
148H LEU* 2.9 58.7 + - + +
164H TRP* 4.1 15.7 - - + -
169H LEU* 3.8 31.9 - - + -
171H SER 3.8 8.5 - - - +
172H GLY 3.4 17.9 - - - +
173H VAL* 3.8 15.7 - - + -
191H VAL* 1.3 75.2 - - - +
193H THR* 1.3 68.1 + - - +
194H VAL* 3.9 8.4 + - + -
204H TYR* 5.1 0.2 - - + -
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Residues in contact with THR 193 (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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145H THR* 4.0 27.4 - - + +
146H ALA 4.0 8.1 - - - +
147H ALA* 4.7 7.8 - - + +
171H SER 4.3 8.0 - - - +
172H GLY* 3.4 17.1 + - - -
191H VAL 5.7 0.2 - - - -
192H VAL* 1.3 76.9 - - - +
194H VAL* 1.3 65.4 + - - +
117L PHE* 5.6 5.8 - - + -
136L LEU* 5.3 1.0 - - - +
138L ASN* 2.8 33.0 + - - +
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Residues in contact with VAL 194 (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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145H THR* 3.5 5.0 - - - -
146H ALA* 2.8 37.4 + - - +
148H LEU* 3.8 28.9 - - + -
169H LEU* 4.5 10.3 - - + -
171H SER 5.5 0.2 - - - +
192H VAL* 4.3 16.2 - - + +
193H THR* 1.3 79.2 - - - +
195H PRO* 1.4 74.9 - - + +
199H LEU* 4.8 4.0 - - + -
204H TYR* 3.5 42.2 - - + +
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Residues in contact with PRO 195 (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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144H GLY 3.8 9.6 - - - +
145H THR* 3.9 12.8 - - + -
146H ALA 4.4 0.2 - - - -
194H VAL* 1.4 91.3 - - + +
196H SER* 1.3 64.2 + - - +
197H SER* 3.3 13.0 - - - +
198H SER* 3.3 37.2 + - - +
199H LEU* 3.8 8.5 + - - +
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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