Contacts of the strand formed by residues 185 - 195 (chain H) in PDB entry 2YMX
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 185 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H LYS 5.1 0.4 - - - +
128H THR* 3.7 25.8 - - + +
155H GLY* 3.5 37.2 - - - +
156H TYR 3.5 6.7 - - - +
157H PHE* 4.2 2.0 - - + -
180H VAL 3.8 0.3 - - - +
181H LEU* 3.5 6.3 - - - +
182H GLN* 2.9 33.8 + - - +
183H SER 4.1 7.9 - - - +
184H ASP* 1.3 87.7 - - + +
186H TYR* 1.3 60.2 + - - +
187H THR* 5.0 1.2 + - - -
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Residues in contact with TYR 186 (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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121H THR* 5.7 2.9 + - - +
155H GLY 2.9 25.3 + - - -
156H TYR* 2.8 60.5 + + + +
157H PHE* 3.5 30.9 - + - -
159H GLU* 3.7 31.0 - - + +
179H ALA* 3.6 22.0 - - + -
180H VAL 3.4 1.1 - - - -
181H LEU* 3.7 44.3 - - + +
185H LEU* 1.3 74.1 - - - +
187H THR* 1.3 61.3 + - - +
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Residues in contact with THR 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H LEU* 3.6 27.6 - - + -
153H VAL 3.3 7.0 - - - +
154H LYS* 3.6 30.1 + - + +
179H ALA* 3.2 3.0 - - - -
180H VAL 2.7 35.7 + - - -
185H LEU 5.0 0.9 + - - -
186H TYR* 1.3 76.2 + - - +
188H LEU* 1.3 63.0 + - - +
160L LEU* 3.8 21.6 - - + +
178L THR* 4.7 8.5 - - + +
1214L GOL 3.0 22.3 + - - +
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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
----------------------------------------------------------
152H LEU* 3.8 3.8 - - - +
153H VAL* 2.8 47.0 + - + +
156H TYR* 3.9 24.2 - - + +
159H GLU* 4.9 2.0 - - - +
161H VAL* 4.2 24.0 - - + +
163H VAL* 3.6 26.7 - - + -
176H THR* 4.3 10.3 - - + -
177H PHE 3.6 17.5 - - - +
178H PRO* 5.7 0.2 - - + -
179H ALA* 4.3 9.2 - - + +
186H TYR 4.3 0.2 - - - -
187H THR* 1.3 75.1 - - - +
189H SER* 1.3 76.5 + - - +
190H SER* 4.6 0.4 - - - +
1214L GOL 3.4 8.7 - - - -
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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
----------------------------------------------------------
135H LEU* 5.2 0.2 - - - -
151H CYS 3.4 10.5 - - - -
152H LEU* 4.4 12.6 - - - -
176H THR* 3.7 0.3 - - - -
177H PHE* 2.9 27.4 + - - -
188H LEU* 1.3 82.6 - - - +
190H SER* 1.3 63.0 + - - +
133L VAL* 5.1 2.7 - - - -
135L PHE* 3.5 14.4 - - - -
176L SER* 2.7 31.1 + - - -
1214L GOL 2.9 18.4 + - - -
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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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150H GLY* 3.1 3.5 - - - -
151H CYS* 2.9 35.9 + - - -
163H VAL* 3.8 20.8 - - - +
165H TRP* 2.9 27.8 + - - -
174H VAL* 3.9 1.4 - - - +
175H HIS 3.1 6.8 + - - -
176H THR* 2.7 29.0 + - - -
177H PHE* 4.4 0.2 - - - -
188H LEU* 4.9 0.4 - - - -
189H SER* 1.3 76.4 - - - +
191H SER* 1.3 61.0 + - - +
135L PHE* 3.8 5.5 - - - -
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Residues in contact with SER 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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148H THR* 4.1 5.2 - - - -
149H LEU 3.3 6.7 - - - -
165H TRP* 4.4 1.8 - - - -
173H GLY 4.3 0.8 + - - -
174H VAL* 3.3 6.9 - - - +
175H HIS* 2.7 47.0 + - - +
177H PHE* 4.1 1.4 - - - -
190H SER* 1.3 75.3 - - - +
192H VAL* 1.3 62.4 + - - +
193H THR* 5.2 0.5 + - - -
135L PHE* 3.7 32.5 - - - -
137L ASN* 3.0 24.8 + - - -
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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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147H VAL 3.8 1.0 - - - +
148H THR* 3.4 1.8 - - - -
149H LEU* 2.8 47.5 + - + +
165H TRP* 3.7 40.6 - - + +
170H LEU* 4.0 23.3 - - + -
172H SER 4.4 1.8 - - - +
173H GLY 3.3 5.8 - - - +
174H VAL* 3.7 21.5 - - + -
191H SER* 1.3 75.2 - - - +
193H THR* 1.3 67.5 + - - +
194H VAL* 4.1 8.9 + - + +
204H VAL* 4.2 9.2 - - + -
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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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146H MET* 3.8 38.6 - - + +
147H VAL 3.4 10.5 - - - +
148H THR* 2.8 24.0 + - - +
172H SER 4.2 10.2 - - - +
173H GLY* 2.9 21.9 + - - +
175H HIS* 5.8 1.4 - - - -
191H SER* 5.2 0.9 + - - -
192H VAL* 1.3 73.8 - - - +
194H VAL* 1.3 67.3 + - - +
137L ASN* 4.9 6.8 + - - -
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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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146H MET* 3.4 7.9 - - - -
147H VAL* 2.8 49.3 + - + +
149H LEU* 4.5 11.0 - - + -
170H LEU* 4.0 37.7 - - + -
192H VAL* 4.3 9.2 - - + +
193H THR* 1.3 78.4 - - - +
195H PRO* 1.3 78.9 - - + +
198H THR* 3.8 7.0 - - - +
199H TRP* 4.0 15.5 - - + -
204H VAL* 4.7 5.6 - - + -
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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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145H SER 3.7 8.3 - - - +
146H MET* 3.9 16.1 - - + -
194H VAL* 1.3 93.1 - - + +
196H SER* 1.3 56.9 + - - +
197H SER* 3.1 18.6 - - - +
198H THR* 2.9 41.1 + - + +
199H TRP 3.6 3.8 + - - -
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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