Contacts of the strand formed by residues 181 - 190 (chain H) in PDB entry 1MHP
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 181 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41H PRO* 5.6 7.1 - - - +
115H THR* 5.6 8.0 - - + +
149H ASP 3.3 3.6 + - - -
150H TYR* 2.8 54.2 + - + +
151H PHE* 4.1 21.8 - + - -
152H PRO* 4.2 3.1 - - + -
153H GLU* 3.2 51.5 - - + +
173H ALA* 4.0 4.9 - - + -
174H VAL* 3.5 15.0 - - - -
175H LEU* 3.6 42.3 - - + +
180H LEU* 1.3 73.2 - - - +
182H SER* 1.3 62.6 + - - +
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Residues in contact with SER 182 (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 LEU* 3.8 11.1 - - - +
147H VAL 3.3 13.5 + - - -
148H LYS* 3.7 14.3 + - - +
150H TYR* 3.9 2.0 - - - -
172H PRO 4.6 0.2 - - - +
173H ALA* 3.4 2.0 - - - -
174H VAL* 3.1 32.4 + - - +
176H GLN* 3.5 27.4 - - - -
181H TYR* 1.3 78.1 - - - +
183H LEU* 1.3 66.1 + - - +
177L THR* 6.1 0.5 - - - +
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Residues in contact with LEU 183 (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 LEU* 3.6 4.1 - - - +
147H VAL* 2.8 57.0 + - + +
150H TYR* 3.4 23.8 - - - +
153H GLU* 5.3 1.6 - - - +
155H VAL* 3.6 19.3 - - + +
157H VAL* 4.5 3.4 - - + -
170H THR* 4.0 15.3 - - - +
171H PHE* 3.5 22.7 - - - +
172H PRO* 4.2 3.4 - - + +
173H ALA* 3.9 14.1 - - + +
182H SER* 1.3 78.1 + - - +
184H SER* 1.3 73.9 + - - +
185H SER 4.3 1.1 - - - +
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Residues in contact with SER 184 (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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129H LEU* 3.9 14.1 - - - +
145H CYS 3.1 12.4 + - - -
146H LEU* 3.3 25.1 - - - +
171H PHE* 2.8 46.8 + - - +
183H LEU* 1.3 77.9 - - - +
185H SER* 1.3 59.8 + - - +
186H VAL* 4.5 4.5 - - - -
132L VAL* 4.3 14.9 - - - +
175L SER* 5.5 3.4 - - - -
177L THR* 5.0 2.8 + - - -
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Residues in contact with SER 185 (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* 3.2 2.6 - - - -
145H CYS* 2.7 35.5 + - - +
147H VAL* 5.6 0.8 - - - +
157H VAL* 3.4 26.9 - - - +
159H TRP* 3.0 23.7 + - - -
168H VAL* 4.0 1.4 - - - +
170H THR* 2.8 35.6 + - - +
183H LEU* 4.3 1.2 - - - +
184H SER* 1.3 74.8 - - - +
186H VAL* 1.3 57.9 + - - +
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Residues in contact with VAL 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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129H LEU* 4.3 18.6 - - + -
142H ALA* 4.9 0.4 - - + -
143H LEU 3.5 14.8 - - - +
144H GLY* 4.0 0.4 - - - -
159H TRP* 4.9 0.7 - - - -
167H GLY 3.7 0.4 - - - +
168H VAL* 3.4 4.6 - - - +
169H HIS* 2.5 49.4 + - + +
171H PHE* 3.7 21.1 - - + -
184H SER* 4.5 3.8 - - - -
185H SER* 1.3 81.0 + - - +
187H VAL* 1.3 69.8 + - - +
188H THR* 5.2 1.8 - - + -
117L PHE* 4.9 7.0 - - + -
132L VAL* 5.9 2.7 - - + -
134L LEU* 3.3 34.5 - - + -
136L ASN* 5.5 2.0 - - - +
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Residues in contact with VAL 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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141H ALA 4.1 0.2 - - - +
142H ALA* 3.4 2.8 - - - -
143H LEU* 2.9 66.4 + - + +
159H TRP* 4.4 10.5 - - + -
164H LEU* 4.1 18.8 - - + -
166H SER 3.9 5.2 - - - +
167H GLY 3.1 19.5 - - - +
168H VAL* 3.8 17.7 - - + -
186H VAL* 1.3 78.1 - - - +
188H THR* 1.3 83.8 + - - +
189H VAL* 4.0 11.2 - - + -
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Residues in contact with THR 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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140H THR* 4.8 10.5 - - - +
141H ALA 3.2 10.3 - - - +
142H ALA* 4.3 12.3 - - + -
166H SER 4.2 7.3 - - - +
167H GLY* 3.2 17.8 + - - +
169H HIS* 6.0 0.4 - - + -
186H VAL* 5.2 3.6 - - + -
187H VAL* 1.3 84.5 - - - +
189H VAL* 1.3 66.6 + - - +
115L PHE* 4.6 8.7 - - + -
136L ASN* 3.7 29.1 + - - +
137L ASN* 5.3 3.8 + - - -
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Residues in contact with VAL 189 (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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140H THR* 3.4 7.4 - - - -
141H ALA* 2.8 34.6 + - + +
143H LEU* 4.0 13.0 - - + -
164H LEU* 4.5 7.2 - - + -
166H SER 5.8 0.2 - - - +
187H VAL* 4.0 18.4 - - + -
188H THR* 1.3 79.9 - - - +
190H PRO* 1.3 73.2 - - + +
193H SER* 3.7 4.9 - - - +
194H LEU* 4.3 8.3 - - + -
199H TYR* 3.2 53.6 - - + +
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Residues in contact with PRO 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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139H GLY 3.7 8.3 - - - +
140H THR* 4.6 1.6 - - + -
189H VAL* 1.3 92.2 - - + +
191H SER* 1.3 67.0 + - - +
192H SER* 3.9 15.3 - - - +
193H SER* 2.6 36.7 + - - +
194H LEU* 4.4 0.2 - - - +
199H TYR* 4.5 0.9 - - - +
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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