Contacts of the strand formed by residues 175 - 182 (chain H) in PDB entry 4MXW
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 175 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H THR* 4.7 16.0 - - + +
143H ASP* 3.1 2.9 + - - -
144H TYR* 2.6 56.3 + - + +
145H PHE* 3.8 31.2 - + - -
146H PRO* 4.7 0.9 - - + -
147H GLU* 2.9 51.4 - - + +
167H ALA* 4.5 5.2 - - + -
168H VAL 3.2 17.7 - - - -
169H LEU* 3.4 34.2 - - + +
174H LEU* 1.3 72.1 - - - +
176H SER* 1.3 66.3 + - - +
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Residues in contact with SER 176 (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 LEU* 5.4 4.0 - - - -
141H VAL 3.5 10.8 - - - -
142H LYS* 3.1 6.7 - - - +
143H ASP 2.9 13.9 + - - -
144H TYR* 4.1 2.6 - - - -
167H ALA* 3.3 1.5 - - - -
168H VAL* 2.7 41.8 + - - +
170H GLN* 2.9 34.1 + - - -
175H TYR* 1.3 80.5 + - - +
177H LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H CYS 5.5 0.2 - - - +
140H LEU* 3.5 7.3 - - - +
141H VAL* 2.9 39.3 + - + +
144H TYR* 3.3 26.5 - - + +
147H GLU* 5.4 0.7 - - - +
149H VAL* 3.7 16.4 - - + +
151H VAL* 4.3 13.9 - - + -
164H THR* 3.9 27.8 - - + -
165H PHE* 3.6 18.4 - - + +
166H PRO 4.4 2.2 - - - +
167H ALA* 3.7 19.1 - - + +
168H VAL* 5.5 2.0 - - - -
176H SER* 1.3 75.4 - - - +
178H SER* 1.3 68.7 + - - +
179H SER* 4.6 0.4 - - - +
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Residues in contact with SER 178 (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* 4.5 13.9 - - - -
139H CYS 3.2 10.1 - - - -
140H LEU* 4.3 11.9 - - - -
165H PHE* 2.9 48.4 + - - +
177H LEU* 1.3 80.5 - - - +
179H SER* 1.3 61.2 + - - +
180H VAL* 5.1 3.3 - - - +
133L VAL* 4.7 7.9 - - - +
176L SER* 3.7 17.0 + - - -
178L THR* 5.3 2.0 - - - -
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Residues in contact with SER 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H CYS* 2.9 37.9 + - - -
151H VAL* 3.4 24.2 - - - +
153H TRP* 2.9 35.1 + - - -
162H VAL* 3.9 1.6 - - - +
163H HIS 3.3 4.7 + - - -
164H THR* 2.8 28.0 + - - +
177H LEU* 4.6 0.6 - - - +
178H SER* 1.3 73.7 - - - +
180H VAL* 1.3 59.7 + - - +
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Residues in contact with VAL 180 (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* 4.9 11.0 - - + -
137H LEU 3.5 11.4 - - - +
138H GLY* 4.5 6.1 - - - -
161H GLY 4.2 0.6 - - - +
162H VAL* 3.5 4.5 - - - +
163H HIS* 2.8 48.2 + - + +
165H PHE* 3.6 26.2 - - + -
178H SER* 4.1 3.8 - - - +
179H SER* 1.3 78.7 - - - +
181H VAL* 1.3 58.9 + - - +
118L PHE* 4.8 8.5 - - + -
133L VAL* 6.1 2.9 - - + -
135L LEU* 3.6 43.7 - - + -
137L ASN* 5.4 1.6 - - - +
176L SER* 6.3 0.2 - - - -
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Residues in contact with VAL 181 (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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136H ALA* 3.6 1.5 - - - +
137H LEU* 2.8 59.7 + - + +
153H TRP* 4.2 14.1 - - + -
158H LEU* 3.6 34.5 - - + -
160H SER 3.9 17.3 - - - +
161H GLY 3.8 5.4 - - - -
162H VAL* 4.0 15.9 - - + +
180H VAL* 1.3 76.0 - - - +
182H THR* 1.3 76.4 + - - +
183H VAL* 3.9 4.0 + - + -
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Residues in contact with THR 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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135H ALA 3.4 13.9 - - - +
136H ALA* 3.9 15.5 - - + -
158H LEU* 5.7 0.9 - - - +
160H SER 4.7 4.7 - - - +
161H GLY* 3.8 17.3 + - - -
181H VAL* 1.3 81.9 - - - +
183H VAL* 1.3 64.7 + - - +
114L SER* 6.3 0.2 - - - -
116L PHE* 4.6 7.9 - - + -
135L LEU* 5.7 2.0 - - + -
137L ASN* 3.2 33.5 + - - +
138L ASN* 5.2 0.7 + - - -
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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