Contacts of the strand formed by residues 203 - 213 (chain Z) 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 THR 203 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152X GLN 4.0 8.1 - - - -
153X LYS* 3.3 21.5 + - - +
140Z GLY* 3.8 0.2 - - - -
141Z TYR* 2.8 58.5 + - + +
143Z GLY* 4.9 2.4 - - - +
157Z VAL* 5.5 4.3 - - + -
183Z GLU* 3.1 28.7 + - + +
185Z VAL* 4.8 13.5 - - + -
202Z TYR* 1.3 75.0 - - - +
204Z SER* 1.3 64.4 + - - +
205Z VAL* 4.6 5.6 - - + -
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Residues in contact with SER 204 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X SER 4.3 2.6 + - - -
151X SER* 3.4 36.3 - - - -
152X GLN 4.0 8.0 + - - -
153X LYS* 5.6 0.4 - - - +
167X MET* 5.8 1.8 - - - -
138Z LEU* 5.0 9.4 - - - +
139Z VAL 3.4 7.4 - - - -
140Z GLY* 3.7 12.1 + - - -
183Z GLU* 4.0 8.8 - - - +
203Z THR* 1.3 79.5 + - - +
205Z VAL* 1.3 67.2 + - - +
235Z LYS* 4.4 2.4 - - - +
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Residues in contact with VAL 205 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Y SER* 5.5 4.9 - - - +
138Z LEU* 3.3 3.5 - - - -
139Z VAL 2.8 37.5 + - - +
141Z TYR* 4.1 22.2 - - + -
157Z VAL* 4.5 4.0 - - + -
158Z THR 5.6 0.2 - - - -
159Z LEU* 2.9 35.8 - - + +
181Z GLY* 4.0 21.1 - - - -
182Z ALA* 4.1 4.5 - - - +
183Z GLU* 3.9 31.0 - - + +
203Z THR* 4.6 2.7 - - + -
204Z SER* 1.3 79.6 - - - +
206Z GLY* 1.3 62.3 + - - +
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Residues in contact with GLY 206 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X TYR 5.8 0.4 - - - -
138Y LEU* 3.4 13.7 - - - +
204Y SER* 5.6 2.6 - - - -
206Y GLY* 5.5 2.8 + - - -
137Z CYS 3.2 9.9 - - - -
138Z LEU* 4.0 16.7 - - - +
159Z LEU* 4.3 0.9 - - - -
181Z GLY* 5.5 0.7 - - - -
204Z SER 4.4 0.2 - - - -
205Z VAL* 1.3 79.2 - - - +
207Z PHE* 1.3 68.0 + - - +
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Residues in contact with PHE 207 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Y LEU* 3.4 26.2 - - + -
237Y PHE* 4.8 3.4 - - + -
136Z TYR* 3.5 3.5 - - - +
137Z CYS* 2.9 59.8 + - + +
159Z LEU* 2.8 42.6 - - + -
161Z SER* 3.2 38.1 - - - -
179Z LEU* 3.5 28.5 - - + -
180Z GLU* 4.4 1.6 - - - -
181Z GLY* 3.8 18.8 - - - -
206Z GLY* 1.3 77.5 - - - +
208Z GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 208 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Y TYR* 4.1 5.5 - - - +
138Y LEU* 4.9 1.3 - - - +
237Y PHE* 3.0 21.9 - - - -
134Z TYR* 3.6 24.7 + - - -
135Z LEU 3.1 12.8 - - - -
136Z TYR* 4.0 1.1 - - - -
179Z LEU* 3.5 7.9 - - - -
207Z PHE* 1.3 76.8 - - - +
209Z GLY* 1.3 59.1 + - - -
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Residues in contact with GLY 209 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Y HIS* 4.8 1.8 - - - -
136Y TYR* 4.1 13.7 - - - -
237Y PHE* 4.3 3.4 - - - -
134Z TYR* 3.9 7.9 - - - -
135Z LEU* 2.9 32.2 + - - +
179Z LEU* 3.3 12.9 - - - +
208Z GLY* 1.3 74.0 - - - -
210Z LEU* 1.3 62.5 + - - -
211Z VAL* 3.5 10.8 + - - +
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Residues in contact with LEU 210 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Y ALA* 4.7 4.9 - - + -
90Y ALA 3.5 11.4 - - - +
91Y HIS* 3.9 14.1 + - - -
110Y GLN* 5.0 3.8 - - - +
112Y PHE* 3.8 26.6 - - + -
136Y TYR* 3.1 31.2 + - + +
240Y ALA 3.4 12.3 - - - +
241Y VAL* 2.9 40.4 - - + -
132Z LEU* 6.0 3.6 - - + -
133Z TYR 3.2 11.2 - - - +
134Z TYR* 3.8 29.6 - - + -
209Z GLY* 1.3 70.2 - - - -
211Z VAL* 1.3 61.2 + - - +
243Z VAL* 4.3 10.5 - - + -
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Residues in contact with VAL 211 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Y HIS* 6.5 0.2 - - + -
110Y GLN* 4.1 14.4 - - + +
132Z LEU* 3.8 2.6 - - - -
133Z TYR* 2.9 31.0 + - - +
135Z LEU* 3.6 30.5 - - + -
163Z LEU* 4.8 2.0 - - + -
178Z LEU* 3.6 40.2 - - + -
179Z LEU* 5.0 8.1 - - + -
209Z GLY 3.7 10.3 - - - +
210Z LEU* 1.3 77.8 - - - +
212Z GLN* 1.3 63.3 + - - +
213Z LEU* 3.3 19.7 + - + +
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Residues in contact with GLN 212 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y GLN* 5.0 3.0 + - - -
112Y PHE* 5.4 12.4 - - + +
131Z GLY* 3.7 11.9 - - - +
132Z LEU* 3.4 30.8 - - + +
210Z LEU 4.3 0.6 + - - -
211Z VAL* 1.3 75.7 - - - +
213Z LEU* 1.3 62.6 + - - +
214Z ARG* 4.1 0.7 + - - +
217Z GLU* 4.6 2.8 - - - +
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Residues in contact with LEU 213 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Z LEU* 3.9 22.0 - - + -
130Z ASP* 3.9 0.5 - - - +
131Z GLY 2.9 34.6 + - - +
133Z TYR* 3.8 21.7 - - + -
135Z LEU* 3.8 31.0 - - + -
163Z LEU* 3.5 25.1 - - + -
178Z LEU* 4.6 0.2 - - + -
211Z VAL* 3.3 17.5 + - + +
212Z GLN* 1.3 76.6 - - - +
214Z ARG* 1.3 62.2 + - - +
217Z GLU* 3.3 18.4 - - + +
219Z VAL* 3.9 19.7 - - + -
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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