Contacts of the strand formed by residues 203 - 213 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B TYR* 2.6 62.4 + - + +
143B GLY 5.4 0.4 - - - +
157B VAL* 5.5 5.2 - - + -
183B GLU* 3.6 20.7 + - + +
185B VAL* 5.1 14.9 - - + +
202B TYR* 1.3 76.3 - - - +
204B SER* 1.3 59.1 + - - +
205B VAL* 4.7 5.2 - - + -
182D ALA 3.1 11.0 - - - -
183D GLU* 3.4 25.7 + - - +
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Residues in contact with SER 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 4.7 11.7 - - - +
139B VAL 3.4 7.6 - - - -
140B GLY* 3.4 17.2 - - - -
141B TYR* 5.1 0.2 - - - -
183B GLU* 4.1 7.4 - - - +
203B THR* 1.3 75.9 + - - +
205B VAL* 1.3 66.6 + - - +
235B LYS* 4.4 3.5 - - - +
180D GLU 4.6 0.5 + - - -
181D GLY* 3.5 13.1 - - - -
182D ALA 3.2 28.7 + - - -
183D GLU* 5.2 2.9 + - - +
205D VAL* 5.2 6.6 - - - +
206D GLY 5.6 1.8 - - - -
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A SER* 5.1 5.4 - - - +
138B LEU* 4.3 2.7 - - - -
139B VAL 2.8 36.4 + - - +
141B TYR* 4.4 11.2 - - + -
157B VAL* 4.8 1.6 - - + -
159B LEU* 2.9 45.7 - - + +
181B GLY* 4.0 24.0 - - - -
182B ALA 4.1 2.5 - - - +
183B GLU* 3.9 33.0 - - + +
203B THR* 4.7 3.6 - - + -
204B SER* 1.3 80.3 - - - +
206B GLY* 1.3 62.1 + - - +
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN* 3.9 2.3 - - - +
166A SER* 5.1 4.2 + - - +
168A TYR* 3.3 22.4 + - - +
137B CYS 3.2 9.4 - - - -
138B LEU* 4.0 16.5 - - - +
181B GLY* 5.7 0.2 - - - -
204B SER 4.3 0.4 + - - -
205B VAL* 1.3 78.0 - - - +
207B PHE* 1.3 67.4 + - - +
206D GLY 5.3 2.6 + - - -
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN* 3.3 21.8 - - - +
168A TYR* 3.7 14.1 - - + -
199A PHE* 5.2 0.9 - - + -
135B LEU* 6.5 0.2 - - + -
136B TYR* 3.3 3.8 - - - +
137B CYS* 2.8 61.7 + - + +
159B LEU* 3.6 31.6 - - + -
160B ARG* 3.8 11.4 - - - -
161B SER* 3.9 9.2 - - - -
179B LEU* 3.4 45.8 - - + -
180B GLU 4.4 2.2 - - - -
181B GLY* 3.6 22.9 - - - -
206B GLY* 1.3 78.2 - - - +
208B GLY* 1.3 61.6 + - - +
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Residues in contact with GLY 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TYR* 4.8 0.2 - - - -
168A TYR* 3.1 37.4 - - - -
199A PHE* 3.4 17.3 - - - -
134B TYR* 3.4 7.2 - - - -
135B LEU 3.2 12.8 - - - -
136B TYR* 3.9 1.8 - - - -
179B LEU* 3.4 8.0 - - - +
207B PHE* 1.3 74.5 - - - +
209B GLY* 1.3 57.9 + - - -
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 5.4 1.3 - - - -
110A TYR* 4.0 14.1 - - - -
199A PHE* 4.7 0.4 - - - -
134B TYR* 3.5 11.7 - - - -
135B LEU* 2.9 30.9 + - - -
179B LEU* 3.2 16.3 - - - +
208B GLY* 1.3 75.5 - - - -
210B LEU* 1.3 63.6 - - - -
211B VAL* 3.5 4.7 + - - +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA* 4.0 11.0 - - + -
65A ALA 3.7 19.5 - - - +
66A HIS* 3.6 24.6 + - + +
87A PHE* 4.5 8.0 - - + -
110A TYR* 3.0 28.3 + - + +
202A ALA 3.9 3.4 - - - +
203A PHE* 3.3 54.1 - - + -
132B LEU* 3.9 22.9 - - + -
133B TYR 3.5 3.8 - - - +
134B TYR* 3.9 17.0 - - + +
209B GLY* 1.3 71.2 - - - -
211B VAL* 1.3 61.5 + - - +
243B VAL* 4.4 3.8 - - + -
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 6.1 0.2 - - - +
85A ARG* 3.1 38.6 - - - +
87A PHE* 5.7 0.4 - - - -
132B LEU* 3.8 3.8 - - - -
133B TYR* 2.8 39.0 + - - +
135B LEU* 3.9 26.7 - - + -
178B LEU* 4.0 30.1 - - + +
179B LEU* 4.6 9.0 - - + -
209B GLY 3.9 9.2 - - - +
210B LEU* 1.3 79.7 - - - +
212B GLN* 1.3 57.7 + - - +
213B LEU* 3.2 15.0 + - + +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 3.2 20.0 + - - +
87A PHE* 4.5 21.5 - - + -
89A GLN* 3.7 25.2 + - - +
131B GLY* 3.4 15.2 - - - +
132B LEU* 3.9 21.7 - - + +
211B VAL* 1.3 71.3 - - - +
213B LEU* 1.3 62.2 + - - +
214B ARG* 4.2 0.5 + - - +
217B GLU* 4.6 1.6 - - - +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 3.8 15.9 - - + -
130B ASP* 3.7 0.7 - - - +
131B GLY 2.9 32.5 + - - +
133B TYR* 3.6 33.2 - - + -
135B LEU* 3.8 28.9 - - + -
163B LEU* 3.5 31.4 - - + -
211B VAL* 3.2 15.6 + - + +
212B GLN* 1.3 77.4 - - - +
214B ARG* 1.3 62.9 + - - +
217B GLU* 3.5 13.0 - - + +
219B VAL* 3.6 18.2 - - + -
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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