Contacts of the strand formed by residues 131 - 141 (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 GLY 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLN 3.6 1.8 + - - -
130B ASP* 1.3 75.0 - - - +
132B LEU* 1.3 62.6 + - - -
133B TYR* 3.6 8.0 + - - -
212B GLN* 3.4 12.0 - - - +
213B LEU 2.9 34.6 + - - +
242B MET* 4.0 13.2 - - - -
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Residues in contact with LEU 132 (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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62A LYS 5.6 0.9 - - - +
64A ALA* 3.4 33.0 - - + -
87A PHE* 3.7 24.9 - - + -
89A GLN* 4.1 19.1 - - - +
131B GLY* 1.3 71.2 - - - -
133B TYR* 1.3 58.2 + - - +
210B LEU* 3.9 24.0 - - + -
211B VAL 3.7 21.8 - - - +
212B GLN* 3.9 19.8 - - + +
242B MET* 3.7 6.5 - - - +
243B VAL* 2.9 41.6 + - + +
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Residues in contact with TYR 133 (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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88B PRO* 4.1 14.6 - - + +
127B LEU* 3.4 41.2 - - + +
129B GLN* 2.6 43.3 + - - +
131B GLY 3.7 12.1 - - - -
132B LEU* 1.3 73.5 - - - +
134B TYR* 1.3 61.3 + - - +
135B LEU* 3.7 8.5 + - + -
209B GLY 3.6 0.2 - - - +
210B LEU* 3.5 6.4 - - - -
211B VAL* 2.8 37.5 + - - +
213B LEU* 3.6 32.3 - - + -
240B ALA* 4.8 1.1 - - + -
241B VAL* 3.1 10.3 - - - +
242B MET* 3.2 45.1 - - + -
243B VAL* 5.0 0.2 - - - -
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Residues in contact with TYR 134 (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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108A PHE* 3.5 22.8 - + - -
110A TYR* 4.4 4.9 - + - -
168A TYR* 2.4 27.2 + - - -
203A PHE* 3.5 23.6 - + + -
132B LEU 4.4 0.2 + - - -
133B TYR* 1.3 72.5 - - - +
135B LEU* 1.3 73.0 + - - +
136B TYR* 3.7 26.7 - + + +
208B GLY* 3.4 5.3 - - - -
209B GLY* 3.5 24.7 - - - -
210B LEU* 3.9 11.2 - - + +
239B GLY 3.8 0.3 - - - +
240B ALA* 3.2 4.7 - - - -
241B VAL* 2.9 36.8 + - + +
243B VAL* 4.3 10.0 - - + +
134D TYR* 3.3 27.1 + + - -
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Residues in contact with LEU 135 (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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125B LEU* 5.8 2.0 - - + -
127B LEU* 5.2 0.4 - - + -
133B TYR* 4.3 3.4 - - + +
134B TYR* 1.3 80.1 - - - +
136B TYR* 1.3 63.6 + - - +
161B SER* 4.4 10.3 - - - +
178B LEU* 4.1 19.1 - - + -
179B LEU* 4.4 9.6 - - + -
207B PHE* 6.5 0.2 - - + -
208B GLY* 3.2 2.4 - - - -
209B GLY 2.9 34.1 + - - +
211B VAL* 3.9 25.6 - - + -
213B LEU* 3.8 26.5 - - + -
219B VAL* 4.1 21.1 - - + -
238B PHE* 6.6 0.4 - - + -
239B GLY 3.4 3.6 - - - +
240B ALA* 3.4 27.8 - - + -
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Residues in contact with TYR 136 (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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91B HIS* 2.9 22.6 + - - -
134B TYR* 3.7 20.2 - + + +
135B LEU* 1.3 76.8 - - - +
137B CYS* 1.3 64.5 + - - +
161B SER* 6.1 0.2 - - - -
207B PHE* 3.3 14.6 - - - +
208B GLY* 3.9 1.3 - - - -
237B PHE* 3.6 36.1 - + - -
238B PHE* 3.2 4.5 - - - +
239B GLY* 2.9 57.3 + - - +
240B ALA* 4.4 0.9 - - - -
241B VAL* 5.3 0.4 - - + -
134D TYR* 3.6 26.9 - + - +
208D GLY 4.2 4.5 - - - +
209D GLY* 3.9 0.7 - - - -
210D LEU* 3.1 49.4 + - + +
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Residues in contact with CYS 137 (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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104B TRP* 5.4 1.6 - - - -
136B TYR* 1.3 79.2 - - - +
138B LEU* 1.3 62.0 + - - +
139B VAL* 4.3 20.0 - - - -
159B LEU* 4.9 2.5 - - - -
160B ARG 5.8 0.2 - - - -
161B SER* 5.3 2.5 - - - -
205B VAL 4.0 0.3 - - - +
206B GLY* 3.2 2.3 - - - -
207B PHE* 2.8 64.9 + - + +
221B VAL* 3.9 22.7 - - + -
237B PHE 3.4 7.9 - - - -
238B PHE* 3.9 17.9 - - + -
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Residues in contact with LEU 138 (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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137B CYS* 1.3 74.1 - - - +
139B VAL* 1.3 68.7 + - - +
140B GLY 4.4 0.2 - - - +
204B SER* 4.7 12.6 - - - +
205B VAL 3.3 9.0 - - - +
206B GLY* 4.1 14.1 - - - +
235B LYS 3.1 29.4 - - - +
236B THR* 3.1 2.9 - - - -
237B PHE* 2.9 65.6 + - + +
180D GLU 4.1 13.2 - - - +
181D GLY* 5.6 0.4 - - - -
206D GLY 3.4 25.6 - - - +
207D PHE* 3.4 18.8 - - + -
208D GLY 5.3 0.9 - - - +
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Residues in contact with VAL 139 (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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104B TRP* 5.1 2.5 - - + -
137B CYS* 4.3 11.0 - - - -
138B LEU* 1.3 80.6 - - - +
140B GLY* 1.3 61.5 - - - +
141B TYR* 3.4 37.4 - - + +
159B LEU* 3.8 22.2 - - + -
204B SER* 3.4 1.0 - - - -
205B VAL 2.8 35.9 + - - -
223B ILE* 3.4 27.1 - - + -
229B VAL* 3.8 9.4 - - + -
235B LYS 3.2 2.5 - - - -
236B THR* 3.5 18.6 - - + -
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Residues in contact with GLY 140 (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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139B VAL* 1.3 73.3 - - - +
141B TYR* 1.3 55.1 + - - +
204B SER* 3.4 17.9 - - - -
229B VAL* 3.5 5.7 - - - +
230B ASP* 2.7 36.7 + - - +
235B LYS* 2.4 30.2 + - - -
236B THR* 3.2 4.1 - - - +
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 3.4 32.0 - - + +
140B GLY* 1.3 73.6 - - - -
142B ARG* 1.3 60.8 + - - +
143B GLY* 3.7 6.7 - - - +
157B VAL* 3.1 34.7 - - + +
158B THR 3.3 2.9 + - - -
159B LEU* 3.3 24.6 - - + +
202B TYR* 3.3 21.0 - - - -
203B THR* 2.6 45.1 + - + +
205B VAL* 4.4 4.5 - - + -
223B ILE* 3.0 26.4 - - + +
224B SER* 4.5 0.9 + - - -
225B HIS* 3.9 18.2 - - + -
228B MET* 3.0 28.9 - - + +
229B VAL* 3.8 7.6 - - + -
230B ASP* 3.9 4.8 - - - +
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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