Contacts of the strand formed by residues 105 - 115 (chain X) 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 105 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103X THR 3.3 4.6 + - - -
104X SER* 1.3 74.1 - - - +
106X ILE* 1.3 63.9 + - - -
107X TYR* 3.8 9.5 - - - -
173X PHE 3.8 0.3 - - - +
174X GLN* 3.7 2.0 - - - -
175X LEU 2.9 31.6 + - - +
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Residues in contact with ILE 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X GLY* 1.3 74.0 - - - -
107X TYR* 1.3 65.6 + - - +
172X ALA* 4.5 4.9 - - + -
173X PHE 3.3 8.1 - - - +
174X GLN* 4.2 18.6 - - + +
204X ALA* 3.7 2.3 - - - +
205X LEU* 2.9 55.5 + - + +
87Z LEU* 4.3 18.9 - - + +
89Z ALA* 3.8 13.5 - - + -
112Z PHE* 3.9 7.9 - - + -
114Z THR* 3.8 28.9 - - + -
241Z VAL* 4.4 10.1 - - + -
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Residues in contact with TYR 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X PRO* 3.8 10.0 - - + +
92X PHE* 3.9 23.8 - + - -
101X VAL* 3.4 15.7 - - + -
102X PRO* 3.2 20.4 - - + +
103X THR* 2.8 33.9 + - - -
105X GLY* 3.8 20.0 - - - -
106X ILE* 1.3 74.5 - - - +
108X PHE* 1.3 64.9 + - - +
109X VAL* 3.7 3.2 + - + +
172X ALA* 3.2 2.9 - - - -
173X PHE* 2.8 34.1 + - - +
175X LEU* 4.0 25.8 - - + -
181X LEU* 6.2 0.4 - - + -
202X ALA* 4.6 6.1 - - + -
203X PHE* 3.2 6.7 - - - +
204X ALA* 3.3 41.5 - - + +
205X LEU* 4.5 3.1 - - - -
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Residues in contact with PHE 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X TYR* 1.3 72.3 - - - +
109X VAL* 1.3 56.9 + - - +
110X TYR* 3.9 22.6 + + + -
168X TYR* 4.8 0.7 - + - -
170X GLY* 3.5 8.3 - - - -
171X ALA* 2.8 45.3 - - - -
172X ALA* 4.0 6.3 - - + +
202X ALA* 3.0 3.4 - - - -
203X PHE* 2.8 75.2 + + + -
205X LEU* 4.3 10.5 - - + +
134Y TYR* 3.6 26.9 - + - -
134Z TYR* 3.9 29.2 - + - -
136Z TYR* 4.0 9.4 - + + -
241Z VAL* 5.0 6.1 - - + -
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Residues in contact with VAL 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X TYR* 3.7 3.8 + - + +
108X PHE* 1.3 73.1 - - - +
110X TYR* 1.3 62.7 + - - +
135X VAL* 4.2 11.0 - - + -
148X LEU* 4.8 9.6 - - + -
149X LEU* 3.2 8.0 - - + +
170X GLY* 3.2 3.1 - - - -
171X ALA 2.9 24.2 + - - -
173X PHE* 3.4 36.1 - - + -
175X LEU* 5.6 2.9 - - + -
181X LEU* 4.4 14.4 - - + -
200X PHE* 4.0 22.9 - - + -
201X GLY 3.5 10.5 - - - +
202X ALA* 3.6 14.8 - - + -
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Residues in contact with TYR 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X HIS* 3.3 19.4 + - - +
108X PHE* 3.9 18.2 - + + -
109X VAL* 1.3 77.2 - - - +
111X SER* 1.3 65.7 + - - +
149X LEU* 4.3 1.6 - - - -
168X TYR* 3.5 18.4 - - - +
169X HIS 3.4 5.4 - - - +
170X GLY* 3.8 8.5 - - - -
199X PHE* 3.9 21.1 - + - -
200X PHE* 3.4 3.4 - - - -
201X GLY* 2.8 61.7 + - - +
202X ALA* 3.8 4.7 - - - -
203X PHE* 4.3 3.6 - + - -
134Y TYR* 4.4 4.9 - + - -
208Y GLY 3.6 14.6 - - - -
209Y GLY* 3.6 14.6 - - - -
210Y LEU* 3.1 46.4 + - + +
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Residues in contact with SER 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X TRP* 4.5 0.7 - - - -
110X TYR* 1.3 82.0 - - - +
112X GLN* 1.3 58.7 + - - +
133X HIS* 2.8 27.1 + - - -
135X VAL* 3.5 26.4 - - - +
168X TYR* 3.7 3.4 - - - -
169X HIS* 2.9 36.9 + - - +
199X PHE* 2.6 22.4 + - - -
200X PHE* 3.5 12.5 - - - +
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Residues in contact with GLN 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X SER* 1.3 75.1 + - - +
113X VAL* 1.3 75.6 + - - +
114X VAL* 4.4 5.4 - - + -
133X HIS* 4.7 0.7 - - - -
166X SER* 4.0 11.3 - - - -
167X MET 3.4 13.2 - - - +
168X TYR* 3.4 17.1 - - + +
196X SER 3.9 0.2 + - - -
197X THR 3.1 20.6 + - - +
198X VAL* 3.1 2.3 - - - -
199X PHE* 2.9 57.0 + - + +
180Y GLU 3.2 23.9 + - - +
181Y GLY* 4.1 1.9 - - - -
206Y GLY 3.5 20.6 - - - +
207Y PHE* 3.5 11.4 - - - +
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Residues in contact with VAL 113 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77X LEU* 5.0 1.8 - - + -
111X SER* 5.1 0.2 - - - +
112X GLN* 1.3 76.8 - - - +
114X VAL* 1.3 65.3 + - - +
115X PHE* 3.8 20.8 - - + -
133X HIS* 3.3 56.7 - - + +
165X HIS 3.9 0.2 - - - +
166X SER* 3.4 3.1 - - - -
167X MET* 3.0 40.1 + - + +
185X THR* 4.6 5.6 - - + -
191X LEU* 3.7 21.8 - - + -
198X VAL* 4.1 10.8 - - + -
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Residues in contact with VAL 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X GLN* 4.4 5.6 - - + +
113X VAL* 1.3 80.6 - - - +
115X PHE* 1.3 77.6 + - - +
164X LEU* 4.6 13.7 - - + -
165X HIS 3.1 11.7 - - - +
166X SER* 3.7 19.7 - - - +
191X LEU* 3.5 1.7 - - - +
192X VAL* 3.1 39.1 + - + -
197X THR* 3.3 44.4 - - + +
198X VAL* 3.9 5.4 - - + +
180Y GLU 4.6 3.1 - - - +
181Y GLY* 5.4 0.7 - - - -
182Y ALA* 5.2 2.9 - - + +
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Residues in contact with PHE 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X VAL* 3.8 20.4 - - + -
114X VAL* 1.3 83.3 - - - +
116X SER* 1.3 60.4 + - - +
131X LEU* 3.2 45.8 - - + -
132X ALA 4.2 5.4 - - - -
153X LYS* 6.2 0.4 - - + -
163X TRP* 4.1 20.1 - - + -
164X LEU* 3.2 12.4 - - - +
165X HIS* 2.7 43.4 + - + +
167X MET* 3.8 22.4 - - + -
185X THR* 5.2 2.7 - - - -
186X ASP 3.8 12.1 - - - -
187X GLY 3.7 19.5 - - - -
190X HIS* 3.6 2.5 - - + -
191X LEU* 3.4 30.7 - - + -
192X VAL* 4.2 0.4 - - - -
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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