Contacts of the strand formed by residues 165 - 175 (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 HIS 165 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113X VAL 3.9 0.5 - - - +
114X VAL* 3.1 5.6 - - - +
115X PHE* 2.7 50.7 + - + +
131X LEU* 4.8 2.5 - - + -
153X LYS* 4.1 29.5 - - + +
155X VAL* 3.6 21.0 - - + +
163X TRP* 3.3 37.2 - + - +
164X LEU* 1.3 91.8 + - - +
166X SER* 1.3 63.7 + - - +
167X MET* 4.1 4.7 - - + +
182Y ALA 3.6 4.4 + - - -
183Y GLU* 3.3 23.6 + - - +
184Y THR 4.5 8.7 - - - -
185Y VAL* 5.8 2.0 - - + -
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Residues in contact with SER 166 (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* 4.0 17.8 - - - +
113X VAL 3.4 7.6 - - - -
114X VAL* 3.7 11.9 - - - +
165X HIS* 1.3 74.6 + - - +
167X MET* 1.3 63.8 + - - +
168X TYR* 3.5 3.8 + - - +
181Y GLY* 3.6 3.2 - - - -
182Y ALA* 2.5 45.7 + - - -
183Y GLU* 5.4 5.1 + - - +
205Y VAL* 5.1 6.8 - - - +
206Y GLY 5.2 4.5 + - - +
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Residues in contact with MET 167 (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 4.2 0.7 - - - +
112X GLN* 3.4 2.8 - - - -
113X VAL* 3.0 36.5 + - + +
115X PHE* 3.8 22.9 - - + -
131X LEU 4.2 1.1 - - - +
132X ALA* 3.4 11.9 - - - +
133X HIS* 3.4 30.3 - - + +
151X SER* 3.3 51.8 - - - +
152X GLN 3.8 18.2 - - - +
153X LYS* 4.3 9.2 - - + -
165X HIS* 4.1 3.1 - - + -
166X SER* 1.3 72.8 - - - +
168X TYR* 1.3 59.7 + - - +
169X HIS* 5.5 0.7 - - - -
204Z SER* 5.8 2.5 - - - -
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Residues in contact with TYR 168 (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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108X PHE* 4.4 1.3 - + - -
110X TYR* 3.5 22.3 - + + +
111X SER 3.7 5.8 - - - -
112X GLN* 3.4 26.0 - - + +
151X SER* 5.2 0.9 + - - -
166X SER 3.5 4.4 + - - -
167X MET* 1.3 74.2 - - - +
169X HIS* 1.3 82.8 + - - +
170X GLY* 4.0 10.5 - - - -
199X PHE* 4.0 7.4 - + - -
134Y TYR* 2.8 27.1 + - - -
206Y GLY 3.2 24.2 - - - +
207Y PHE* 3.8 11.0 - - + -
208Y GLY* 3.0 42.6 + - - -
134Z TYR* 5.3 3.8 - - - -
138Z LEU* 3.8 11.1 - - - +
206Z GLY* 5.8 0.7 - - - -
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Residues in contact with HIS 169 (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 2.9 33.3 + - - -
133X HIS* 3.0 41.4 + + - -
135X VAL* 4.2 10.8 - - + -
149X LEU* 3.3 44.0 + - + +
150X SER 3.9 6.7 - - - -
151X SER* 3.2 22.6 + - - -
167X MET 5.3 0.9 - - - -
168X TYR* 1.3 87.5 - - - +
170X GLY* 1.3 59.7 + - - +
138Z LEU* 3.5 23.1 - - + -
237Z PHE* 4.9 2.0 - - + -
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Residues in contact with GLY 170 (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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108X PHE* 3.5 16.6 - - - -
109X VAL 3.2 12.1 - - - -
110X TYR* 3.7 8.7 - - - -
149X LEU* 3.8 3.6 - - - -
168X TYR* 4.0 7.5 - - - -
169X HIS* 1.3 75.2 - - - +
171X ALA* 1.3 65.8 + - - +
136Z TYR* 4.3 6.8 - - - +
138Z LEU* 5.7 0.7 - - - +
237Z PHE* 3.6 13.9 - - - -
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Residues in contact with ALA 171 (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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108X PHE* 2.8 28.0 - - - -
109X VAL 2.9 23.6 + - - -
149X LEU* 3.5 3.1 - - + -
170X GLY* 1.3 76.4 - - - +
172X ALA* 1.3 60.5 + - - +
173X PHE* 3.4 23.6 - - + -
91Z HIS* 3.9 3.8 - - + -
136Z TYR* 3.7 11.9 - - + +
237Z PHE* 3.5 21.8 - - + -
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Residues in contact with ALA 172 (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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106X ILE* 4.5 7.0 - - + -
107X TYR 3.2 9.6 - - - +
108X PHE* 4.4 6.3 - - + -
171X ALA* 1.3 75.4 - - - +
173X PHE* 1.3 66.4 + - - +
205X LEU* 4.7 0.4 - - + -
90Z ALA 5.2 1.1 - - - +
91Z HIS* 3.5 18.4 - - - +
112Z PHE* 3.6 6.8 - - + -
136Z TYR* 2.9 24.8 + - + +
240Z ALA 5.2 0.4 - - - +
241Z VAL* 3.5 31.2 - - + -
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Residues in contact with PHE 173 (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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105X GLY 3.8 0.3 - - - +
106X ILE* 3.3 5.0 - - - -
107X TYR* 2.8 33.7 + - - +
109X VAL* 3.4 26.0 - - + -
148X LEU* 3.2 47.1 - - + -
149X LEU* 3.6 17.9 - - + -
171X ALA* 3.4 26.2 - - + -
172X ALA* 1.3 78.3 - - - +
174X GLN* 1.3 65.5 + - - +
175X LEU* 3.9 20.2 + - + +
91Z HIS* 4.1 13.7 - + - -
110Z GLN* 3.8 34.5 - - + +
112Z PHE* 4.0 6.3 - - - -
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Residues in contact with GLN 174 (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 3.7 5.2 - - - +
106X ILE* 4.2 10.3 - - + +
137X LEU* 5.3 2.1 - - - +
173X PHE* 1.3 73.6 - - - +
175X LEU* 1.3 66.9 + - - +
176X THR* 5.6 1.1 - - - +
110Z GLN* 4.8 8.6 + - - +
112Z PHE* 3.4 58.1 - - + +
113Z LEU 5.5 1.4 - - - +
114Z THR* 4.8 6.4 - - - +
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Residues in contact with LEU 175 (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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101X VAL* 3.6 32.1 - - + -
103X THR 4.1 0.2 - - - +
104X SER* 3.1 3.3 - - - -
105X GLY 2.9 33.6 + - - -
107X TYR* 4.0 26.5 - - + -
109X VAL* 5.6 3.6 - - + -
137X LEU* 3.7 28.9 - - + -
148X LEU* 5.4 1.1 - - + -
173X PHE* 4.4 17.3 - - + +
174X GLN* 1.3 81.6 - - - +
176X THR* 1.3 62.6 + - - +
179X ASP* 3.4 16.2 - - + +
181X LEU* 3.9 23.1 - - + -
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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