Contacts of the strand formed by residues 191 - 198 (chain X) in PDB entry 4MXV
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 VAL 191 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149X LYS 3.9 0.5 - - - +
150X VAL* 3.5 5.2 - - - +
151X ASP* 2.7 53.3 + - - +
152X ASN 6.0 0.7 - - - +
190X LYS* 1.3 77.1 - - + +
192X TYR* 1.3 70.1 + - - +
193X ALA* 4.1 4.0 - - + +
208X SER* 4.7 12.3 - - - +
209X PHE 3.6 7.0 - - - +
210X ASN* 3.2 21.1 - - - +
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Residues in contact with TYR 192 (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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117X ILE* 3.5 6.4 - - - +
132X VAL* 4.4 17.0 - - + -
148X TRP* 5.4 2.0 - + + -
149X LYS 3.8 2.2 - - - -
150X VAL* 3.9 33.1 - - + +
179X LEU* 4.5 4.7 - - + -
181X LEU* 4.5 11.6 - - + +
185X ASP 3.9 1.0 + - - -
186X TYR* 2.7 58.3 + + - -
189X HIS* 3.6 26.3 + - - +
190X LYS 3.5 11.9 - - - -
191X VAL* 1.3 75.2 - - - +
193X ALA* 1.3 60.3 + - - +
208X SER* 3.2 3.7 - - - -
209X PHE* 3.0 61.6 + + + -
211X ARG* 4.3 3.6 - - + -
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Residues in contact with ALA 193 (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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117X ILE* 4.5 0.2 - - - -
148X TRP* 3.2 13.6 - - - -
149X LYS* 2.9 48.7 + - + +
191X VAL* 4.1 5.1 - - + -
192X TYR* 1.3 75.2 - - - +
194X CYS* 1.3 61.4 + - - +
195X GLU 4.1 0.7 - - - -
206X THR* 3.7 14.4 - - + -
207X LYS 3.3 10.1 - - - +
208X SER* 3.7 12.3 - - - -
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Residues in contact with CYS 194 (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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115X VAL* 4.4 6.5 - - - +
116X PHE 5.1 0.2 - - - -
117X ILE* 4.0 8.7 - - + -
134X CYS* 2.0 54.1 - - + -
146X VAL* 4.4 9.0 - - - -
147X GLN 3.6 4.7 - - - -
148X TRP* 3.9 14.6 - - + -
193X ALA* 1.3 77.2 - - - +
195X GLU* 1.3 58.3 + - - +
196X VAL* 4.0 3.9 + - - +
205X VAL 3.8 1.2 - - - +
206X THR* 3.4 2.2 - - - -
207X LYS* 2.8 38.2 + - + +
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Residues in contact with GLU 195 (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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145X LYS 3.5 4.2 - - - +
146X VAL* 3.5 1.0 - - - -
147X GLN* 2.8 65.9 + - + +
149X LYS* 2.6 37.1 + - + +
193X ALA 5.8 0.2 - - - -
194X CYS* 1.3 72.3 - - - +
196X VAL* 1.3 63.2 + - - +
197X THR* 4.1 3.8 + - - +
204X PRO* 3.8 28.7 - - + +
205X VAL 3.4 5.2 - - - +
206X THR* 3.5 22.2 + - + +
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Residues in contact with VAL 196 (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 PRO* 4.0 9.4 - - + -
115X VAL* 3.8 25.4 - - + -
134X CYS* 4.4 5.4 - - - -
136X LEU* 3.5 49.6 - - + -
145X LYS 3.4 4.0 - - - +
146X VAL* 4.7 2.0 - - + -
194X CYS* 4.5 2.5 - - - +
195X GLU* 1.3 76.1 - - - +
197X THR* 1.3 71.3 + - - +
201X LEU* 3.8 20.3 - - + +
204X PRO* 3.3 7.7 - - - +
205X VAL 2.5 38.5 + - - +
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Residues in contact with THR 197 (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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144X ALA* 3.6 2.3 - - - -
145X LYS* 2.9 53.0 + - + +
147X GLN* 5.4 4.2 + - - +
195X GLU* 4.7 7.1 + - - +
196X VAL* 1.3 77.8 + - - +
198X HIS* 1.3 69.2 + - - +
201X LEU* 4.7 0.2 - - - -
204X PRO* 3.8 17.6 - - + +
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Residues in contact with HIS 198 (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 ALA 3.4 14.1 - - - -
113X PRO* 3.4 32.3 - - + +
139X PHE* 3.6 14.3 - + + -
140X TYR 3.3 26.4 - - - -
141X PRO* 2.9 29.5 + - + +
143X GLU 3.1 28.6 + - - -
144X ALA* 4.0 4.5 - - + -
196X VAL* 4.7 0.7 - - + -
197X THR* 1.3 81.3 - - - +
199X GLN* 1.3 65.9 + - - +
200X GLY* 3.0 25.2 + - - -
201X LEU* 3.3 27.9 - - + +
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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