Contacts of the strand formed by residues 164 - 173 (chain B) in PDB entry 1MPX
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 SER 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASN* 4.0 9.0 + - - -
73B ALA 3.1 14.8 - - - -
75B ILE* 3.8 29.5 - - - +
113B ILE* 4.0 5.8 - - - -
157B LEU 4.5 3.3 + - - -
158B VAL* 4.6 3.3 + - - -
161B VAL* 3.1 18.8 + - - +
162B SER 4.0 6.9 - - - +
163B GLU* 1.3 82.1 - - - +
165B ASN* 1.3 60.0 + - - +
166B GLY* 3.2 15.7 + - - -
167B LYS 5.6 0.2 - - - -
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Residues in contact with ASN 165 (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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72B ASN* 3.5 35.6 + - - +
73B ALA 3.2 5.2 + - - +
74B PRO* 3.4 17.3 - - - +
164B SER* 1.3 71.8 - - - +
166B GLY* 1.3 58.9 + - - +
167B LYS* 3.1 27.9 + - + +
376B LEU 2.8 28.1 + - - -
378B ASP* 3.1 29.7 + - - +
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 6.0 0.7 - - - -
158B VAL* 3.3 38.8 - - - +
164B SER* 3.2 14.5 + - - -
165B ASN* 1.3 78.6 + - - +
167B LYS* 1.3 60.3 + - - +
168B VAL* 4.9 0.2 - - - -
190B ALA* 3.5 13.3 - - - +
192B LYS* 5.1 1.6 - - - -
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Residues in contact with LYS 167 (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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74B PRO* 3.7 3.8 - - - +
75B ILE* 3.1 25.3 + - - +
164B SER* 5.8 0.2 - - - -
165B ASN* 3.1 20.0 + - - +
166B GLY* 1.3 81.7 - - - +
168B VAL* 1.3 62.5 + - - +
190B ALA 3.9 4.0 - - - -
192B LYS* 4.0 20.0 - - + +
375B TYR 3.6 19.3 - - - +
376B LEU* 3.9 27.1 + - + +
377B VAL 5.1 1.0 + - - -
378B ASP* 2.8 33.1 + - - +
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Residues in contact with VAL 168 (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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75B ILE* 3.4 26.0 - - + +
77B LEU* 4.1 19.3 - - + -
154B ILE* 4.1 40.8 - - + +
157B LEU* 5.1 4.0 - - + -
158B VAL* 4.1 16.2 - - + -
167B LYS* 1.3 79.6 - - - +
169B GLY* 1.3 72.6 + - - +
170B MSE 4.6 0.4 - - + -
190B ALA 3.0 11.7 + - - +
191B LEU* 3.4 7.4 - - + +
192B LYS 2.9 26.0 + - - -
376B LEU* 3.5 6.5 - - - +
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Residues in contact with GLY 169 (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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75B ILE 2.9 9.4 + - - -
76B VAL* 3.3 3.1 - - - -
77B LEU 2.8 25.3 + - - -
168B VAL* 1.3 75.8 - - - +
170B MSE 1.3 62.9 + - - -
193B VAL* 3.3 25.6 - - - -
372B PHE* 4.2 8.1 - - - -
376B LEU* 3.7 9.8 - - - +
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Residues in contact with MSE 170 (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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77B LEU* 3.3 25.8 - - + +
78B THR* 5.4 0.2 - - - -
79B ARG* 3.7 37.9 - - + +
150B ALA* 4.5 1.6 - - + -
154B ILE* 4.2 11.9 - - - -
168B VAL* 4.6 1.8 - - + -
169B GLY* 1.3 75.3 - - - +
171B ILE* 1.3 64.5 + - - +
179B THR* 3.8 18.4 - - - +
180B VAL* 4.1 24.7 - - + +
183B ALA* 3.5 25.8 - - + -
191B LEU* 3.7 22.9 - - + +
193B VAL 3.0 8.4 + - - +
194B ALA* 3.4 2.9 - - + -
195B VAL 3.0 23.7 + - - -
372B PHE* 3.7 3.8 - - - -
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Residues in contact with ILE 171 (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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76B VAL* 3.5 26.7 - - + -
77B LEU 3.2 4.0 + - - +
78B THR* 2.6 38.8 + - - +
107B PHE* 4.0 12.1 - - + -
114B ARG* 3.7 10.3 - - - +
170B MSE 1.3 75.8 - - - +
172B GLY* 1.3 64.4 + - - +
176B GLU 3.9 0.3 - - - +
180B VAL* 3.7 11.0 - - - +
195B VAL* 3.5 28.7 - - + +
197B GLU* 3.7 24.9 - - - +
344B ASN* 5.9 1.1 - - - +
368B LEU* 3.7 30.1 - - + -
372B PHE* 4.2 4.3 - - + -
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Residues in contact with GLY 172 (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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78B THR* 4.4 3.6 - - - -
114B ARG* 5.9 0.2 - - - -
171B ILE* 1.3 84.4 - - - +
173B SER* 1.3 58.9 + - - -
176B GLU* 3.4 19.9 + - - -
177B GLY* 3.1 14.3 - - - -
180B VAL* 4.1 0.2 - - - +
195B VAL 3.6 1.4 + - - -
197B GLU* 2.9 30.6 + - - +
344B ASN* 5.9 0.4 - - - -
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Residues in contact with SER 173 (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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82B TYR* 5.4 1.7 - - - -
172B GLY* 1.3 74.3 - - - -
174B SER* 1.3 68.2 + - - +
175B TYR 3.3 0.2 + - - -
176B GLU* 3.1 26.5 + - - +
177B GLY 3.5 0.4 - - - -
197B GLU* 3.1 24.6 + - - +
198B SER* 4.0 8.8 + - - -
341B SER* 2.8 34.5 + - - -
343B VAL* 5.0 1.4 - - - +
344B ASN* 4.0 14.6 - - - +
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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