Contacts of the strand formed by residues 161 - 167 (chain B) in PDB entry 1MMM
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 PHE 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B VAL* 3.3 2.0 - - - -
133B LEU* 2.9 43.3 + - + +
150B LEU* 4.3 15.3 - - + -
160B GLY* 1.3 71.2 - - - -
162B PRO* 1.3 82.2 - - + +
163B ILE* 3.4 11.4 + - + +
200B ARG* 3.4 56.3 - - + -
204B LYS* 4.1 18.2 - - - +
205B LYS* 3.4 38.4 - - - -
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Residues in contact with PRO 162 (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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83B LEU* 3.8 24.7 - - + -
130B TRP* 4.0 15.0 - - + -
131B LEU 3.9 5.4 - - - +
132B VAL* 4.2 4.5 - - + -
148B SER* 4.4 2.7 - - - +
149B PRO* 4.1 23.3 - - + -
150B LEU* 3.6 32.3 - - + -
160B GLY 3.6 5.8 - - - +
161B PHE* 1.3 95.1 - - + +
163B ILE* 1.3 59.8 + - - +
164B MET 5.0 0.4 - - - +
200B ARG* 2.8 29.4 + - - +
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Residues in contact with ILE 163 (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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83B LEU* 5.2 0.6 - - - +
98B LEU* 4.4 10.1 - - + -
131B LEU* 2.8 35.0 + - + +
133B LEU* 4.1 13.9 - - + +
138B LEU* 4.1 19.7 - - + -
161B PHE* 3.9 27.1 - - + +
162B PRO* 1.3 73.7 - - - +
164B MET* 1.3 63.3 + - + +
197B ALA* 3.5 35.4 - - + +
200B ARG* 3.3 24.2 - - - +
201B PHE* 3.9 28.5 - - + +
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Residues in contact with MET 164 (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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83B LEU* 4.7 8.3 - - - -
87B GLY* 5.4 6.1 - - - +
112B PHE* 3.6 19.5 - - + -
116B PHE* 3.7 25.8 - - + -
130B TRP* 3.6 10.1 - - - -
131B LEU* 3.1 56.7 + - + +
162B PRO 3.7 0.4 - - - -
163B ILE* 1.3 82.6 - - + +
165B GLY* 1.3 64.2 + - - +
188B PHE* 3.9 12.3 - - + -
189B TRP* 4.9 1.1 - - + -
192B VAL* 3.5 25.1 - - + -
193B ASN 5.9 0.2 - - - +
194B TRP* 4.2 13.2 - - + -
197B ALA* 4.3 14.1 - - + -
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Residues in contact with GLY 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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83B LEU* 4.4 7.8 - - - +
84B PHE* 3.4 21.5 - - - -
87B GLY 5.7 0.7 - - - +
128B TRP* 4.2 6.1 - - - -
129B ALA 3.3 11.0 - - - -
130B TRP* 3.9 15.3 - - - -
164B MET* 1.3 82.8 - - - +
166B LEU* 1.3 60.3 + - - -
188B PHE* 3.7 12.6 - - - -
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Residues in contact with LEU 166 (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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18B PHE* 4.4 1.6 - - + -
84B PHE* 4.0 4.7 - - + -
116B PHE* 3.9 18.4 - - + -
120B ALA* 4.3 5.8 - - + -
128B TRP* 3.4 8.4 - - - -
129B ALA* 2.9 34.3 + - + +
165B GLY* 1.3 73.4 - - - +
167B ASP* 1.3 67.5 + - - +
168B VAL* 3.5 18.2 + - + +
184B TYR* 3.4 32.5 - - + +
185B ILE* 4.1 32.5 - - + -
188B PHE* 3.5 39.5 - - + -
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Residues in contact with ASP 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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26B HIS* 2.9 13.9 - - - -
81B HIS* 3.5 0.2 + - - -
84B PHE* 3.8 15.8 - - + -
128B TRP* 3.5 33.6 - - + -
166B LEU* 1.3 73.5 - - - +
168B VAL* 1.3 59.4 + - - +
169B TRP* 3.2 21.6 + - - -
171B HIS* 3.3 2.8 + - - -
172B ALA* 3.7 6.2 - - + +
184B TYR* 2.8 30.3 + - - -
206B FE 2.0 30.6 - - - -
207B OH 2.9 14.7 + - - -
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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