Contacts of the strand formed by residues 166 - 173 (chain B) in PDB entry 5MOM
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 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B CYS* 3.8 0.9 - - - -
163B ALA* 2.8 42.3 + - - +
165B ASP* 1.3 80.5 - - - +
167B VAL* 1.3 58.1 + - - +
182B LEU 3.2 13.2 - - - -
183B SER* 4.2 2.0 - - - -
197B ILE* 3.3 11.9 - - - -
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Residues in contact with VAL 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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137B VAL* 4.4 19.3 - - + -
160B ILE* 3.8 24.0 - - + -
161B SER 3.4 11.9 - - - +
162B CYS* 4.2 12.1 - - - -
166B GLY* 1.3 75.4 - - - +
168B LYS* 1.3 62.4 + - - +
169B PHE* 3.9 26.1 - - + -
180B ILE 3.9 1.0 - - - +
181B LYS* 3.7 1.5 - - - +
182B LEU* 2.9 51.5 + - + +
195B VAL* 5.1 1.1 - - + -
197B ILE* 4.0 14.4 - - + -
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Residues in contact with LYS 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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159B VAL 3.4 1.2 - - - +
160B ILE* 3.4 5.2 - - - -
161B SER* 2.9 53.7 + - - +
167B VAL* 1.3 76.5 - - - +
169B PHE* 1.3 65.4 + - - +
170B SER* 3.6 22.4 + - - +
179B ASN* 4.1 13.6 - - + +
180B ILE 3.4 9.4 - - - +
181B LYS* 3.7 35.8 - - + +
204B GLN* 5.9 0.2 - - - -
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Residues in contact with PHE 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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137B VAL* 5.4 0.4 - - + -
139B MET* 4.1 20.9 - - - -
144B PHE* 4.2 22.2 - + - -
147B ILE* 3.8 35.2 - - + -
148B CYS* 6.2 0.4 - - - -
151B LEU* 3.8 16.2 - - + +
158B VAL* 3.7 13.0 - - + -
159B VAL 3.5 4.9 - - - -
160B ILE* 4.0 32.3 - - + -
167B VAL* 3.9 31.6 - - + -
168B LYS* 1.3 72.3 - - - +
170B SER* 1.3 62.8 + - - +
179B ASN* 3.1 2.4 - - - -
180B ILE* 2.8 46.9 + - + +
182B LEU* 4.0 8.7 - - + -
227B LEU* 4.3 7.4 - - + -
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Residues in contact with SER 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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151B LEU* 4.4 0.9 - - - -
158B VAL* 3.2 7.7 - - - +
159B VAL* 2.8 49.2 + - - +
168B LYS* 3.6 19.1 + - - +
169B PHE* 1.3 74.6 - - - +
171B ALA* 1.3 62.0 + - - +
178B GLY 3.3 9.2 - - - -
179B ASN* 3.2 18.3 - - - +
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Residues in contact with ALA 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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151B LEU* 4.0 37.6 - - + +
154B ILE* 4.3 4.3 - - + -
155B GLY* 4.4 6.7 - - - +
157B ALA 3.3 20.6 - - - +
159B VAL* 5.7 2.2 - - - -
170B SER* 1.3 74.1 - - - +
172B SER* 1.3 63.3 + - - +
177B ASN* 3.3 4.9 - - - +
178B GLY 2.9 32.5 + - - +
209B LEU* 4.6 0.7 - - + -
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Residues in contact with SER 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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154B ILE* 3.7 5.8 - - - -
155B GLY* 3.5 11.8 - - - -
156B ASP 4.5 1.9 + - - -
157B ALA 4.7 1.5 + - - +
171B ALA* 1.3 79.0 - - - +
173B GLY* 1.3 59.2 + - - +
176B GLY 3.5 6.1 - - - -
177B ASN* 3.8 14.8 - - - -
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Residues in contact with GLY 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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117A LYS* 4.2 5.2 + - - -
154B ILE 3.3 15.0 + - - -
155B GLY* 4.5 2.2 - - - -
172B SER* 1.3 74.8 - - - +
174B GLU* 1.3 66.6 + - - +
175B LEU 3.2 3.4 - - - -
176B GLY* 2.9 20.6 + - - +
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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