Contacts of the strand formed by residues 166 - 174 (chain M) in PDB entry 3P4P
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 166 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162M VAL* 3.6 4.4 - - - +
163M ASP 3.0 28.2 + - - +
164M ASP* 4.3 4.0 - - + +
165M GLY* 1.3 80.9 - - - +
167M VAL* 1.3 80.0 + - + +
168M ARG* 3.6 40.1 + - - +
186M ASN* 3.7 26.0 - - + -
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Residues in contact with VAL 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M ILE* 4.1 17.5 - - + -
161M LEU 3.2 13.5 - - - +
162M VAL* 3.7 19.1 - - + +
166M HIS* 1.3 83.8 + - + +
168M ARG* 1.3 63.9 + - - +
169M GLY 4.0 5.8 - - - +
185M ALA 4.0 4.9 - - - +
186M ASN* 4.2 10.4 - - - +
187M ALA* 4.8 0.7 - - - -
188M VAL* 3.9 46.4 - - + +
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Residues in contact with ARG 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161M LEU* 2.3 35.4 + - + +
163M ASP* 4.2 22.1 + - + +
164M ASP* 5.5 2.4 - - - +
166M HIS* 3.6 43.9 + - - +
167M VAL* 1.3 73.2 - - - +
169M GLY* 1.3 55.4 + - - +
184M ARG* 3.9 20.8 + - - +
185M ALA 3.3 13.1 + - - +
186M ASN* 3.5 23.1 + - - -
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Residues in contact with GLY 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M ILE* 3.9 2.3 - - - -
161M LEU* 3.1 24.7 + - - +
167M VAL* 3.7 2.7 - - - +
168M ARG* 1.3 77.4 - - - +
170M LEU* 1.3 64.7 + - - +
183M ILE 3.1 12.3 - - - -
185M ALA* 3.2 19.3 + - - -
188M VAL* 4.0 16.8 - - - +
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Residues in contact with LEU 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M ALA* 3.5 25.4 - - + -
10M VAL* 3.7 17.3 - - + -
35M ILE* 3.3 36.6 - - + -
157M VAL* 3.9 17.9 - - + -
159M ASP 3.8 11.7 - - - +
160M ILE* 4.4 8.5 - - + -
161M LEU* 3.7 5.3 - - - +
169M GLY* 1.3 73.9 - - - +
171M VAL* 1.3 65.8 - - - +
172M ALA* 4.1 6.1 - - + -
182M GLN* 3.7 0.7 - - - -
183M ILE* 2.6 65.9 + - + +
188M VAL* 4.6 6.3 - - + -
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Residues in contact with VAL 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0M MET* 4.4 14.6 - - + -
157M VAL* 3.6 1.7 - - - +
158M LEU* 2.8 34.0 + - + -
159M ASP* 3.1 23.9 + - + +
161M LEU* 3.6 24.4 - - + +
170M LEU* 1.3 77.9 - - - +
172M ALA* 1.3 56.2 + - - +
180M LEU* 4.2 20.0 - - + -
181M VAL 3.5 11.4 - - - +
182M GLN* 4.1 20.9 - - + +
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Residues in contact with ALA 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M ILE* 4.9 4.9 - - + -
155M HIS* 4.8 8.3 - - + +
156M PHE 3.4 17.5 - - - +
157M VAL* 3.6 21.1 - - + +
158M LEU* 4.1 2.0 - - - +
170M LEU* 4.1 9.5 - - + +
171M VAL* 1.3 74.8 - - - +
173M MET* 1.3 56.7 - - - +
174M ASN 4.2 0.2 - - - -
180M LEU* 3.7 7.4 - - - +
181M VAL* 2.7 38.8 + - + +
183M ILE* 4.6 8.5 - - + +
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Residues in contact with MET 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155M HIS* 3.2 5.2 + - - -
156M PHE* 2.8 40.4 + - + +
158M LEU* 5.1 12.5 - - + +
172M ALA* 1.3 72.8 - - - +
174M ASN* 1.3 77.6 + - - +
175M MET* 3.1 15.6 + - + +
178M GLY* 4.0 21.1 - - - +
179M THR 3.9 7.0 - - - +
180M LEU* 4.1 19.5 - - + -
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Residues in contact with ASN 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153M ASP 5.5 0.6 + - - -
154M GLU 4.9 1.4 + - - -
155M HIS* 2.3 53.1 + - + -
173M MET* 1.3 76.6 - - - +
175M MET* 1.3 63.1 + - - +
176M MET* 3.5 8.0 + - - +
177M GLU* 2.6 51.8 + - + +
178M GLY* 2.9 23.9 + - - -
179M THR* 2.9 22.9 + - - +
181M VAL* 3.9 1.5 - - + +
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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