Contacts of the strand formed by residues 173 - 182 (chain M) in PDB entry 4DKE
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 TYR 173 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164I HIS* 5.5 1.1 - - - -
83M PHE* 5.6 1.8 - + - -
105M GLU* 3.5 22.1 + - - +
138M ASN* 3.0 4.7 + - - -
139M PHE* 2.9 55.8 + - + +
140M TYR* 3.8 13.5 - + - -
141M PRO 4.3 0.4 - - - -
142M ARG* 3.5 54.5 - - + +
163M VAL* 4.1 6.5 - - + -
164M THR* 3.6 24.7 - - - +
165M GLU* 5.1 1.6 - - - -
166M GLN* 3.4 51.0 + - + +
172M THR* 1.3 73.7 - - - +
174M SER* 1.3 68.3 + - - +
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Residues in contact with SER 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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164I HIS* 3.1 25.3 + - - -
166I PHE* 3.5 14.3 - - - -
136M LEU 3.1 11.4 - - - -
137M ASN* 3.0 12.2 + - - -
138M ASN 2.9 23.9 + - - -
139M PHE* 3.5 4.0 - - - -
163M VAL* 3.5 4.2 - - - +
164M THR* 3.0 35.4 + - - -
173M TYR* 1.3 70.6 + - - +
175M LEU* 1.3 64.0 + - - +
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Residues in contact with LEU 175 (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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166I PHE* 3.4 6.0 - - - -
135M LEU* 3.7 7.4 - - - +
136M LEU* 2.9 52.2 + - + -
139M PHE* 4.0 20.6 - - + -
142M ARG 5.5 2.7 - - - +
144M ALA* 4.8 17.3 - - + +
146M VAL* 4.2 12.6 - - + -
161M GLU* 3.6 22.9 - - + +
162M SER 3.2 10.3 - - - +
163M VAL* 4.0 17.9 - - + -
174M SER* 1.3 77.7 - - - +
176M SER* 1.3 65.2 + - - +
177M SER* 3.6 16.4 - - - +
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Residues in contact with SER 176 (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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166I PHE* 3.0 41.6 - - - +
179I SER* 5.0 8.1 - - - -
133M VAL* 5.4 7.1 - - - +
134M CYS 3.9 4.9 - - - -
135M LEU* 5.0 1.9 - - - +
160M GLN 3.4 1.7 - - - +
161M GLU* 3.0 7.1 - - - -
162M SER* 2.7 39.4 + - - -
175M LEU* 1.3 74.1 - - - +
177M SER* 1.3 60.0 + - - +
178M THR* 4.0 9.9 + - - -
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Residues in contact with SER 177 (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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133M VAL* 3.8 0.5 - - - +
134M CYS* 3.0 38.0 + - - +
136M LEU* 5.6 0.2 - - - -
146M VAL* 3.8 28.3 + - - +
148M TRP* 3.1 24.8 + - - -
159M SER* 3.3 10.0 + - - -
160M GLN 3.4 2.9 - - - -
161M GLU* 3.9 17.4 + - - +
175M LEU* 3.6 6.0 - - - +
176M SER* 1.3 74.3 - - - +
178M THR* 1.3 59.4 + - - +
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Residues in contact with THR 178 (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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141I LEU* 5.5 3.1 - - + +
177I SER* 6.1 1.1 - - - +
179I SER* 4.9 4.9 + - - -
131M SER* 4.5 10.5 - - - +
132M VAL 3.3 9.2 - - - +
133M VAL* 3.6 23.1 - - + +
158M ASN 4.0 0.2 - - - +
159M SER* 3.3 8.7 + - - -
160M GLN* 2.9 38.9 + - + +
176M SER* 4.8 8.0 - - - -
177M SER* 1.3 75.3 + - - +
179M LEU* 1.3 69.8 + - - +
180M THR* 3.9 11.7 + - - +
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Residues in contact with LEU 179 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130M ALA 3.9 0.5 - - - +
131M SER* 3.4 5.2 - - - -
132M VAL* 2.7 46.3 + - + +
148M TRP* 3.6 59.2 - - + -
150M VAL* 4.0 22.2 - - + -
155M GLN* 4.3 2.0 - - + -
158M ASN* 3.3 46.4 - - - +
159M SER* 4.4 0.2 - - - -
178M THR* 1.3 73.3 - - - +
180M THR* 1.3 61.2 + - - +
181M LEU* 4.1 17.2 + - + -
192M TYR* 5.3 2.2 - - + -
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Residues in contact with THR 180 (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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143I LYS* 5.2 7.9 - - - +
171I GLN* 5.1 6.6 + - - +
129M THR* 4.6 11.2 - - - +
130M ALA 3.7 5.8 - - - +
131M SER* 4.2 8.2 + - - +
158M ASN* 3.2 32.4 + - - +
178M THR* 3.9 13.4 + - - +
179M LEU* 1.3 74.7 + - - +
181M LEU* 1.3 72.1 + - - +
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Residues in contact with LEU 181 (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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129M THR* 3.5 5.6 + - - -
130M ALA* 2.7 49.9 + - + +
132M VAL* 5.0 7.4 - - + -
150M VAL* 4.8 6.7 - - + -
155M GLN* 5.4 3.8 - - - +
158M ASN* 4.7 10.3 - - - +
179M LEU* 4.1 25.3 + - + +
180M THR* 1.3 83.5 - - - +
182M SER* 1.3 64.7 + - - +
185M ASP* 3.8 28.7 - - + +
186M TYR* 4.7 10.3 - - + -
192M TYR* 4.2 25.8 - - + +
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Residues in contact with SER 182 (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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128M GLY 4.3 6.1 - - - -
129M THR* 4.8 2.9 - - - -
181M LEU* 1.3 76.4 - - - +
183M LYS* 1.3 67.7 + - - +
184M ALA* 3.1 7.5 + - - +
185M ASP* 3.2 27.7 + - - -
186M TYR* 3.2 17.4 + - - +
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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