Contacts of the strand formed by residues 173 - 181 (chain M) in PDB entry 4R2G
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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83M GLU* 4.8 5.1 + - - -
108M GLN* 6.1 0.4 - - - -
139M ASP 3.3 15.1 + - - -
140M PHE* 2.5 57.3 + - + +
141M TYR* 3.8 28.3 - + - -
143M GLY* 3.7 26.5 - - - -
165M PRO 3.8 10.1 - - - -
166M SER* 3.3 28.0 - - - +
167M LYS* 3.3 32.0 - - + +
168M GLN* 4.5 0.9 - - - -
171M ASN 5.2 0.7 - - - -
172M LYS* 1.3 79.9 - - - +
174M ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 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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137M ILE 3.4 10.8 - - - +
138M SER* 4.4 0.9 - - - -
139M ASP 5.3 0.2 - - - +
140M PHE* 3.9 2.9 - - - -
163M THR* 4.7 0.5 + - - -
164M THR 4.6 1.0 - - - +
165M PRO* 3.6 0.5 - - - +
166M SER* 2.9 29.9 + - - +
168M GLN* 3.5 27.6 - - + +
173M TYR* 1.3 77.2 - - - +
175M ALA* 1.3 62.0 + - - +
182N HIS* 3.8 18.8 - - + +
184N PHE* 4.2 9.0 - - + -
185N PRO* 4.7 7.4 - - + +
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Residues in contact with ALA 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M ILE* 2.8 44.1 + - + +
140M PHE* 4.1 4.2 - - + -
145M VAL* 4.3 13.2 - - + -
162M THR* 5.0 3.1 - - + -
163M THR* 3.3 21.5 - - - +
165M PRO* 4.3 17.5 - - + -
174M ALA* 1.3 75.3 - - - +
176M SER* 1.3 65.4 + - - +
184N PHE* 3.6 5.3 - - - -
185N PRO* 5.6 0.4 - - - -
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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
----------------------------------------------------------
135M CYS 3.3 8.7 - - - -
136M LEU* 4.1 9.2 - - - -
137M ILE* 4.7 1.1 - - - -
161M GLU 3.9 0.7 - - - +
162M THR* 3.3 6.5 - - - +
163M THR* 2.6 41.8 + - - +
175M ALA* 1.3 76.6 - - - +
177M SER* 1.3 60.2 + - - +
178M TYR* 3.4 29.1 + - - -
184N PHE* 3.6 16.3 - - - +
185N PRO* 3.7 16.3 + - - +
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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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134M VAL 3.7 0.2 - - - -
135M CYS* 2.8 42.5 + - - +
137M ILE* 4.5 1.4 - - - +
147M VAL* 3.6 25.5 - - - +
149M TRP* 3.1 22.7 + - - -
160M VAL* 3.4 6.4 - - - +
161M GLU 3.4 2.5 - - - -
162M THR* 2.5 26.0 + - - -
176M SER* 1.3 74.6 - - - +
178M TYR* 1.3 65.3 + - - +
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Residues in contact with TYR 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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132M THR* 5.0 7.4 - - - -
133M LEU 3.5 5.6 - - - +
134M VAL* 3.6 24.7 - - + -
149M TRP* 4.5 1.8 - - - -
159M GLY 3.1 6.1 - - - +
160M VAL* 3.5 1.1 - - - -
161M GLU* 2.9 42.0 + - + +
163M THR* 5.0 0.2 - - + -
176M SER* 3.4 30.7 + - - -
177M SER* 1.3 78.2 + - - +
179M LEU* 1.3 61.1 + - - +
180M SER* 5.4 0.6 - - - -
159N LEU* 3.8 16.2 - - + -
184N PHE* 5.3 0.2 - - - +
185N PRO 4.9 1.8 + - - -
187N VAL* 3.4 35.9 - - + -
195N SER* 3.9 6.0 + - - -
196N LEU* 3.2 10.0 - - - -
197N SER* 3.0 43.1 + - - -
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Residues in contact with LEU 179 (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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131M ALA 4.3 0.2 - - - +
132M THR* 3.2 4.7 - - - -
133M LEU* 2.8 38.8 + - + +
149M TRP* 3.6 45.2 - - + -
156M VAL* 4.0 15.5 - - + -
158M ALA 3.4 25.6 - - - +
159M GLY 3.5 8.1 - - - -
160M VAL* 4.2 7.0 - - + +
178M TYR* 1.3 73.2 - - - +
180M SER* 1.3 70.8 + - - +
181M LEU* 3.8 15.7 - - + -
192M TYR* 3.6 33.0 - - + -
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Residues in contact with SER 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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131M ALA 3.6 3.1 - - - -
132M THR* 3.7 20.0 - - - -
158M ALA 4.5 1.2 - - - +
159M GLY* 3.1 27.0 + - - -
161M GLU* 5.6 1.4 + - - -
178M TYR* 5.4 1.1 - - - -
179M LEU* 1.3 79.3 - - - +
181M LEU* 1.3 70.0 + - - +
185M GLN* 4.7 0.9 - - - +
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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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130M LYS* 4.7 1.0 - - - -
131M ALA* 2.8 30.3 + - + +
133M LEU* 3.5 28.3 - - + -
156M VAL* 5.4 3.8 - - + -
158M ALA 5.2 2.7 - - - +
179M LEU* 3.8 23.1 - - + -
180M SER* 1.3 83.6 - - - +
182M THR* 1.3 71.4 + - - +
183M PRO* 4.3 0.2 - - - +
185M GLN* 3.4 19.3 - - + +
186M TRP* 4.3 10.3 - - + +
192M TYR* 3.5 45.1 - - + +
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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