Contacts of the strand formed by residues 173 - 184 (chain A) in PDB entry 3ME9
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 GLU 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ARG* 3.6 17.8 + - + +
166A VAL 3.3 16.3 - - - +
167A LYS* 3.1 27.1 + - + +
171A GLY 3.3 10.9 + - - +
172A ASP* 1.3 73.1 - - - +
174A GLN* 1.3 69.7 + - - +
209A ARG* 2.8 44.6 + - - -
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ALA 3.3 2.3 - - - +
165A ARG* 3.4 4.1 - - - -
166A VAL* 2.8 35.9 + - + +
172A ASP* 4.1 13.0 + - + +
173A GLU* 1.3 81.0 + - - +
175A TRP* 1.3 61.9 + - - +
176A ILE* 3.6 18.2 + - + -
243A CYS* 3.8 8.0 - - - +
245A TYR* 2.7 37.6 + - - -
3C THR* 3.6 32.2 - - + +
5C GLN* 5.7 4.2 - - - +
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Residues in contact with TRP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ALA* 3.5 28.9 - - + -
164A ALA 3.4 8.5 - - - -
165A ARG* 3.2 54.2 - - + +
174A GLN* 1.3 72.6 + - - +
176A ILE* 1.3 60.1 + - - +
208A ARG 4.0 14.1 - - - -
209A ARG 3.5 12.6 - - - -
211A ILE* 3.6 28.9 - - + -
235A LEU* 3.8 33.7 - - + +
243A CYS* 3.2 6.9 - - - +
244A PHE* 2.8 56.3 + - + +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ALA* 3.4 4.2 - - - -
164A ALA* 2.8 45.2 + - + +
166A VAL* 3.6 32.1 - - + -
174A GLN* 3.9 14.4 - - + -
175A TRP* 1.3 75.8 - - - +
177A LEU* 1.3 64.5 + - - +
178A ALA* 3.5 3.7 + - + -
194A ASP* 3.8 38.4 - - + +
203A HIS* 4.0 15.0 - - + +
242A THR 3.7 3.6 - - - -
243A CYS* 4.0 2.2 - - - -
244A PHE* 4.0 3.4 - - - -
1C ALA* 3.9 24.5 - - + -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.3 33.9 - - + -
126A SER* 6.1 0.9 - - - -
161A LYS* 4.4 9.4 - - + -
162A VAL 3.7 10.1 - - - +
176A ILE* 1.3 74.0 - - - +
178A ALA* 1.3 64.0 + - - +
194A ASP* 3.7 8.1 - - - +
195A ILE* 3.3 44.0 + - + +
213A LEU* 3.6 31.4 - - + -
237A LEU* 4.5 2.5 - - + -
242A THR* 2.8 23.3 + - - +
244A PHE* 3.8 12.0 - - + -
283A TYR* 3.8 17.3 - - + +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS* 3.4 9.5 - - - +
162A VAL* 2.9 33.8 + - + +
164A ALA* 4.0 16.4 - - + -
176A ILE* 4.2 6.7 - - + +
177A LEU* 1.3 76.0 - - - +
179A GLU* 1.3 61.8 + - - +
192A VAL* 3.9 24.0 - - + -
193A ASP 3.2 16.4 - - - +
194A ASP* 4.4 0.2 - - - -
195A ILE* 4.0 5.8 - - - -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLY* 3.5 37.8 + - - +
160A ASP 3.4 3.6 - - - +
161A LYS* 3.6 24.0 + - + -
178A ALA* 1.3 75.2 - - - +
180A VAL* 1.3 69.4 + - - +
181A VAL* 3.4 2.6 + - + +
192A VAL* 3.3 4.2 - - - -
193A ASP* 2.8 39.0 + - + +
195A ILE* 4.2 6.5 - - + +
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ALA* 3.9 20.6 - - + +
157A ARG 3.4 27.6 - - - +
158A PRO* 3.4 2.9 - - + +
159A GLY* 2.8 24.8 + - - -
160A ASP 2.9 12.5 + - - +
162A VAL* 3.7 27.8 - - + -
179A GLU* 1.3 77.6 - - - +
181A VAL* 1.3 63.4 + - - +
182A SER 3.7 23.1 - - - +
190A TYR* 4.0 19.1 - - + -
191A GLU 3.8 4.0 - - - +
192A VAL* 4.2 6.7 - - + -
210A VAL* 5.0 0.4 - - + -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PRO* 3.5 18.8 - - - +
179A GLU* 4.0 2.0 - - + +
180A VAL* 1.3 79.2 - - - +
182A SER* 1.3 61.8 + - - +
191A GLU* 2.8 28.8 + - + +
192A VAL 4.3 0.4 - - - -
193A ASP* 3.4 47.1 - - + +
202A ARG* 3.7 28.0 - - - +
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PRO* 4.6 6.5 - - - -
180A VAL* 3.7 6.6 - - - +
181A VAL* 1.3 82.6 - - - +
183A TYR* 1.3 66.4 + - - +
184A SER* 5.0 0.9 + - - -
190A TYR* 3.3 8.7 - - - -
191A GLU* 2.8 55.9 + - - +
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 3.4 37.7 - - + +
156A ALA 4.7 2.9 - - - +
158A PRO* 5.7 1.0 - - - +
182A SER* 1.3 78.6 - - - +
184A SER* 1.3 67.5 + - - +
185A HIS* 3.6 44.1 + + - -
188A ASN* 2.7 49.8 + - - +
189A LYS 3.4 14.8 - - - -
190A TYR* 3.8 22.4 - + + -
207A ARG* 3.4 26.4 + - + -
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A SER* 5.0 1.3 + - - -
183A TYR* 1.3 73.8 - - - +
185A HIS* 1.3 52.7 + - - +
186A ALA* 3.3 21.7 + - - +
187A THR* 3.4 20.1 + - - +
188A ASN* 2.7 36.7 + - - -
189A LYS* 2.8 13.7 + - - -
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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