Contacts of the strand formed by residues 163 - 176 (chain A) in PDB entry 1O9S
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A PHE* 3.1 6.8 - - - -
160A ILE* 2.9 36.9 + - + +
161A ASP 3.2 3.0 + - - +
162A GLY* 1.3 78.4 - - - +
164A MET* 1.3 63.1 + - - +
165A ILE* 3.3 18.6 + - + +
193A PHE* 3.6 43.8 - - + +
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Residues in contact with MET 164 (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 LEU* 3.6 38.6 - - + -
159A PHE* 3.5 31.8 - - + -
162A GLY 3.8 1.2 + - - -
163A GLU* 1.3 71.1 - - - +
165A ILE* 1.3 62.9 + - - +
167A GLY* 3.8 11.9 - - - +
191A TYR* 3.6 23.1 - - + +
192A HIS* 3.5 30.3 - - - +
193A PHE* 2.8 32.0 + - - +
311A PRO* 3.7 35.5 + - + +
312A ARG* 4.2 3.4 - - + +
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Residues in contact with ILE 165 (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 LYS* 2.8 39.6 + - + +
159A PHE* 4.2 0.4 - - - -
160A ILE* 3.9 35.2 - - + -
163A GLU* 3.7 32.3 - - + +
164A MET* 1.3 79.9 - - - +
166A GLU* 1.3 60.0 + - + +
192A HIS* 3.1 21.7 - - - +
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Residues in contact with GLU 166 (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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142A GLU* 5.5 0.7 - - - +
156A TYR 4.0 0.5 - - - +
157A GLY* 3.3 5.8 - - - -
158A LYS* 3.0 44.7 + - + +
165A ILE* 1.3 80.5 - - + +
167A GLY* 1.3 58.0 + - - +
168A LYS* 3.0 33.4 + - + +
190A VAL* 3.9 26.3 - - + +
191A TYR 3.6 3.8 - - - -
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Residues in contact with GLY 167 (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 LEU* 4.2 3.6 - - - -
156A TYR 3.7 14.6 - - - -
157A GLY 4.4 0.4 - - - -
159A PHE* 5.0 1.1 - - - -
164A MET* 3.8 18.6 - - - +
166A GLU* 1.3 74.0 - - - +
168A LYS* 1.3 62.5 + - - -
190A VAL* 3.8 1.3 - - - -
191A TYR* 2.9 45.4 + - - -
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Residues in contact with LYS 168 (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 LEU* 3.4 3.3 - - - -
156A TYR* 2.8 37.2 + - - +
166A GLU* 3.0 31.9 + - + +
167A GLY* 1.3 76.2 - - - -
169A LEU* 1.3 65.6 + - - +
170A ALA* 3.3 0.5 + - - +
184A LEU* 3.5 36.0 - - + +
189A SER 4.4 7.2 - - - +
190A VAL* 4.5 12.8 - - + -
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Residues in contact with LEU 169 (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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153A THR* 3.9 16.8 - - + -
154A ALA 3.6 10.3 - - - +
155A LEU* 4.3 4.5 - - + -
167A GLY 4.2 0.8 + - - -
168A LYS* 1.3 72.0 - - - +
170A ALA* 1.3 66.6 + - - +
184A LEU* 3.6 5.5 - - - +
185A MET* 2.9 46.2 + - + +
186A PRO 5.2 5.6 - - - +
189A SER* 4.4 5.5 + - - +
191A TYR* 4.4 16.0 - - + +
210A PRO* 3.7 36.6 - - + -
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Residues in contact with ALA 170 (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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153A THR* 3.9 4.3 - - - +
154A ALA* 2.8 32.9 + - + +
156A TYR* 3.9 25.6 - - + -
168A LYS 3.9 0.2 - - - +
169A LEU* 1.3 80.7 - - - +
171A THR* 1.3 66.3 + - - +
182A PHE* 4.3 14.4 - - + -
183A GLU 3.2 17.3 - - - +
184A LEU* 4.4 4.3 - - + -
185A MET* 3.7 6.1 - - - +
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Residues in contact with THR 171 (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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152A ARG* 3.2 42.5 + - + +
153A THR* 5.7 0.5 - - - -
170A ALA* 1.3 73.8 + - - +
172A LEU* 1.3 71.7 + - - +
173A MET* 3.3 5.9 + - + -
182A PHE* 3.3 6.6 - - - -
183A GLU* 2.9 53.3 + - + +
185A MET* 3.0 24.1 - - - +
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Residues in contact with LEU 172 (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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120A TRP* 4.0 22.9 - - + -
147A VAL* 4.2 19.1 - - + -
151A GLU* 3.8 23.8 - - + +
152A ARG* 2.7 25.5 + - - +
154A ALA* 4.6 0.2 - - - +
171A THR* 1.3 77.1 - - - +
173A MET* 1.3 62.0 + - - +
174A SER* 3.6 17.5 - - - +
175A THR* 4.3 5.2 - - - +
180A PRO* 3.6 29.8 - - + -
181A HIS 3.8 4.0 - - - +
182A PHE* 3.7 20.0 - - + -
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Residues in contact with MET 173 (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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171A THR* 3.9 14.4 - - + +
172A LEU* 1.3 76.5 - - - +
174A SER* 1.3 64.9 + - - +
181A HIS* 2.8 20.5 + - + +
182A PHE 3.9 8.7 - - - +
183A GLU* 3.7 47.8 - - + +
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Residues in contact with SER 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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172A LEU* 3.6 6.1 - - - +
173A MET* 1.3 81.7 - - - +
175A THR* 1.3 69.1 + - - +
176A GLU* 5.5 2.1 - - - +
180A PRO* 3.5 0.5 - - - +
181A HIS* 2.8 45.7 + - - +
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Residues in contact with THR 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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120A TRP* 3.7 25.0 - - + -
172A LEU* 4.3 4.7 - - - +
174A SER* 1.3 80.5 + - - +
176A GLU* 1.3 71.9 + - - +
177A GLU 4.1 1.0 + - - +
178A GLY* 3.4 33.0 - - - +
179A ARG 3.1 13.7 - - - +
180A PRO* 4.0 2.4 - - - +
181A HIS* 4.1 0.7 - - - -
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Residues in contact with GLU 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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174A SER* 5.5 2.2 - - - +
175A THR* 1.3 77.2 - - - +
177A GLU* 1.3 83.5 + - - +
178A GLY 3.2 0.4 - - - -
179A ARG* 2.6 30.0 + - + +
181A HIS* 3.2 23.3 + - + +
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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