Contacts of the strand formed by residues 177 - 185 (chain A) in PDB entry 5ODS
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 VAL 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ILE* 3.8 36.3 - - + -
171A SER 3.6 6.5 - - - +
172A ALA* 4.7 7.0 - - + +
176A ARG* 1.3 74.9 - - - +
178A VAL* 1.3 55.0 + - - +
197A HIS* 2.7 29.9 + - - +
221A ARG 5.0 0.7 - - - +
260A PHE* 3.6 49.1 - - + +
278A LYS* 6.0 0.7 - - - +
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Residues in contact with VAL 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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151A CYS* 5.3 0.2 - - - -
170A ILE* 3.3 4.5 - - - -
171A SER* 2.7 40.7 + - - +
173A GLN* 3.5 39.9 - - + +
176A ARG* 3.6 13.5 - - + +
177A VAL* 1.3 73.6 - - - +
179A GLY* 1.3 68.0 + - - +
180A ALA* 3.8 2.5 + - + +
195A GLU* 3.9 22.2 - - + +
197A HIS* 3.9 1.8 - - - -
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Residues in contact with GLY 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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169A GLY 3.6 4.9 - - - -
170A ILE* 3.9 3.4 - - - -
178A VAL* 1.3 75.8 - - - +
180A ALA* 1.3 59.9 + - - -
195A GLU* 3.2 29.3 + - - +
196A GLY 3.3 25.9 + - - -
197A HIS* 3.4 22.0 + - - -
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Residues in contact with ALA 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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147A SER* 3.9 26.2 - - - +
148A LEU* 3.8 12.6 - - + +
151A CYS* 4.0 14.1 - - - -
168A THR* 3.5 1.9 - - - -
169A GLY 2.7 44.1 + - - +
178A VAL* 3.8 2.6 + - + +
179A GLY* 1.3 74.1 - - - +
181A MET* 1.3 61.6 + - - +
194A ILE 3.9 1.8 - - - -
195A GLU* 4.9 0.2 - - - +
196A GLY 3.8 0.4 + - - -
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Residues in contact with MET 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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147A SER* 4.5 0.7 + - - -
148A LEU* 3.7 6.7 - - - +
166A LEU* 4.0 9.6 - - + -
167A LEU 3.2 7.2 - - - +
168A THR* 3.6 23.6 - - + +
180A ALA* 1.3 75.9 - - - +
182A GLN* 1.3 60.6 + - - +
183A LEU 4.1 0.4 - - - -
193A PRO* 3.3 6.6 - - - +
194A ILE* 2.7 63.6 + - + +
196A GLY* 3.4 32.8 - - - +
197A HIS 4.6 0.2 - - - -
198A ALA 4.9 1.6 - - - -
199A ALA* 3.9 17.5 - - - -
216A PHE* 3.8 12.8 - - + -
218A PHE* 3.7 26.2 - - + -
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Residues in contact with GLN 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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142A PHE* 3.4 21.2 - - + -
143A ASP 2.9 23.0 + - - -
144A ARG* 3.6 9.5 - - - +
145A HIS* 2.9 36.5 + - + +
148A LEU* 3.7 14.6 - - + +
165A LEU 3.5 1.6 - - - +
166A LEU* 3.4 7.0 - - - +
167A LEU* 3.0 36.9 + - + +
181A MET* 1.3 74.4 - - - +
183A LEU* 1.3 61.8 + - - +
184A TYR* 3.6 1.2 + - - +
191A SER* 2.9 37.5 + - - +
192A GLN 3.7 4.0 - - - +
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Residues in contact with LEU 183 (chain A).
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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164A TRP* 3.8 20.4 - - + +
165A LEU 3.6 13.5 - - - +
166A LEU* 3.9 11.6 - - + +
181A MET 4.1 0.6 - - - -
182A GLN* 1.3 70.1 - - - +
184A TYR* 1.3 59.2 + - - +
185A SER 4.1 0.3 + - - -
190A VAL 3.7 1.6 - - - +
191A SER* 3.4 2.4 - - - -
192A GLN* 2.9 47.3 + - + +
194A ILE* 3.9 23.1 - - + +
201A PHE* 3.7 28.3 - - + -
216A PHE* 4.1 21.8 - - + -
231A ILE* 5.4 2.2 - - + -
233A VAL* 4.2 16.4 - - + -
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Residues in contact with TYR 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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141A MET* 3.4 25.2 + - + -
142A PHE* 3.6 43.6 - + + -
164A TRP* 3.5 6.9 - - - -
165A LEU* 2.8 56.2 + - + +
182A GLN* 3.6 1.7 + - - +
183A LEU* 1.3 72.8 - - - +
185A SER* 1.3 73.5 + - - +
186A VAL* 3.9 10.7 + - + +
189A LYS* 3.4 43.6 - - - +
190A VAL 3.6 7.6 - - - -
191A SER* 3.1 24.9 - - - +
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Residues in contact with SER 185 (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 LYS 3.6 4.9 + - - -
164A TRP* 3.6 34.9 - - - +
183A LEU 4.1 0.6 + - - -
184A TYR* 1.3 76.7 - - - +
186A VAL* 1.3 60.0 + - - +
187A ASP* 3.8 4.2 + - - +
188A ARG* 3.6 32.1 + - - +
189A LYS* 2.9 29.5 + - - -
190A VAL* 3.1 14.7 + - - -
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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