Contacts of the strand formed by residues 169 - 175 (chain C) in PDB entry 1O97
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 LEU 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C ALA* 4.5 11.4 - - + -
148C ASP* 6.1 0.7 - - + -
161C ARG* 4.2 32.8 - - + +
162C ARG 3.2 6.3 - - - +
163C GLU* 3.7 29.8 - - + +
164C LEU* 4.2 3.4 - - - -
167C GLY 3.9 9.6 - - - +
168C MET* 1.3 83.2 - - - +
170C GLN* 1.3 61.5 + - - +
188D TYR* 3.4 10.4 - - - +
189D VAL* 2.8 42.4 + - + +
191D VAL* 3.6 29.8 - - + -
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Residues in contact with GLN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ARG* 3.2 3.1 - - - -
162C ARG* 2.8 80.3 + - + +
164C LEU* 4.0 7.2 - - + -
169C LEU* 1.3 76.2 - - - +
171C GLU* 1.3 73.3 + - - +
172C VAL* 3.6 6.9 + - - +
69D ASP* 4.6 2.1 - - - +
70D PHE 4.5 0.8 + - - -
185D ASN* 3.4 39.2 + - - +
186D LYS 4.6 4.4 - - - +
187D ASP 3.8 5.2 - - - +
188D TYR* 3.4 40.5 + - + -
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Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C VAL* 3.3 22.8 - - + +
160C ILE 3.2 5.6 - - - +
161C ARG* 2.9 49.1 + - + +
169C LEU 4.3 0.4 - - - -
170C GLN* 1.3 76.9 - - - +
172C VAL* 1.3 58.5 + - - +
186D LYS* 2.7 42.4 + - + +
187D ASP* 2.9 23.3 + - - +
189D VAL* 4.0 15.6 - - + +
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C VAL* 3.5 4.6 - - - -
160C ILE* 2.8 61.8 + - + +
162C ARG* 4.5 9.0 - - - +
170C GLN* 3.9 22.2 - - - +
171C GLU* 1.3 79.6 - - - +
173C GLU* 1.3 64.2 + - - +
174C ILE* 3.7 3.7 + - + +
72D PRO* 6.5 0.2 - - + -
183D SER* 3.6 32.3 - - - +
184D GLN 3.5 11.0 - - - +
185D ASN* 3.6 17.7 - - - +
186D LYS* 4.3 0.4 - - - +
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Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LYS* 4.3 25.5 - - + +
158C ALA 3.4 10.1 - - - +
159C VAL* 4.4 16.1 - - + +
172C VAL* 1.3 73.9 - - - +
174C ILE* 1.3 60.2 + - - +
175C ASN* 4.5 1.3 + - - +
183D SER* 3.2 3.8 - - - -
184D GLN* 2.8 48.0 + - + +
186D LYS* 4.1 28.5 + - + +
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C MET* 5.9 0.2 - - + -
141C PRO* 3.9 6.5 - - + -
142C HIS* 3.5 44.6 - - - +
143C ALA* 4.0 10.5 - - + +
157C LYS* 3.3 5.0 - - - -
158C ALA* 2.9 56.4 + - + +
160C ILE* 4.1 20.6 - - + -
172C VAL* 4.6 4.3 - - + -
173C GLU* 1.3 73.3 - - - +
175C ASN* 1.3 77.8 + - - +
176C CYS* 3.9 1.0 - - - -
178C ALA* 3.9 12.6 - - + -
180C LEU* 4.2 7.2 - - + -
182D ARG 3.8 6.5 - - - +
183D SER* 4.0 11.2 - - - -
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Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C PRO* 3.3 31.0 - - + +
156C ASN 3.6 7.0 - - - +
157C LYS* 4.1 14.9 - - - +
173C GLU* 5.5 0.6 + - - +
174C ILE* 1.3 76.1 - - - +
176C CYS* 1.3 60.2 + - - +
177C PRO 4.1 0.4 - - - -
178C ALA* 3.5 10.2 - - - +
181D SER 5.2 0.3 - - - +
182D ARG* 3.0 38.2 + - - +
183D SER* 5.4 0.6 - - - +
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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