Contacts of the strand formed by residues 170 - 179 (chain H) in PDB entry 1CBV
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 SER 170 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169H SER* 1.3 74.5 - - - +
171H VAL* 1.3 65.2 + - - +
172H HIS* 3.5 27.9 + - - -
188H SER* 3.6 6.5 + - - +
189H VAL* 4.0 6.6 - - - -
190H THR* 3.9 20.6 + - - +
143L ASN* 4.9 6.3 + - - -
172L ASP* 4.7 6.8 + - - -
174L LYS* 5.6 8.8 + - - +
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Residues in contact with VAL 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H VAL 5.4 2.9 - - - +
162H TRP* 3.7 20.2 - - + -
169H SER* 4.0 7.4 - - - -
170H SER* 1.3 72.4 + - - +
172H HIS* 1.3 70.9 + - - +
173H THR* 4.0 11.1 + - - +
187H SER* 3.6 17.3 - - - +
188H SER 3.0 11.4 - - - +
189H VAL* 3.3 28.3 - - + -
172L ASP* 4.9 4.2 - - - +
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Residues in contact with HIS 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H SER* 3.7 22.6 + - - -
171H VAL* 1.3 73.8 - - - +
173H THR* 1.3 61.6 + - - +
174H PHE* 3.8 23.0 + - + -
187H SER* 3.3 10.4 + - - -
188H SER* 3.1 30.0 + - - +
142L ASN* 3.3 17.2 + - - -
143L ASN* 2.9 34.2 + - - -
169L THR* 4.8 10.5 - - + +
172L ASP* 3.8 27.8 + - + -
179L SER* 2.8 30.5 + - - -
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Residues in contact with THR 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H VAL* 4.5 21.9 + - + +
171H VAL* 3.9 14.1 + - - +
172H HIS* 1.3 72.6 + - - +
174H PHE* 1.3 68.3 + - - +
175H PRO* 3.7 8.5 - - + +
185H MET* 5.0 5.8 - - + -
186H SER 4.6 1.6 - - - -
187H SER* 4.5 4.3 + - - -
169L THR* 3.8 15.4 + - - +
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Residues in contact with PHE 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H HIS* 4.0 19.1 - - + -
173H THR* 1.3 72.8 - - - +
175H PRO* 1.3 77.8 - - + +
185H MET* 3.1 25.1 - - - +
186H SER* 3.1 40.0 + - - +
187H SER 4.2 0.2 - - - -
188H SER* 3.9 14.1 - - - -
140L PHE* 3.8 16.2 - + - -
142L ASN* 4.1 19.3 - - - -
167L SER* 3.9 15.9 - - - +
169L THR* 3.2 25.8 - - - -
179L SER* 3.6 3.6 - - - -
180L MET 3.5 21.1 - - - -
181L SER* 2.9 27.8 - - - +
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Residues in contact with PRO 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H THR* 3.7 8.3 - - + +
174H PHE* 1.3 90.5 - - + +
176H ALA* 1.3 65.3 + - - +
177H LEU* 4.1 2.1 + - + -
184H THR 4.5 1.4 - - - +
185H MET* 4.6 4.3 - - + -
186H SER 5.2 0.2 + - - -
167L SER* 2.9 25.1 + - - +
168L TRP 3.6 22.4 - - - +
169L THR* 4.5 8.1 - - + +
170L ASP 5.8 0.2 - - - +
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Residues in contact with ALA 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H TYR* 3.1 28.3 - - - +
156H GLU 4.8 3.4 - - - +
174H PHE 3.6 2.0 + - - -
175H PRO* 1.3 78.5 - - - +
177H LEU* 1.3 66.3 + - - +
183H TYR* 4.2 17.5 - - + -
184H THR 3.0 19.1 - - - +
185H MET* 4.0 8.8 - - + +
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Residues in contact with LEU 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H PRO* 4.1 2.2 + - + +
176H ALA* 1.3 81.2 - - - +
178H LEU* 1.3 69.1 + - - +
179H GLN* 4.5 0.7 - - - +
183H TYR* 3.1 9.1 - - - +
184H THR* 2.9 29.8 + - - +
165L LEU* 4.2 28.7 - - + -
166L ASN 2.8 34.5 - - - +
167L SER* 3.9 15.7 - - - +
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Residues in contact with LEU 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H PHE* 6.0 0.4 - - + -
177H LEU* 1.3 80.6 - - - +
179H GLN* 1.3 62.9 + - - +
180H SER 5.4 0.7 - - - +
181H GLY* 3.8 31.2 - - - +
182H LEU 4.1 0.4 - - - -
183H TYR* 3.5 40.7 - - + +
165L LEU* 4.5 5.4 - - - +
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Residues in contact with GLN 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H LYS* 5.0 8.4 - - - +
177H LEU 4.5 0.4 - - - +
178H LEU* 1.3 78.5 - - - +
180H SER* 1.3 79.5 + - - +
182H LEU* 2.5 32.4 + - - +
184H THR* 3.6 23.3 + - - +
165L LEU* 3.6 37.0 - - + +
185L THR* 3.5 37.6 + - - +
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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