Contacts of the strand formed by residues 171 - 177 (chain C) in PDB entry 1VBF
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 GLN 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C THR* 3.1 34.0 - - - +
164C PRO* 4.7 0.2 - - + -
165C ILE 3.4 15.0 - - - +
166C GLY* 3.8 13.7 - - - +
168C GLY 3.4 15.7 + - - +
169C ARG* 4.0 6.7 + - - +
170C VAL* 1.3 83.6 - - - +
172C LYS* 1.3 67.1 + - - +
190C GLU* 3.4 6.8 - - - +
191C VAL* 2.8 51.7 + - + +
192C MSE 3.3 0.5 - - - -
193C PHE* 2.9 41.3 + - - +
195C ARG* 5.8 0.8 - - - +
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Residues in contact with LYS 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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164C PRO* 3.2 3.8 - - - +
165C ILE 2.8 35.7 + - - +
171C GLN* 1.3 78.3 - - - +
173C LEU* 1.3 60.1 + - - +
174C TYR* 3.0 31.8 + - + +
187C ASN* 2.8 32.6 - - - +
189C GLY 3.5 4.9 - - - +
190C GLU* 4.8 12.3 - - + -
191C VAL* 4.3 1.6 - - - -
203D TYR 5.1 7.8 + - - +
204D ASP* 6.4 1.3 - - + -
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Residues in contact with LEU 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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58C LEU* 5.1 1.3 - - + -
61C PHE* 4.6 6.7 - - + -
62C MSE 4.0 33.0 - - + -
162C ILE* 4.0 16.4 - - + -
163C LEU 3.7 21.5 - - - +
164C PRO* 4.1 11.9 - - + -
172C LYS* 1.3 70.5 - - - +
174C TYR* 1.3 59.5 + - - +
187C ASN* 3.6 1.9 - - - -
188C LEU* 2.7 73.2 + - + +
189C GLY 2.9 18.0 + - - +
191C VAL* 3.9 23.7 - - + +
193C PHE* 4.5 0.2 - - + -
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Residues in contact with TYR 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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161C MSE 3.5 1.2 - - - +
162C ILE* 3.2 9.0 - - - +
163C LEU* 2.8 45.2 + - + +
165C ILE* 3.4 44.4 - - + -
172C LYS* 3.0 46.9 + - + +
173C LEU* 1.3 73.2 - - - +
175C LYS* 1.3 59.0 + - - +
176C VAL* 3.6 10.3 - - + -
185C LEU* 3.9 24.7 - - + -
186C GLU 3.5 11.9 - - - -
187C ASN* 4.0 19.9 + - + -
188C LEU* 4.3 3.1 - - - -
203D TYR* 4.1 22.8 + + + +
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Residues in contact with LYS 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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65C GLU* 3.4 46.5 + - - +
67C ASP* 5.6 2.4 - - - +
160C ILE* 4.4 29.2 - - + +
161C MSE 3.6 3.4 - - - -
162C ILE* 4.1 6.7 - - + -
174C TYR* 1.3 72.2 - - - +
176C VAL* 1.3 57.5 + - - +
177C ILE* 3.9 14.6 + - + +
184C SER 3.2 5.7 - - - +
186C GLU* 2.9 56.5 + - + +
188C LEU* 3.6 17.0 - - + +
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Residues in contact with VAL 176 (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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147C LEU* 4.9 11.7 - - + -
152C TYR* 3.8 23.3 - - + -
155C LEU* 5.0 0.8 - - + +
159C GLY 3.9 0.2 - - - +
160C ILE* 3.4 4.5 - - - +
161C MSE 2.7 52.6 + - + +
163C LEU* 4.3 12.8 - - + -
165C ILE* 5.2 0.7 - - + -
174C TYR* 4.3 16.8 - - + -
175C LYS* 1.3 74.5 - - - +
177C ILE* 1.3 63.9 + - - +
178C LYS 4.2 0.4 + - - +
183C PRO* 3.7 25.1 - - + -
184C SER 3.7 3.6 - - - -
185C LEU* 3.8 20.4 - - + -
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Residues in contact with ILE 177 (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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158C GLY* 4.0 11.9 - - - +
159C GLY 3.5 9.6 - - - +
160C ILE* 4.3 21.3 - - + -
175C LYS* 4.6 17.3 - - + +
176C VAL* 1.3 82.2 - - - +
178C LYS* 1.3 71.8 + - - +
179C LYS* 3.4 7.3 + - + +
183C PRO* 3.5 1.6 - - - +
184C SER* 3.3 41.2 + - - +
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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