Contacts of the strand formed by residues 161 - 167 (chain C) in PDB entry 4S10
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 ARG 161 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159C VAL 5.6 0.4 - - - -
160C GLN* 1.3 81.9 - - - +
162C LEU* 1.3 60.5 + - - +
163C PHE* 3.1 37.9 - - + -
175C GLU* 3.5 26.1 + - - +
176C VAL 5.4 0.2 - - - -
178C VAL* 3.6 6.7 - - - -
190C ILE 4.3 0.9 - - - -
191C LEU* 3.4 8.7 - - - +
192C ASP* 2.8 61.3 + - + +
220C ILE* 3.8 8.1 - - - +
224C GLU* 2.7 36.8 + - - -
225C ARG* 3.6 2.7 - - - +
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Residues in contact with LEU 162 (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* 1.3 75.1 - - - +
163C PHE* 1.3 61.0 + - - +
175C GLU* 3.1 8.5 - - - +
176C VAL* 2.7 55.9 + - + +
177C PRO 3.2 20.9 - - - +
178C VAL* 3.8 9.4 - - + +
179C SER 3.9 6.5 - - - +
182C SER* 3.8 10.5 - - - -
183C PHE* 3.4 31.6 - - + -
189C PHE* 3.8 22.2 - - + -
190C ILE 3.4 23.3 - - - +
191C LEU* 3.9 11.9 - - + +
247C LEU* 5.4 0.2 - - + -
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Residues in contact with PHE 163 (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* 3.1 61.2 - - + -
162C LEU* 1.3 73.3 - - - +
164C GLN* 1.3 61.2 + - - +
165C VAL* 3.8 2.2 + - + +
173C ALA* 4.7 14.6 - - + -
174C THR 3.0 11.2 - - - +
175C GLU* 3.4 37.7 - - + -
176C VAL* 4.0 3.1 - - - -
189C PHE* 3.3 8.6 - - - -
190C ILE* 2.9 53.8 + - + +
192C ASP* 4.4 1.6 - - + -
216C VAL* 5.0 8.7 - - + -
220C ILE* 4.1 12.1 - - + -
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Residues in contact with GLN 164 (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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163C PHE* 1.3 71.7 - - - +
165C VAL* 1.3 62.3 + - - +
166C LYS* 3.9 24.7 - - + +
172C ARG 3.1 5.2 - - - +
173C ALA* 3.2 1.4 - - - -
174C THR* 2.5 51.0 + - - +
176C VAL* 3.9 17.6 - - + +
182C SER 5.0 2.8 - - - +
184C ASN* 3.6 13.5 - - - +
187C ASP* 3.0 24.2 + - + +
189C PHE* 3.5 29.6 - - + -
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Residues in contact with VAL 165 (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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163C PHE* 4.2 6.1 - - + +
164C GLN* 1.3 75.8 - - - +
166C LYS* 1.3 59.0 + - - +
171C VAL* 3.6 22.7 - - + -
172C ARG 3.4 4.5 - - - +
173C ALA* 4.4 11.0 - - + -
187C ASP* 3.5 4.0 - - - +
188C CYS* 2.7 46.6 + - + +
190C ILE* 4.0 27.1 - - + -
209C GLU* 3.6 28.4 - - - +
212C LYS* 3.9 13.2 - - + -
213C ALA* 3.9 4.7 - - + +
216C VAL* 4.7 0.9 - - + -
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Residues in contact with LYS 166 (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 GLN* 3.8 19.8 - - + +
165C VAL* 1.3 74.0 - - - +
167C GLY* 1.3 65.1 + - - +
170C VAL 4.3 0.5 - - - +
171C VAL* 3.6 4.4 - - - -
172C ARG* 3.1 35.5 + - + +
184C ASN* 5.5 0.6 - - - +
187C ASP* 3.1 28.3 + - - +
209C GLU* 3.4 3.6 - - - -
256C GLY* 5.1 0.2 - - - -
257C THR* 3.0 38.2 + - - +
258C GLU 3.4 13.9 + - - -
259C ASP* 3.2 20.5 + - - +
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Residues in contact with GLY 167 (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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166C LYS* 1.3 79.0 - - - +
168C ARG* 1.3 58.2 + - - -
170C VAL 3.8 7.9 - - - -
171C VAL* 4.1 8.5 - - - +
206C ASN* 2.7 32.4 + - - +
209C GLU* 2.6 20.0 + - - +
259C ASP* 4.0 17.7 - - - -
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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