Contacts of the strand formed by residues 182 - 186 (chain C) in PDB entry 5D4D
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 182 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LEU* 6.4 0.9 - - + -
175C GLU 3.1 12.1 - - - +
176C VAL* 3.7 21.1 - - + +
180C GLY 4.6 3.8 - - - +
181C VAL* 1.3 75.9 - - - +
183C SER* 1.3 58.8 + - - +
192C PRO* 3.6 6.1 - - - +
193C LEU* 3.0 47.3 + - + +
194C VAL* 5.0 1.6 - - + +
217C LEU 5.2 0.7 - - - +
220C GLY 4.2 2.2 + - - -
221C LEU* 3.7 28.0 - - + +
307C LEU* 4.5 5.4 - - + -
310C LEU* 5.7 1.3 - - + -
311C PHE* 3.7 29.6 - - + -
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ASP 3.1 4.3 - - - +
174C LEU* 3.6 1.7 - - - -
175C GLU* 2.9 39.2 + - - +
177C GLU* 2.5 31.4 + - - -
181C VAL* 3.4 5.3 + - - -
182C VAL* 1.3 74.1 - - - +
184C MET* 1.3 58.9 + - - +
185C LYS* 4.0 0.5 + - - +
190C LYS* 3.6 25.0 - - - -
191C PHE 3.6 9.9 - - - -
192C PRO* 4.7 0.2 - - - -
193C LEU* 5.0 1.3 - - - -
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Residues in contact with MET 184 (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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172C ILE* 3.6 22.9 - - + -
173C ASP 3.2 4.5 - - - -
174C LEU* 4.3 4.0 - - + -
182C VAL 4.1 1.2 + - - -
183C SER* 1.3 72.9 - - - +
185C LYS* 1.3 61.4 + - - +
186C VAL* 3.4 24.0 - - + -
189C ARG 3.4 2.1 - - - +
190C LYS* 3.2 5.1 - - - -
191C PHE* 2.9 61.9 + - + +
193C LEU* 3.7 21.7 - - + +
196C LEU* 3.5 28.7 - - + -
260C LEU* 5.9 2.5 - - + -
261C ILE* 4.6 5.2 - - + -
303C PHE* 3.6 26.0 - - + -
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Residues in contact with LYS 185 (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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171C TRP 3.5 2.4 - - - +
172C ILE* 3.3 9.2 - - - -
173C ASP* 2.9 53.3 + - + +
175C GLU* 5.5 3.4 - - - -
183C SER 5.4 0.7 - - - +
184C MET* 1.3 73.5 - - - +
186C VAL* 1.3 64.0 + - - +
188C LYS* 4.3 16.2 - - + +
189C ARG 3.6 15.9 - - - +
190C LYS* 2.9 45.3 - - + +
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Residues in contact with VAL 186 (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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170C PRO* 4.0 18.2 - - + -
171C TRP 4.2 3.8 - - - -
172C ILE* 3.9 9.9 - - + -
184C MET* 3.4 37.5 - - + -
185C LYS* 1.3 80.1 - - - +
187C ASN* 1.3 89.2 + - - +
188C LYS 3.2 0.9 - - - -
189C ARG* 3.0 25.1 + - - +
191C PHE* 4.2 9.4 - - + -
242C LEU* 5.0 8.7 - - + +
256C TYR* 6.0 0.2 - - - +
260C LEU* 4.1 22.2 - - + -
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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