Contacts of the strand formed by residues 184 - 188 (chain C) in PDB entry 5IPN
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 184 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ALA 4.0 0.5 - - - +
175C ARG* 3.9 0.3 - - - -
176C ILE* 3.0 54.2 + - + +
182C SER 3.9 0.8 + - - -
183C TRP* 1.3 74.9 - - - +
185C ASP* 1.3 63.2 + - - +
186C PHE* 3.7 25.5 + - + -
196C VAL* 3.9 25.4 - - + -
197C ARG 4.0 4.5 - - - +
198C ILE* 4.1 4.3 - - + -
209C ILE* 4.1 16.2 - - + -
389C PHE* 3.7 35.7 - - + -
395C TYR* 5.5 0.7 - - - +
420C LEU* 4.3 13.2 - - + -
425C ILE* 4.9 7.9 - - + -
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Residues in contact with ASP 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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173C ASN* 6.3 0.2 - - + -
174C ALA 3.4 7.4 - - - +
175C ARG* 3.3 36.8 + - - +
183C TRP* 3.7 17.2 - - - +
184C LEU* 1.3 85.0 + - - +
186C PHE* 1.3 68.3 - - - +
187C GLU* 4.3 2.2 + - + -
196C VAL* 3.3 7.8 - - - +
197C ARG* 2.9 63.1 + - + +
199C ASP 5.0 0.2 + - - -
200C ARG* 4.5 14.5 + - - +
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Residues in contact with PHE 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ASN* 3.0 6.2 - - - +
174C ALA* 2.6 48.9 + - + +
176C ILE* 4.3 10.8 - - + -
184C LEU* 3.7 38.1 - - + -
185C ASP* 1.3 75.5 - - - +
187C GLU* 1.3 62.5 + - - +
194C LEU* 5.0 2.5 - - + -
195C PHE 3.4 5.6 - - - +
196C VAL* 3.2 35.0 - - + -
206C ALA* 4.8 1.3 - - + -
209C ILE* 4.4 5.2 - - + -
425C ILE* 3.9 22.9 - - + -
428C VAL* 4.8 8.3 - - + -
429C MET* 3.6 35.0 - - + -
432C LEU* 3.5 22.0 - - + -
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Residues in contact with GLU 187 (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 LEU* 5.9 1.7 - - - +
172C TYR 3.6 5.6 - - - +
173C ASN* 3.8 16.0 + - + +
185C ASP* 5.3 2.0 - - + -
186C PHE* 1.3 79.7 - - - +
188C PHE* 1.3 69.9 + - - +
194C LEU* 3.5 8.5 - - - +
195C PHE* 2.7 46.6 + - + +
196C VAL 5.9 0.2 - - - -
197C ARG* 2.9 49.0 + - + +
203C LYS* 4.0 13.7 - - - +
432C LEU* 4.4 1.5 - - - +
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Residues in contact with PHE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 4.0 21.1 - - + +
172C TYR* 3.1 42.3 + - + +
187C GLU* 1.3 88.9 - - - +
189C ASP* 1.3 65.8 + - - +
192C ASP* 4.2 21.5 - - - +
193C ASN 3.6 3.4 - - - -
194C LEU* 3.5 24.2 - - + -
195C PHE* 4.8 1.7 - - - -
203C LYS* 5.5 0.9 + - - -
346C TYR* 4.0 28.7 - + + -
432C LEU* 3.9 22.0 - - + -
433C ILE* 4.3 16.2 - - + -
436C ARG* 3.5 41.7 - - + +
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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