Contacts of the strand formed by residues 179 - 183 (chain C) in PDB entry 5HP1
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 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C LYS* 6.6 0.2 - - - -
103C LYS* 5.0 16.2 - - + -
178C ILE* 1.3 78.3 - - - +
180C ILE* 1.3 60.9 + - - +
181C TYR* 3.7 32.3 - - + -
188C TYR* 3.4 10.0 - - + +
189C VAL* 3.2 5.7 - - - -
190C GLY* 2.9 39.5 + - - +
138D GLU* 4.0 11.7 - - - +
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Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C LEU* 4.6 6.7 - - + -
171C PHE* 4.0 26.7 - - + -
172C LYS* 3.4 42.7 + - + +
178C ILE* 3.5 26.9 + - + -
179C VAL* 1.3 73.4 - - - +
181C TYR* 1.3 70.3 + - - +
182C GLN* 3.7 6.2 + - + +
187C LEU* 4.2 24.2 - - + -
188C TYR 3.1 9.0 - - - +
189C VAL* 4.2 6.7 - - + -
205C LEU* 4.5 16.4 - - + -
138D GLU* 3.3 18.7 + - - +
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Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 3.8 21.1 - - + -
99C GLY 3.9 12.0 + - - -
100C LEU* 3.5 28.8 - - + -
179C VAL* 3.7 21.5 - - + -
180C ILE* 1.3 71.8 - - - +
182C GLN* 1.3 61.1 + - - +
183C TYR 3.9 0.6 + - - -
186C ASP 3.5 5.2 - - - +
187C LEU* 3.5 0.3 - - - -
188C TYR* 2.9 47.0 + + + +
229C TRP* 4.2 9.1 + + + -
135D ILE* 4.5 1.7 + - - +
136D ASN* 3.5 41.0 + - - +
138D GLU* 3.3 49.2 + - + +
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Residues in contact with GLN 182 (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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91C GLN* 5.1 2.4 + - - +
95C PRO* 5.2 1.7 - - - +
161C GLN* 4.1 2.8 + - - +
164C MET* 3.5 25.7 - - - +
165C THR* 3.1 38.5 + - - +
168C LEU* 3.3 21.3 - - + +
172C LYS* 5.6 6.5 - - + +
180C ILE* 3.7 5.8 + - + +
181C TYR* 1.3 73.6 - - - +
183C TYR* 1.3 60.4 + - - +
184C MET 4.0 8.1 + - - +
186C ASP 3.5 4.3 - - - -
187C LEU* 3.5 20.0 - - + -
137D ASN 4.4 5.0 - - - +
138D GLU 3.1 18.2 + - - +
139D THR* 4.3 4.9 - - + +
140D PRO* 3.5 27.6 - - + +
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Residues in contact with TYR 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLN* 3.3 38.4 - - + -
94C ILE* 3.6 27.1 - - + +
95C PRO* 3.8 22.2 - - + -
181C TYR 3.9 1.7 + - - +
182C GLN* 1.3 72.6 - - - +
184C MET* 1.3 66.7 + - + +
185C ASP* 3.0 1.0 + - - +
186C ASP* 2.9 34.5 + - + +
229C TRP* 6.1 2.9 - - + +
230C MET* 3.7 28.9 - - + -
3E C 3.8 0.7 + - - -
32E G 2.4 49.5 + - + -
33E G 3.4 30.0 - - - +
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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