Contacts of the strand formed by residues 183 - 189 (chain A) in PDB entry 1P4A
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 ILE 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ASN* 4.3 28.5 - - + +
175A TYR 3.5 9.2 - - - +
176A VAL* 3.8 14.4 - - + -
182A ARG* 1.3 76.5 - - + +
184A GLN* 1.3 62.3 + - - +
185A THR* 5.6 1.1 - - - +
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS* 4.8 20.0 + - - +
174A ASN* 3.4 6.7 - - - +
175A TYR* 2.8 59.0 + - + +
177A SER* 3.1 30.6 - - - -
180A SER* 4.2 10.7 + - - +
182A ARG* 3.4 17.6 + - + +
183A ILE* 1.3 79.4 - - - +
185A THR* 1.3 63.6 + - - +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG 3.9 0.2 - - - +
161A LYS* 3.5 28.8 + - - +
162A ASP* 5.4 3.5 - - + +
172A SER* 3.9 21.5 - - - +
173A ILE 3.5 10.1 - - - +
174A ASN* 2.7 20.8 + - - +
175A TYR* 3.7 4.8 - - - -
183A ILE* 5.6 1.4 - - - +
184A GLN* 1.3 74.8 - - - +
186A MET* 1.3 71.1 + - - +
187A SER* 4.9 2.0 - - - -
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Residues in contact with MET 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 4.1 14.8 - - + -
159A VAL* 3.5 18.6 - - + -
160A ARG 3.2 7.2 - - - +
161A LYS* 5.2 0.4 - - - -
172A SER* 3.4 1.0 - - - -
173A ILE* 3.1 49.1 + - + +
175A TYR* 3.7 33.1 - - + +
185A THR* 1.3 75.2 - - - +
187A SER* 1.3 63.4 + - - +
211A THR* 3.5 24.5 - - + +
214A GLY* 3.4 8.5 - - - +
215A MET* 3.4 35.4 - - + +
218A LEU* 4.3 4.9 - - + -
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A VAL* 3.6 6.1 - - - +
160A ARG* 2.9 46.0 + - - +
162A ASP* 4.3 12.6 + - - -
170A THR* 3.9 13.3 - - - +
171A VAL 3.1 12.8 - - - -
172A SER* 3.3 16.8 - - - -
185A THR* 4.9 2.7 - - - -
186A MET* 1.3 76.8 - - - +
188A LEU* 1.3 64.9 + - - +
218A LEU* 4.4 2.2 - - - -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET* 3.9 17.5 - - + -
157A VAL* 3.4 30.3 - - + -
158A ILE 3.4 26.2 - - - +
159A VAL* 3.9 6.7 - - - -
160A ARG* 6.0 0.4 - - + -
170A THR* 3.5 4.7 - - - -
171A VAL* 2.8 34.7 + - - +
187A SER* 1.3 78.1 - - - +
189A ALA* 1.3 71.8 + - - +
190A LYS 3.5 0.2 + - - -
192A SER* 4.2 9.6 - - - -
193A MET* 3.8 20.0 - - + -
218A LEU* 4.1 12.8 - - + -
222A PHE* 4.0 19.6 - - + -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A SER 3.9 10.3 - - - +
170A THR* 3.7 13.3 - - + +
188A LEU* 1.3 79.2 - - - +
190A LYS* 1.3 60.0 + - - +
191A ARG* 4.0 15.3 - - + +
192A SER* 2.9 39.0 + - - +
193A MET 3.8 3.3 + - - -
222A PHE* 4.0 2.6 - - - -
104B TYR* 6.1 1.6 - - + -
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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