Contacts of the strand formed by residues 158 - 163 (chain A) in PDB entry 1PTG
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 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PHE* 4.9 3.1 - - + -
95A ILE* 4.3 14.6 - - + +
98A ALA* 3.7 26.9 - - + -
99A LYS* 5.3 0.4 - - + -
102A LEU* 3.8 16.4 - - + -
110A ILE* 3.4 16.4 - - + +
112A MET* 4.0 15.9 - - + -
141A ILE* 2.7 37.9 + - + +
142A PHE* 3.4 32.8 - - + -
143A LEU 3.1 20.2 + - - +
157A LYS* 1.3 75.4 - - - +
159A VAL* 1.3 69.2 + - - +
160A LEU* 3.7 1.2 + - - +
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Residues in contact with VAL 159 (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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23A LEU* 4.0 11.7 - - + -
109A THR* 3.8 10.1 - - - +
110A ILE 2.8 7.4 + - - +
111A ILE* 3.1 18.1 - - + -
112A MET* 2.7 32.4 + - - -
143A LEU* 4.7 11.2 - - + -
149A ILE* 3.8 29.4 - - + -
154A ALA* 3.7 30.7 - - + +
158A ILE* 1.3 75.4 - - - +
160A LEU* 1.3 58.2 - - - +
172A GLY* 4.3 2.7 - - - -
173A TYR* 3.9 22.2 - - + -
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Residues in contact with LEU 160 (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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111A ILE* 4.9 0.2 - - - -
112A MET* 3.3 40.2 - - + +
114A LEU* 4.1 12.6 - - + -
132A PHE* 4.2 7.2 - - + -
137A PHE* 3.9 29.8 - - + -
142A PHE* 4.8 4.3 - - + -
143A LEU 5.3 1.2 + - - +
158A ILE 3.7 1.0 + - - -
159A VAL* 1.3 75.6 - - - +
161A LEU* 1.3 69.9 + - - +
162A LYS* 3.4 40.4 - - + +
164A TYR* 3.9 12.1 - - + +
171A GLY 4.4 4.3 - - - +
172A GLY* 3.5 4.0 - - - -
173A TYR* 2.8 35.9 + - - +
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Residues in contact with LEU 161 (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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65A ILE* 5.5 4.0 - - + -
111A ILE* 4.0 16.2 - - + -
112A MET 2.9 7.4 + - - +
113A SER* 3.2 24.8 + - - +
114A LEU 3.1 24.9 + - - -
160A LEU* 1.3 73.7 - - - +
162A LYS* 1.3 72.0 + - - +
163A ARG* 3.5 6.1 + - + -
173A TYR* 4.1 24.2 - - + +
174A ASN 5.3 0.2 - - - +
176A PHE* 4.1 28.0 - - + -
178A TRP* 5.1 6.5 - - + -
228A LEU* 6.1 1.8 - - + -
230A ILE* 4.2 23.1 - - + -
270A TRP* 4.7 8.7 - - + -
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Residues in contact with LYS 162 (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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114A LEU 4.4 1.1 - - - -
133A GLU* 4.6 0.7 - - - -
137A PHE* 4.9 2.2 - - - -
146A GLU* 4.5 1.6 + - - -
160A LEU* 3.4 28.0 - - + -
161A LEU* 1.3 76.7 - - - +
163A ARG* 1.3 60.9 + - - +
164A TYR* 3.4 22.2 - - + +
167A SER* 2.8 36.5 + - - +
169A GLU 3.0 19.6 + - - -
171A GLY 3.5 25.4 + - - +
173A TYR 3.2 19.5 + - - +
174A ASN* 4.3 15.8 + - - -
175A ASN* 3.1 34.8 - - + +
176A PHE* 4.5 1.6 + - - -
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Residues in contact with ARG 163 (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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67A ASP* 3.6 20.6 + - - -
69A ARG* 3.9 6.6 - - - +
113A SER* 3.3 23.8 - - - +
114A LEU 2.8 21.0 + - - +
115A LYS* 3.4 33.8 - - + +
116A LYS* 3.4 18.2 - - - +
161A LEU* 3.5 7.6 + - + +
162A LYS* 1.3 75.1 - - - +
164A TYR* 1.3 55.4 + - - +
175A ASN* 3.8 8.5 - - - -
178A TRP* 3.3 58.2 - - + +
232A PHE* 4.3 1.8 - - - -
801A INS 2.7 45.6 + - - -
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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