Contacts of the strand formed by residues 181 - 188 (chain A) in PDB entry 2PNT
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A THR* 4.1 22.4 - - + -
104A LEU 3.4 4.3 - - - +
105A GLU* 4.6 6.3 - - + +
112A PHE* 4.5 0.4 - - - -
159A ASN* 4.8 3.8 - - - +
178A SER* 2.8 26.9 + - - +
179A GLY 3.4 0.2 - - - -
180A ASN* 1.3 78.2 - - + +
182A LEU* 1.3 63.0 + - - +
183A ARG* 6.5 0.2 - - + -
160B GLY 5.9 2.2 - - - +
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Residues in contact with LEU 182 (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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102A LEU 3.6 1.0 - - - +
103A THR* 3.2 3.4 - - - -
104A LEU* 2.6 47.9 + - + +
112A PHE* 3.7 23.6 - - + -
114A PHE* 4.2 9.4 - - + -
158A VAL* 3.5 25.8 - - + -
159A ASN* 4.3 0.2 - - - -
175A ILE* 3.7 31.2 - - + +
178A SER* 3.2 31.2 - - - +
181A VAL* 1.3 75.9 - - - +
183A ARG* 1.3 60.0 + - - +
184A LEU* 3.8 31.0 - - + -
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Residues in contact with ARG 183 (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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101A VAL* 3.6 23.3 - - + -
102A LEU 3.1 12.3 - - - +
103A THR* 3.7 15.9 - - + +
157A SER 3.8 0.5 - - - +
158A VAL* 3.3 7.1 - - - +
159A ASN* 2.9 63.9 + - - +
160A GLY* 3.8 21.2 - - - +
181A VAL* 6.5 0.2 - - + -
182A LEU* 1.3 72.4 - - - +
184A LEU* 1.3 61.1 + - - +
185A GLU 4.3 0.2 + - - -
159B ASN 6.3 0.2 - - - -
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Residues in contact with LEU 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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100A LYS 3.5 0.2 - - - +
101A VAL* 3.4 3.7 - - - -
102A LEU* 2.7 41.2 + - + +
104A LEU* 3.7 30.1 - - + -
114A PHE* 4.2 11.4 - - + -
149A LEU* 4.3 16.8 - - + -
155A ILE* 3.9 21.3 - - + -
157A SER 3.5 2.0 - - - +
158A VAL* 3.8 28.5 - - + -
175A ILE* 5.1 2.2 - - + -
182A LEU* 3.8 31.4 - - + -
183A ARG* 1.3 73.2 - - - +
185A GLU* 1.3 60.5 + - - +
186A THR* 3.5 14.4 + - + +
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Residues in contact with GLU 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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99A ARG* 4.1 26.5 + - + +
100A LYS 3.7 4.9 - - - +
101A VAL* 4.1 22.2 - - + +
155A ILE* 3.7 3.1 - - - -
156A ALA* 2.8 43.8 + - + +
157A SER* 3.0 39.9 + - - +
183A ARG 4.2 0.4 - - - -
184A LEU* 1.3 69.7 - - - +
186A THR* 1.3 69.2 + - - +
187A LEU* 4.6 4.7 - - + -
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Residues in contact with THR 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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99A ARG* 3.2 6.6 - - - +
100A LYS* 2.9 49.3 + - - +
102A LEU* 3.7 28.6 - - + +
149A LEU* 3.8 18.6 - - + -
153A ASP* 4.0 16.7 + - + +
154A THR 3.2 9.6 - - - +
155A ILE* 5.3 2.5 - - + -
184A LEU* 4.1 10.5 - - + +
185A GLU* 1.3 77.7 - - - +
187A LEU* 1.3 63.2 + - - +
188A TYR* 3.8 9.9 - - - -
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Residues in contact with LEU 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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97A GLN* 3.7 33.7 - - + +
98A GLN 3.3 6.3 - - - +
99A ARG* 3.7 20.4 - - + +
152A GLY 4.2 0.7 - - - +
153A ASP* 3.6 2.1 - - - -
154A THR* 2.9 50.9 + - + -
156A ALA* 3.8 20.9 - - + -
164A GLU* 3.6 24.2 - - - +
185A GLU* 4.6 5.8 - - - -
186A THR* 1.3 80.9 - - - +
188A TYR* 1.3 63.8 + - - +
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Residues in contact with TYR 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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97A GLN* 3.7 3.6 - - - +
98A GLN* 2.8 79.8 + - + +
99A ARG 4.9 1.2 + - - -
100A LYS* 3.7 40.7 + - + +
152A GLY 5.0 4.7 - - - +
153A ASP* 3.5 24.2 - - - +
186A THR* 3.8 21.3 - - - -
187A LEU* 1.3 80.4 - - - +
189A SER* 1.3 67.1 + - - +
190A SER* 5.3 3.4 - - - -
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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