Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 1PNG
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 LYS 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A THR 3.4 1.2 + - - -
40A VAL* 1.3 73.4 - - - +
42A THR* 1.3 67.3 + - - +
101A THR* 3.5 14.6 - - - +
134A VAL* 2.7 25.5 + - + +
135A TYR 4.6 2.2 - - - +
136A GLY* 3.8 13.2 - - - +
137A THR* 3.1 40.4 + - - +
138A PRO* 4.0 21.7 - - + +
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Residues in contact with THR 42 (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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40A VAL* 3.7 1.4 - - - +
41A LYS* 1.3 87.8 + - - +
43A ILE* 1.3 74.5 + - - +
44A LYS* 3.7 23.8 - - + -
99A ASP* 3.4 25.5 + - - +
101A THR* 3.3 7.3 + - - +
132A ASP 3.6 1.1 - - - +
133A ILE* 3.6 0.2 - - - -
134A VAL* 2.9 42.5 + - + +
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Residues in contact with ILE 43 (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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33A PHE* 5.4 0.7 - - + -
37A VAL* 5.8 1.6 - - + -
40A VAL* 3.7 16.2 - - + -
42A THR* 1.3 77.8 - - - +
44A LYS* 1.3 63.0 + - - +
99A ASP* 3.7 2.1 - - - +
100A VAL* 2.9 47.4 + - + +
101A THR* 2.9 18.2 + - - +
104A LYS* 3.8 27.4 - - + +
107A LEU* 3.9 25.6 - - + +
131A PHE* 3.9 22.9 - - + -
132A ASP 3.3 7.4 - - - +
133A ILE* 4.3 21.1 - - + -
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Residues in contact with LYS 44 (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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42A THR* 3.7 15.0 - - + +
43A ILE* 1.3 75.8 - - - +
45A MET* 1.3 60.1 + - - +
46A PHE* 3.7 25.2 - - + -
97A GLU* 3.3 30.6 + - + +
98A ILE 3.8 1.6 - - - -
99A ASP* 2.8 39.2 + - - +
131A PHE* 3.2 6.6 - - - +
132A ASP* 2.9 39.5 + - + +
134A VAL* 6.0 2.5 - - + -
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Residues in contact with MET 45 (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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43A ILE 4.0 0.6 + - - -
44A LYS* 1.3 73.0 - - - +
46A PHE* 1.3 61.2 + - - +
47A ILE* 4.4 14.4 - - + +
65A VAL* 3.3 43.5 - - + -
78A ILE* 4.0 20.2 - - + -
79A GLY 5.6 1.3 - - - -
96A LEU 3.5 0.9 - - - +
97A GLU* 3.3 5.0 - - - +
98A ILE* 2.8 51.0 + - + +
100A VAL* 4.0 10.8 - - + -
113A LEU* 5.6 0.7 - - + -
129A VAL* 3.3 29.8 - - + -
130A ASP 3.8 2.9 - - - -
131A PHE* 3.6 28.3 - - + -
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Residues in contact with PHE 46 (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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44A LYS* 3.7 25.1 - - + -
45A MET* 1.3 74.5 - - - +
47A ILE* 1.3 62.0 + - - +
48A LYS* 5.5 0.4 - - - -
94A ARG* 3.4 67.8 - - + +
95A GLY 4.6 1.1 - - - -
96A LEU 3.2 4.7 - - - -
97A GLU* 3.4 44.6 - - + -
128A SER 3.8 0.7 - - - +
129A VAL* 3.4 8.8 - - - +
130A ASP* 2.9 46.0 + - - +
132A ASP* 3.6 23.3 - - - -
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Residues in contact with ILE 47 (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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45A MET* 4.4 18.2 - - + -
46A PHE* 1.3 77.0 - - - +
48A LYS* 1.3 62.9 + - - +
49A ASN* 4.0 1.5 + - + +
65A VAL* 4.6 10.5 - - + -
81A PHE* 3.7 39.9 - - + -
89A THR* 4.0 3.7 + - + +
95A GLY* 3.2 1.7 - - - -
96A LEU* 2.7 51.6 + - + +
98A ILE* 3.9 22.4 - - + -
115A ILE* 4.6 2.5 - - + -
127A TYR* 3.9 27.8 - - + -
128A SER 3.7 2.0 - - - -
129A VAL* 4.5 16.4 - - + +
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Residues in contact with LYS 48 (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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46A PHE 5.5 0.2 - - - -
47A ILE* 1.3 71.1 - - - +
49A ASN* 1.3 60.0 + - - +
50A GLU* 3.7 15.0 - - + +
89A THR* 3.6 5.4 - - - +
92A LEU 5.8 0.7 - - - +
93A PRO 4.0 8.9 + - - +
94A ARG* 3.5 45.5 - - - +
95A GLY* 4.1 2.2 - - - +
127A TYR* 3.1 8.4 - - - +
128A SER* 2.8 50.8 + - - +
130A ASP* 4.6 13.3 + - - +
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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