Contacts of the strand formed by residues 110 - 118 (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 ASN 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A THR* 4.0 19.4 - - + +
31A PHE 3.4 6.7 + - - -
32A THR* 2.7 32.8 + - - +
70A LYS* 2.9 31.2 - - - +
109A GLY* 1.3 68.3 - - - -
111A THR* 1.3 61.2 + - - +
112A GLU 4.3 0.5 + - - -
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Residues in contact with THR 111 (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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29A GLY 3.9 0.2 - - - +
30A THR* 3.5 2.0 - - - -
31A PHE* 2.8 38.3 + - - +
33A PHE* 3.8 17.1 - - + -
67A VAL* 3.4 31.9 - - + -
68A LYS 5.3 1.8 - - - +
70A LYS* 4.8 3.3 - - - +
106A LEU 3.4 10.6 + - - +
107A LEU* 4.2 7.0 - - + -
108A SER 3.4 20.8 + - - -
109A GLY 3.1 12.0 + - - -
110A ASN* 1.3 73.5 - - - +
112A GLU* 1.3 64.4 + - - +
113A LEU* 3.8 13.1 + - + +
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Residues in contact with GLU 112 (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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28A GLU* 5.5 4.0 - - - +
29A GLY 3.2 13.7 + - - +
30A THR* 3.5 20.2 + - + +
67A VAL* 3.7 3.8 - - - +
68A LYS* 2.8 79.4 + - + +
70A LYS* 6.3 0.4 - - - +
75A TRP* 3.4 11.2 - - + -
110A ASN 4.2 0.8 + - - -
111A THR* 1.3 74.8 - - - +
113A LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 113 (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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11A THR* 3.8 24.9 - - + +
12A PHE* 3.6 19.1 - - + -
28A GLU* 3.4 5.2 - - - +
29A GLY 3.0 26.6 + - - +
31A PHE* 3.7 25.1 - - + -
33A PHE* 4.3 6.1 - - + -
65A VAL* 4.8 6.7 - - + -
66A TYR 3.3 12.6 - - - +
67A VAL* 4.1 10.5 - - + -
75A TRP* 3.8 3.1 - - - -
78A ILE* 5.1 2.5 - - + -
107A LEU* 4.4 9.2 - - + -
111A THR* 3.8 18.8 + - + +
112A GLU* 1.3 80.5 - - - +
114A LYS* 1.3 62.3 + - - +
129A VAL* 5.7 0.4 - - + -
131A PHE* 3.9 18.2 - - + -
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Residues in contact with LYS 114 (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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12A PHE* 4.1 2.2 - - - -
26A SER* 3.9 26.6 + - - -
27A ALA 3.3 6.7 - - - +
28A GLU* 3.8 19.7 + - + -
64A ASN 3.9 0.4 - - - +
65A VAL* 3.2 7.6 - - - +
66A TYR* 2.8 53.9 + - + -
75A TRP* 3.5 52.1 - - + +
113A LEU* 1.3 77.2 - - - +
115A ILE* 1.3 63.5 + - - +
116A TYR* 5.1 3.4 - - - +
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Residues in contact with ILE 115 (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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12A PHE* 3.8 23.1 - - + -
15A VAL* 4.0 21.1 - - + -
17A ASN* 3.4 14.0 + - - +
26A SER* 3.1 4.1 - - - -
27A ALA* 2.8 41.5 + - + +
47A ILE* 4.6 5.4 - - + -
64A ASN 3.5 9.0 - - - +
65A VAL* 4.1 18.2 - - + -
81A PHE* 4.7 5.6 - - + -
114A LYS* 1.3 76.1 - - - +
116A TYR* 1.3 67.5 + - - +
127A TYR* 3.8 37.2 - - + -
129A VAL* 4.3 11.7 - - + -
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Residues in contact with TYR 116 (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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17A ASN* 3.4 1.8 - - - -
25A GLN* 3.3 47.6 + - + -
26A SER* 3.9 12.6 - - - -
62A TYR* 4.2 11.0 - + - -
63A ALA* 3.1 6.8 - - - +
64A ASN* 2.9 51.5 + - - +
66A TYR* 4.8 8.5 - + + -
114A LYS* 4.3 3.6 - - - -
115A ILE* 1.3 77.2 - - - +
117A THR* 1.3 61.0 + - - +
118A GLU* 3.4 41.8 - - + +
120A TRP* 5.3 1.4 - - - -
153A LYS* 3.4 25.1 - - + -
154A SER* 3.5 12.7 - - - -
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Residues in contact with THR 117 (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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17A ASN* 2.7 29.5 + - - -
25A GLN* 2.9 27.0 + - - +
61A ARG* 4.0 17.7 - - + -
62A TYR 3.5 6.5 - - - +
63A ALA* 3.8 2.9 - - + +
83A THR* 4.6 1.6 - - + -
116A TYR* 1.3 77.8 + - - +
118A GLU* 1.3 57.3 - - - +
119A THR* 2.7 32.6 + - - +
125A ARG* 4.2 10.1 - - + -
127A TYR* 2.7 31.1 + - - +
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Residues in contact with GLU 118 (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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25A GLN* 4.1 2.7 - - - +
61A ARG* 3.0 33.9 + - - +
62A TYR* 2.8 27.8 + - + +
116A TYR* 3.4 23.5 - - + +
117A THR* 1.3 66.9 - - - +
119A THR* 1.3 58.4 + - - +
120A TRP* 3.7 25.2 + - + +
154A SER* 3.7 10.6 + - - -
155A SER* 2.6 43.1 + - - -
156A ILE* 3.7 25.8 - - - +
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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