Contacts of the strand formed by residues 65 - 72 (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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.4 29.8 - - + +
29A PRO 3.6 1.9 + - - +
30A GLY* 3.1 8.3 - - - -
31A THR* 3.0 24.0 + - - +
63A ALA* 3.7 0.9 - - - +
64A ARG* 1.3 85.4 - - - +
66A PHE* 1.3 75.0 + - - +
111A ILE* 3.2 28.7 - - + +
113A SER* 5.3 5.8 - - - -
161A LEU* 5.5 3.6 - - + -
270A TRP* 3.6 46.4 - - + -
272A ILE* 4.6 17.0 - - + -
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Residues in contact with PHE 66 (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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31A THR* 3.7 3.8 - - - -
34A SER* 3.5 16.2 - - - +
55A PHE* 3.9 13.5 - + - -
58A GLN* 3.2 33.0 - - + -
59A MET* 3.4 35.4 - - + -
63A ALA* 3.5 30.1 - - + -
64A ARG* 4.1 2.0 - - - -
65A ILE* 1.3 86.4 - - - +
67A ASP* 1.3 60.8 + - - +
68A ILE* 3.4 8.5 + - + +
94A PHE* 3.7 26.5 - + + -
110A ILE* 3.8 18.6 - - + -
111A ILE 2.8 8.4 + - - +
112A MET* 3.9 0.8 - - - -
113A SER* 2.9 31.3 + - - -
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Residues in contact with ASP 67 (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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31A THR 3.0 21.0 + - - +
32A HIS* 3.8 6.1 - - - -
33A ASP* 2.7 28.6 + - - +
34A SER* 2.8 27.6 + - - -
35A GLY 4.6 1.0 + - - -
66A PHE* 1.3 69.3 - - - +
68A ILE* 1.3 59.1 + - - +
69A ARG* 2.7 42.4 + - - +
113A SER* 4.2 10.9 + - - -
163A ARG* 3.6 13.0 + - - -
232A PHE* 4.0 11.4 - - - -
272A ILE* 4.9 3.4 - - + -
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Residues in contact with ILE 68 (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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34A SER* 4.3 2.5 - - - -
35A GLY 5.1 0.4 - - - +
55A PHE* 4.2 13.5 - - + -
66A PHE* 4.1 15.7 - - + +
67A ASP* 1.3 77.9 - - - +
69A ARG* 1.3 63.2 + - - +
80A LEU* 3.8 31.0 - - + -
91A LEU* 4.2 15.0 - - + -
94A PHE* 4.0 27.1 - - + -
112A MET* 3.7 24.0 - - + -
113A SER* 2.9 22.0 + - - +
114A LEU* 3.3 16.8 - - + +
115A LYS* 2.9 24.4 + - - +
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Residues in contact with ARG 69 (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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32A HIS* 4.1 3.8 + - - -
33A ASP* 3.0 22.6 + - - +
67A ASP* 2.7 43.7 + - - +
68A ILE* 1.3 74.8 - - - +
70A GLY* 1.3 61.1 + - - +
80A LEU* 3.3 13.3 - - - +
81A HIS 3.1 29.9 + - - +
87A LEU* 5.6 0.2 - - - +
113A SER* 5.8 0.4 + - - -
115A LYS* 3.4 36.2 - - - +
117A GLU* 3.3 42.9 + - + +
163A ARG* 3.9 3.5 - - - +
801A INS 3.3 42.7 + - - -
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Residues in contact with GLY 70 (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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68A ILE 4.0 1.0 + - - -
69A ARG* 1.3 74.6 - - - +
71A ARG* 1.3 63.9 + - - +
78A ILE* 4.2 11.0 - - - -
79A VAL 2.9 12.1 - - - -
80A LEU* 4.5 2.7 - - - -
81A HIS* 4.8 1.3 - - - -
114A LEU* 4.1 7.7 - - - +
115A LYS 3.0 10.3 + - - -
116A LYS* 3.8 2.3 - - - -
117A GLU* 2.9 28.0 + - - +
118A TYR 3.8 0.7 + - - -
128A PHE* 4.1 6.5 - - - -
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Residues in contact with ARG 71 (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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70A GLY* 1.3 76.8 - - - +
72A LEU* 1.3 76.7 + - - +
73A THR* 4.8 2.2 - - - -
77A THR 3.6 0.2 - - - +
78A ILE* 3.3 10.2 - - - +
79A VAL* 2.9 31.8 + - + +
81A HIS* 3.7 45.9 + - + +
84A PRO 5.5 0.2 + - - -
118A TYR* 3.9 37.0 - - + +
119A GLU 2.7 29.8 + - - +
120A ASP 4.3 1.2 + - - -
121A MET* 3.1 44.6 - - - +
122A LYS* 4.4 11.9 - - - +
128A PHE* 4.4 5.2 - - - -
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Residues in contact with LEU 72 (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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71A ARG* 1.3 83.5 - - - +
73A THR* 1.3 63.9 + - - +
76A ASN* 3.9 14.4 - - - +
77A THR 3.3 17.7 - - - +
78A ILE* 4.3 4.5 - - + +
120A ASP* 3.6 25.5 + - + +
121A MET* 3.0 23.8 + - - +
124A ALA* 3.6 15.5 - - + -
126A ASP 3.1 28.5 - - - +
127A SER 3.6 10.5 - - - +
128A PHE* 4.5 9.9 - - + -
131A THR* 3.5 37.9 - - + +
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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