Contacts of the strand formed by residues 102 - 106 (chain A) in PDB entry 1PJJ
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 GLN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ARG 3.6 1.0 - - - +
81A LEU* 3.4 8.4 - - - -
82A ALA* 2.8 40.5 + - - +
83A THR 2.9 21.8 + - - +
84A LEU* 3.6 18.1 + - + +
86A ALA* 4.2 10.3 + - - +
95A THR* 2.6 33.8 + - - +
96A MET 3.3 8.1 - - - +
97A LYS* 3.7 25.0 - - + +
98A PHE* 4.1 2.0 - - - -
101A GLY* 1.3 76.3 - - - +
103A LEU* 1.3 58.9 + - - +
104A ILE* 3.8 23.7 + - + +
1002A GOL 4.4 1.4 + - - -
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Residues in contact with LEU 103 (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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13A LEU* 3.8 19.5 - - + -
17A ILE* 4.1 14.4 - - + -
61A PHE* 3.9 32.5 - - + -
79A TYR* 3.7 34.0 - - + -
80A ARG 3.5 14.4 - - - +
81A LEU* 3.8 15.5 - - + -
94A LEU 4.0 0.3 - - - +
95A THR* 3.2 3.1 - - - -
96A MET* 2.8 54.7 + - + +
98A PHE* 3.9 10.0 - - + -
102A GLN* 1.3 72.0 - - - +
104A ILE* 1.3 59.5 + - - +
114A TRP* 6.0 1.9 - - + -
225A LEU* 4.3 0.4 - - + -
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Residues in contact with ILE 104 (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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78A LYS 3.6 1.4 - - - +
79A TYR* 3.3 8.8 - - - -
80A ARG* 2.9 69.2 + - + +
82A ALA* 4.1 13.0 - - + -
86A ALA* 5.0 3.8 - - + +
87A PRO 5.7 1.3 - - - +
88A ARG* 6.5 0.2 - - - -
92A ASP* 3.6 35.4 - - + +
94A LEU 3.4 9.4 - - - +
95A THR* 3.8 5.8 - - - +
102A GLN* 3.8 37.5 - - + +
103A LEU* 1.3 75.5 - - - +
105A TYR* 1.3 63.3 + - - +
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Residues in contact with TYR 105 (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 MET* 3.4 42.6 - - + -
71A SER* 4.9 2.2 - - - -
72A HIS 4.6 1.6 - - - -
73A LEU* 3.7 28.2 - - + -
77A GLY* 3.2 20.2 - - - -
78A LYS 3.6 10.3 - - - -
79A TYR* 3.6 35.0 - + + -
92A ASP* 3.7 1.6 - - - -
93A HIS* 2.8 27.4 + - + -
94A LEU* 2.8 25.8 + - + +
103A LEU 4.2 0.8 + - - -
104A ILE* 1.3 73.7 - - - +
106A ALA* 1.3 59.8 + - - +
107A ASP* 2.8 38.5 + - + -
112A GLY* 3.3 13.3 - - - -
114A TRP* 4.6 5.4 - + + -
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Residues in contact with ALA 106 (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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76A GLU 4.0 0.8 - - - +
77A GLY* 3.4 0.7 - - - -
78A LYS* 2.8 42.9 + - + +
80A ARG* 4.5 7.6 - - - +
89A GLU* 5.9 0.9 - - - +
91A HIS* 3.2 19.3 - - + +
92A ASP* 3.5 19.1 - - - +
93A HIS 4.4 0.2 - - - +
104A ILE 4.0 0.2 + - - -
105A TYR* 1.3 77.0 - - - +
107A ASP* 1.3 65.1 + - - +
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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