Contacts of the strand formed by residues 100 - 108 (chain A) in PDB entry 2JXP
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 GLU 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ARG* 2.7 39.8 + - - +
83A VAL 3.5 8.7 - - - +
84A ALA* 4.9 4.0 - - + +
99A GLN* 1.3 91.2 + - - +
101A ILE* 1.3 62.7 + - - +
102A ARG* 3.4 18.6 + - + +
139A GLN* 4.5 1.4 + - - -
150A HIS* 5.6 2.3 + - - -
152A HIS* 2.8 41.5 + - + +
153A HIS* 4.3 2.7 - - - +
154A HIS* 3.3 32.1 + - + +
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Residues in contact with ILE 101 (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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81A TYR 3.5 16.8 - - - +
82A ARG* 4.1 6.5 + - - -
83A VAL* 3.0 39.9 + - + +
99A GLN 5.0 2.7 - - - +
100A GLU* 1.3 76.6 - - - +
102A ARG* 1.3 61.0 + - - +
103A LEU* 3.7 32.8 - - + -
132A ALA* 3.5 15.3 - - + +
135A GLN* 3.9 19.5 - - + +
136A ILE* 3.5 32.5 - - + +
139A GLN* 4.3 16.4 - - - +
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Residues in contact with ARG 102 (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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81A TYR 4.8 0.2 - - - -
82A ARG* 4.0 10.8 - - - +
100A GLU* 3.4 32.7 + - + +
101A ILE* 1.3 73.2 - - - +
103A LEU* 1.3 70.2 + - - +
104A THR* 4.2 3.2 + - + -
150A HIS* 5.4 15.7 + - - -
152A HIS* 4.7 17.9 - - - +
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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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79A LEU 3.4 2.0 - - - +
80A VAL* 4.7 0.2 - - - +
81A TYR* 2.8 44.1 + - + +
101A ILE* 3.6 19.5 + - + +
102A ARG* 1.3 82.2 - - - +
104A THR* 1.3 63.6 + - - +
105A ARG* 4.2 2.9 - - - +
128A MET* 3.3 48.0 - - + +
131A ASP* 3.3 21.5 - - + +
132A ALA* 3.6 27.8 - - + +
135A GLN* 5.0 2.9 - - - +
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Residues in contact with THR 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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64A ARG* 5.9 0.7 - - - +
78A GLU* 4.2 26.7 + - + +
79A LEU 3.2 4.9 - - - -
80A VAL* 4.0 25.6 - - + -
102A ARG* 4.1 3.6 + - + -
103A LEU* 1.3 78.0 - - - +
105A ARG* 1.3 68.8 + - - +
106A ILE* 4.2 8.6 + - - +
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Residues in contact with ARG 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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77A PHE 3.4 2.9 - - - +
78A GLU* 3.8 3.3 - - - -
79A LEU* 2.9 50.8 + - + +
103A LEU* 5.8 2.5 - - - -
104A THR* 1.3 80.4 - - - +
106A ILE* 1.3 63.5 + - - +
107A LEU 3.9 0.2 - - - -
124A LEU* 3.4 46.5 - - + +
127A ASP* 2.7 37.7 + - - +
128A MET* 3.5 33.3 - - + +
131A ASP* 6.2 0.2 - - - +
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Residues in contact with ILE 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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66A LEU* 3.6 24.2 - - + -
76A GLU* 3.6 33.4 - - + -
77A PHE 4.1 1.3 - - - -
78A GLU* 5.5 3.6 - - + -
104A THR* 4.8 8.1 - - - +
105A ARG* 1.3 78.9 - - - +
107A LEU* 1.3 61.0 + - - +
108A PRO* 3.1 14.7 - - + +
124A LEU* 3.2 14.4 - - - +
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Residues in contact with LEU 107 (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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63A LYS* 5.2 5.2 - - - +
76A GLU* 3.3 3.4 - - - -
77A PHE* 2.7 58.7 + - + +
79A LEU* 3.9 30.1 - - + -
105A ARG 3.6 0.6 + - - -
106A ILE* 1.3 72.2 - - - +
108A PRO* 1.3 79.1 - - + +
109A PHE* 3.3 11.0 + - + +
117A LYS* 4.5 12.3 - - + +
120A GLU* 3.4 30.1 - - + -
121A GLU* 4.0 20.0 - - + +
124A LEU* 3.9 0.9 - - + -
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Residues in contact with PRO 108 (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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75A ARG 4.2 2.9 - - - +
76A GLU* 4.7 10.3 - - + +
106A ILE* 3.1 14.5 - - + +
107A LEU* 1.3 82.1 - - + +
109A PHE* 1.3 62.0 + - - +
110A LEU* 3.3 16.7 + - + +
117A LYS* 3.0 24.8 + - - -
120A GLU* 3.7 32.5 - - + +
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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