Contacts of the strand formed by residues 52 - 65 (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 ALA 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PHE* 4.2 30.7 - - + -
16A ARG 3.3 3.0 + - - -
17A VAL* 3.5 8.3 - - + -
18A TYR 2.9 23.4 + - - -
50A SER* 3.5 3.3 - - - -
51A GLU* 1.3 81.3 - - - +
53A ILE* 1.3 68.7 + - - +
54A ILE* 5.7 1.8 - - + -
87A LEU* 5.3 7.6 - - + -
88A LEU 4.0 7.0 - - - +
89A ASP* 4.4 0.7 - - - +
90A ALA* 4.0 8.1 - - - +
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Residues in contact with ILE 53 (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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18A TYR* 3.3 38.1 - - + +
20A THR* 4.0 19.1 - - + -
47A ALA* 4.2 4.3 - - + -
50A SER* 4.3 0.9 - - - +
52A ALA* 1.3 79.4 - - - +
54A ILE* 1.3 67.9 + - - +
55A GLN* 3.9 2.8 + - + +
87A LEU* 3.9 3.7 - - - +
88A LEU* 2.9 45.5 + - + +
89A ASP 3.3 17.2 + - - +
90A ALA* 3.1 27.8 - - - +
92A ASN* 3.5 29.8 - - - +
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Residues in contact with ILE 54 (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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14A PHE* 6.2 0.7 - - + -
17A VAL* 5.0 17.0 - - + -
18A TYR 2.8 13.6 + - - +
19A ILE* 3.5 6.7 - - + +
20A THR* 3.1 25.8 + - - +
31A LEU* 3.9 25.6 - - + -
35A ILE* 3.8 29.2 - - + -
52A ALA* 6.1 1.8 - - + -
53A ILE* 1.3 74.8 - - - +
55A GLN* 1.3 66.0 + - - +
56A ILE* 6.3 0.4 - - + -
85A ALA* 5.9 2.7 - - + -
86A ARG 4.2 6.3 - - - +
87A LEU* 5.2 6.1 - - + +
98A LEU* 6.0 2.0 - - + -
136A ILE* 4.6 13.9 - - + -
140A VAL* 4.1 33.9 - - + -
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Residues in contact with GLN 55 (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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20A THR* 3.6 24.0 - - + +
22A PRO* 4.9 4.9 - - - +
53A ILE* 3.9 1.9 + - + -
54A ILE* 1.3 77.3 - - - +
56A ILE* 1.3 85.8 + - - +
57A VAL* 3.5 19.5 - - - +
85A ALA* 3.1 5.6 - - - +
86A ARG* 2.8 54.6 + - - +
88A LEU* 3.6 26.0 - - + -
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Residues in contact with ILE 56 (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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19A ILE* 5.9 4.9 - - + -
20A THR 3.4 14.7 + - - +
21A ALA* 3.8 11.9 - - + -
22A PRO* 3.0 35.7 - - + +
25A LEU* 4.5 7.9 - - + -
27A ILE* 3.6 39.0 - - + -
28A GLY* 6.4 0.7 - - - -
54A ILE* 4.3 1.3 + - + +
55A GLN* 1.3 88.1 + - - +
57A VAL* 1.3 61.9 + - - +
58A HIS* 3.9 7.9 - - - +
59A ALA* 3.7 21.8 - - + -
83A VAL* 5.1 3.1 - - + -
84A ALA 3.7 9.0 - - - +
85A ALA* 3.9 8.1 - - + -
136A ILE* 5.9 2.5 - - + -
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Residues in contact with VAL 57 (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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22A PRO* 3.7 14.1 - - - +
55A GLN* 3.5 23.1 - - - +
56A ILE* 1.3 74.4 - - - +
58A HIS* 1.3 93.2 + - + +
84A ALA* 2.8 28.0 + - + +
85A ALA* 4.0 11.9 - - - -
86A ARG* 4.4 11.9 - - + +
154A HIS* 6.3 0.9 - - - +
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Residues in contact with HIS 58 (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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22A PRO* 5.6 3.3 - - + +
25A LEU* 5.3 2.7 - - - -
56A ILE* 3.8 6.5 - - - +
57A VAL* 1.3 110.8 + - + +
59A ALA* 1.3 63.2 + - - +
60A ILE* 3.7 19.3 - - + +
82A ARG* 3.9 3.1 - - + +
83A VAL* 3.4 0.9 - - - -
84A ALA* 2.9 35.6 + - + +
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Residues in contact with ALA 59 (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 LEU* 3.8 23.0 - - + +
27A ILE* 4.6 4.0 - - + -
56A ILE* 3.7 20.2 - - + -
58A HIS* 1.3 77.4 - - - +
60A ILE* 1.3 65.7 + - - +
61A ARG 4.2 0.5 + - - -
81A TYR* 3.5 29.9 + - + +
82A ARG 3.1 7.0 - - - +
83A VAL* 4.4 6.7 - - + -
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Residues in contact with ILE 60 (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 LEU* 6.0 0.9 - - + -
58A HIS* 3.7 23.6 - - + +
59A ALA* 1.3 87.8 - - - +
61A ARG* 1.3 69.3 + - - +
62A GLU* 4.2 15.8 - - + +
80A VAL 3.5 3.3 - - - +
81A TYR* 3.4 4.9 - - - -
82A ARG* 2.9 40.0 + - + +
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Residues in contact with ARG 61 (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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59A ALA 4.2 0.4 + - - -
60A ILE* 1.3 74.4 - - - +
62A GLU* 1.3 68.9 + - - +
63A LYS* 4.1 12.3 - - - +
79A LEU* 3.4 28.1 - - - +
80A VAL 3.5 3.4 - - - -
81A TYR* 3.5 22.4 - - + -
121A GLU* 2.8 42.4 + - - -
125A TYR* 3.3 56.1 + - + +
128A MET* 3.4 30.2 - - + +
129A GLN* 4.4 0.2 - - - +
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Residues in contact with GLU 62 (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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60A ILE* 3.8 15.3 + - + +
61A ARG* 1.3 83.9 - - - +
63A LYS* 1.3 68.9 + - - +
64A ARG* 4.1 20.9 + - - +
79A LEU 3.6 0.2 - - - -
80A VAL* 3.0 52.2 + - + +
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Residues in contact with LYS 63 (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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61A ARG* 4.1 10.5 - - - +
62A GLU* 1.3 82.5 - - - +
64A ARG* 1.3 63.2 + - - +
77A PHE* 3.5 30.1 - - + +
78A GLU 3.5 5.6 - - - -
79A LEU* 3.5 20.9 - - + -
107A LEU* 5.2 4.8 - - - +
121A GLU* 3.6 38.0 - - - +
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Residues in contact with ARG 64 (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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62A GLU* 4.1 17.7 + - - +
63A LYS* 1.3 77.1 - - - +
65A ILE* 1.3 63.9 + - - +
77A PHE* 3.3 15.3 - - - -
78A GLU* 2.6 74.1 + - + +
80A VAL* 4.2 22.6 - - + +
104A THR* 5.9 0.2 - - - +
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Residues in contact with ILE 65 (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* 1.3 84.1 - - - +
66A LEU* 1.3 70.7 + - - +
67A SER 3.1 27.6 - - - +
68A LEU* 3.6 29.4 - - + -
74A VAL* 3.6 24.2 - - + -
76A GLU 3.4 9.0 - - - +
77A PHE* 3.7 18.8 - - + -
78A GLU* 4.3 2.5 - - - +
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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