Contacts of the strand formed by residues 8 - 15 (chain B) in PDB entry 1JEY
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 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B LYS* 1.3 79.2 - - - +
9B ALA* 1.3 59.2 + - - +
10B VAL* 4.0 2.2 - - + -
52B ASP* 3.0 23.2 + - + +
53B GLU 2.8 27.2 + - - +
127B PHE* 3.4 7.9 - - - -
129B LYS* 3.2 24.5 - - + +
240B ILE* 4.1 27.1 - - + +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ALA* 1.3 71.6 - - - +
10B VAL* 1.3 61.2 + - - +
53B GLU 3.6 4.5 - - - -
83B LEU* 4.2 9.6 - - + -
118B ILE* 4.4 6.1 - - + +
122B THR* 3.7 30.1 - - + -
127B PHE* 3.4 19.6 - - + -
129B LYS 2.7 11.4 + - - +
130B ARG* 3.2 6.9 - - + +
131B HIS 2.8 26.3 + - - +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ALA* 4.8 3.8 - - + +
9B ALA* 1.3 81.4 - - - +
11B VAL* 1.3 75.6 + - - +
12B LEU* 4.1 12.8 - - + -
41B PHE* 4.0 29.4 - - + -
52B ASP* 5.5 2.0 - - + -
53B GLU 2.8 15.4 + - - +
54B ILE* 3.2 9.1 - - + +
55B ALA* 2.8 25.6 + - - +
83B LEU* 4.3 1.9 - - - +
131B HIS* 3.2 16.4 - - + +
133B GLU* 4.8 7.4 - - + +
240B ILE* 3.8 31.9 - - + -
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 1.3 80.2 - - - +
12B LEU* 1.3 66.2 + - - +
13B CYS 3.6 1.0 + - - -
55B ALA* 3.5 21.1 - - + +
57B VAL* 4.0 18.4 - - + -
83B LEU* 5.3 2.2 - - + -
114B SER* 3.8 33.2 - - - +
117B VAL* 4.3 7.2 - - + -
118B ILE* 3.4 33.4 - - + -
131B HIS 2.9 8.7 + - - -
132B ILE* 3.4 12.8 - - + +
133B GLU 2.9 25.1 + - - -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 4.1 12.6 - - + -
11B VAL* 1.3 72.7 - - - +
13B CYS* 1.3 59.3 + - - +
14B MET 3.8 0.7 - - - -
38B ILE* 3.9 17.9 - - + -
41B PHE* 3.9 17.7 - - + -
42B VAL* 3.9 28.5 - - + -
54B ILE* 4.1 15.3 - - + -
55B ALA 2.9 10.5 + - - +
56B LEU* 3.4 20.0 - - + +
57B VAL* 2.9 26.0 + - - +
90B LEU* 5.9 0.4 - - + -
133B GLU* 3.5 33.4 - - + +
135B PHE* 3.9 15.0 - - + -
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Residues in contact with CYS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL 3.6 0.6 + - - -
12B LEU* 1.3 70.5 - - - +
14B MET* 1.3 59.7 + - - +
57B VAL* 3.4 10.3 - - - -
59B PHE* 3.9 9.0 - - - -
110B ALA* 3.4 36.6 - - - -
111B LEU* 4.2 3.6 - - - -
114B SER* 3.2 27.8 - - - +
132B ILE* 4.6 2.5 - - + -
133B GLU 2.7 15.4 + - - +
134B ILE* 3.4 19.7 - - + +
135B PHE* 2.9 26.9 + - - +
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Residues in contact with MET 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU 3.7 0.6 + - - -
13B CYS* 1.3 74.0 - - - +
15B ASP* 1.3 63.5 + - - +
16B VAL* 3.7 14.1 + - + -
31B PHE* 3.7 46.0 - - + +
34B ALA* 4.1 8.5 - - + -
35B LYS* 4.0 23.3 - - + +
38B ILE* 3.9 25.4 - - + -
56B LEU* 4.4 3.6 - - + -
57B VAL 2.7 9.5 + - - +
58B LEU* 3.2 22.8 - - + +
59B PHE* 2.8 35.8 + - - -
94B ILE* 6.2 3.8 - - - -
98B ILE* 5.1 7.2 - - - -
135B PHE* 3.8 8.7 - - + +
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B MET* 1.3 76.3 - - - +
16B VAL* 1.3 62.2 + - - +
17B GLY* 2.9 27.4 + - - -
20B MET* 3.1 33.5 - - + +
31B PHE* 4.2 3.6 - - - -
59B PHE* 3.1 32.9 - - + +
60B GLY* 5.0 0.2 - - - -
104B GLN* 4.8 7.4 + - - -
105B ALA 5.9 0.3 + - - -
135B PHE 2.8 22.0 + - - +
136B THR* 2.5 28.3 + - - -
137B ASP* 4.0 6.5 - - - +
139B SER* 5.6 0.2 + - - -
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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