Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 1EJN
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 MET 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A TYR* 3.5 8.0 - - - -
68A LEU 2.9 29.8 + - - -
79A GLY* 3.8 6.3 - - - +
80A GLU* 1.3 92.8 - - - +
82A LYS* 1.3 62.0 + - - +
83A PHE* 3.6 30.5 - - + -
110A SER* 6.0 6.5 - - - -
113A GLN* 5.8 11.4 - - + +
118A ILE* 3.7 21.1 - - + -
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Residues in contact with LYS 82 (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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36A ARG* 4.3 13.2 - - - +
65A ILE* 3.8 40.2 - - + +
66A VAL 3.6 3.1 - - - -
67A TYR* 3.6 32.1 + - + +
80A GLU* 5.6 0.2 - - - +
81A MET* 1.3 75.5 - - - +
83A PHE* 1.3 73.0 + - - +
84A GLU* 5.5 0.9 - - - -
110A SER* 4.1 32.8 + - - +
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Residues in contact with PHE 83 (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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65A ILE* 3.6 9.5 - - - +
66A VAL* 2.8 40.3 + - + +
68A LEU* 3.4 28.0 - - + -
81A MET* 3.6 39.0 - - + -
82A LYS* 1.3 79.8 - - - +
84A GLU* 1.3 63.6 + - - +
108A ILE* 3.8 27.6 - - + -
109A ARG 3.6 9.2 - - - -
110A SER* 3.5 30.3 - - + +
111A CYS 3.7 8.1 - - - -
112A ALA* 3.7 38.4 - - + -
118A ILE* 5.7 0.2 - - + -
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Residues in contact with GLU 84 (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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36A ARG* 2.9 43.9 + - - -
62A GLU* 4.0 15.3 + - - +
64A TYR 4.2 4.8 - - - +
82A LYS* 5.5 1.2 - - - -
83A PHE* 1.3 78.3 - - - +
85A VAL* 1.3 65.2 + - - +
86A GLU 3.9 0.2 - - - -
108A ILE* 3.4 7.0 - - - +
109A ARG* 2.8 46.3 + - + +
110A LYS* 3.8 34.5 + - - +
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Residues in contact with VAL 85 (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 LYS* 3.6 42.6 + - + +
64A TYR* 3.9 31.0 + - + +
66A VAL* 3.9 23.6 - - + -
84A GLU* 1.3 77.7 + - - +
86A GLU* 1.3 60.4 + - - +
87A ASN 3.4 28.9 - - - +
88A LEU* 4.1 7.4 - - + +
106A LEU* 4.1 17.3 - - + -
107A LYS 3.5 6.3 - - - +
108A ILE* 5.0 0.4 - - + -
109A ARG* 5.6 0.2 - - - -
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Residues in contact with GLU 86 (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 LYS* 2.8 27.1 + - - +
84A GLU 3.8 2.6 + - - -
85A VAL* 1.3 72.1 - - - +
87A ASN* 1.3 61.5 + - + +
107A LYS* 2.8 49.3 + - + +
108A ILE 4.6 0.5 - - - +
109A ARG* 3.4 57.1 + - + +
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Residues in contact with ASN 87 (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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51A TRP* 4.9 3.5 - - + -
62A LYS* 4.2 8.7 - - - +
85A VAL* 3.4 8.4 - - - +
86A GLU* 1.3 83.9 + - + +
88A LEU* 1.3 71.1 + - - +
89A ILE* 3.9 23.9 - - + +
105A LEU 3.7 1.0 - - - +
106A LEU* 3.4 2.8 - - - -
107A LYS* 2.9 48.8 + - + +
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Residues in contact with LEU 88 (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 PHE* 4.0 37.5 - - + -
60A PRO* 3.8 32.3 - - + -
62A LYS* 3.9 28.4 - - + +
64A TYR* 4.3 8.5 - - + -
85A VAL* 4.1 3.1 - - + +
87A ASN* 1.3 79.8 + - - +
89A ILE* 1.3 63.9 + - - +
90A LEU* 3.8 17.2 + - + +
104A ALA* 5.3 0.2 - - + -
105A LEU 3.8 0.4 - - - +
106A LEU* 3.7 30.7 - - + -
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Residues in contact with ILE 89 (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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51A TRP* 3.8 23.3 - - + -
87A ASN* 3.9 20.0 - - - +
88A LEU* 1.3 75.5 - - - +
90A LEU* 1.3 65.2 + - - +
104A ALA* 3.3 6.4 - - - +
105A LEU* 2.8 41.8 + - + +
237A TRP* 3.9 19.3 - - + -
241A HIS* 3.6 56.3 - - + +
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Residues in contact with LEU 90 (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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56A THR* 3.6 20.9 - - + +
59A PHE* 3.8 39.3 - - + +
60A ILE* 4.2 51.6 - - + +
88A LEU* 3.8 16.6 + - + +
89A ILE* 1.3 83.2 - - - +
91A HIS* 1.3 65.5 + - - +
92A LYS* 3.4 2.9 + - - +
104A ALA* 3.9 6.7 - - + -
237A TRP* 4.2 2.8 + - - -
241A HIS* 5.8 0.9 - - - -
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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