Contacts of the strand formed by residues 47 - 56 (chain A) in PDB entry 4EJX
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 LEU 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A THR* 3.9 27.1 - - + +
14A TRP 3.2 4.9 - - - -
15A ASP* 3.6 37.9 - - + +
44A ILE 4.3 4.3 - - - +
46A ARG* 1.3 89.5 - - + +
48A TYR* 1.3 70.4 + - - +
220A TYR* 3.7 33.4 - - + -
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Residues in contact with TYR 48 (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 THR* 4.4 0.7 - - - -
14A TRP* 2.9 30.7 + - - +
16A TYR* 3.4 36.8 - + + -
44A ILE* 3.2 34.6 - - + +
45A GLY 3.2 25.9 + - - -
46A ARG 4.0 1.3 - - - -
47A LEU* 1.3 86.8 - - - +
49A LYS* 1.3 63.4 + - - +
50A LYS* 3.3 10.7 + - + +
207A GLU* 3.2 41.7 - - + +
213A LEU* 5.2 0.9 - - + -
216A ASN* 3.4 20.4 - - + -
220A TYR* 4.4 2.2 - - - -
237A SER 4.6 1.0 + - - -
238A ASN* 2.6 32.0 + - + +
240A MET* 5.1 6.1 - - - -
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Residues in contact with LYS 49 (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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11A GLU* 4.4 32.7 + - - +
12A THR 3.7 13.0 - - - +
13A THR* 4.3 14.8 - - - +
48A TYR* 1.3 69.3 - - - +
50A LYS* 1.3 60.8 + - - +
207A GLU* 4.7 0.2 - - - +
210A SER* 5.2 0.2 + - - -
212A TYR* 3.5 33.5 - - + +
215A ASP* 5.2 14.8 - - - +
216A ASN* 2.8 35.3 + - - +
220A TYR* 3.8 11.9 + - - +
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Residues in contact with LYS 50 (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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11A GLU* 3.6 3.7 - - - +
12A THR 3.1 24.2 + - - +
14A TRP* 4.4 11.7 - - + -
16A TYR* 3.3 29.0 + - + +
48A TYR* 3.3 13.7 + - + +
49A LYS* 1.3 79.2 - - - +
51A ALA* 1.3 60.0 + - - +
52A LEU* 3.2 24.2 - - + +
73A PHE* 4.5 17.9 - - - -
171A ALA 2.8 17.4 + - - -
172A SER* 3.2 17.8 - - - +
173A GLY* 3.4 11.0 - - - +
205A VAL* 4.0 5.2 - - - +
207A GLU* 2.5 33.3 + - - +
210A SER* 5.3 0.4 - - - +
212A TYR* 4.1 7.2 - - - -
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Residues in contact with ALA 51 (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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9A ILE* 4.4 0.9 - - + -
10A ILE 3.5 8.7 - - - +
50A LYS* 1.3 71.0 - - - +
52A LEU* 1.3 65.5 + - - +
98A TYR* 3.4 38.1 - - + +
172A SER* 2.8 22.7 + - - +
173A GLY* 3.3 15.9 - - - -
174A LEU* 3.8 13.5 - - + -
212A TYR* 3.4 16.2 - - + +
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Residues in contact with LEU 52 (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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8A GLY 3.4 2.3 - - - +
9A ILE* 3.2 6.1 - - - -
10A ILE* 3.1 37.9 + - + +
12A THR* 3.8 29.6 - - + +
14A TRP* 4.8 15.5 - - + -
50A LYS* 3.2 38.4 - - + +
51A ALA* 1.3 80.6 - - - +
53A TYR* 1.3 62.1 + - - +
54A LEU* 3.8 2.6 + - + -
67A LYS* 4.2 12.3 - - + +
72A GLY 5.2 0.4 - - - +
73A PHE* 3.8 42.6 - - + +
173A GLY 5.0 0.7 - - - -
174A LEU* 3.5 7.6 - - - +
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Residues in contact with TYR 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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7A ILE* 3.5 20.6 - - + -
8A GLY 3.8 0.7 - - - -
9A ILE* 3.5 28.5 - - + -
52A LEU* 1.3 73.3 - - - +
54A LEU* 1.3 59.2 + - - +
67A LYS* 3.0 22.9 + - - -
73A PHE 4.6 4.0 + - - -
74A LEU 3.8 0.2 - - - +
75A GLY* 3.2 18.6 - - - -
76A PRO* 3.4 12.9 - - + +
90A LEU* 4.1 7.4 - - + -
99A THR 2.5 25.3 + - - -
100A PHE* 4.1 3.8 - + - -
160A TYR* 3.8 22.2 - + - -
161A HIS* 3.2 11.8 - - - -
162A SER* 2.8 18.5 + - - -
173A GLY 5.3 0.2 + - - -
174A LEU* 3.4 36.8 - - + +
175A ILE* 3.6 18.2 - - - -
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Residues in contact with LEU 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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7A ILE* 3.4 3.8 - - - -
8A GLY 2.8 44.9 + - - +
10A ILE* 3.6 35.0 - - + -
12A THR* 6.0 0.4 - - + -
52A LEU* 5.4 3.4 - - + -
53A TYR* 1.3 75.6 - - - +
55A GLN* 1.3 63.3 + - - +
56A TYR* 3.3 17.6 - - + +
64A THR* 4.0 22.9 - - + +
65A ILE 4.6 10.5 - - - +
67A LYS* 3.5 34.5 - - + +
76A PRO* 3.7 6.1 - - - -
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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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5A TYR* 3.1 46.1 - - + +
6A TYR 4.0 2.9 - - - +
7A ILE* 4.6 2.2 - - + -
54A LEU* 1.3 73.8 - - - +
56A TYR* 1.3 67.7 + - - +
64A THR* 3.4 8.3 - - - -
65A ILE* 2.7 70.4 + - + +
76A PRO* 3.4 32.1 - - + +
77A ILE 4.6 6.5 + - - +
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Residues in contact with TYR 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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5A TYR* 5.2 0.2 - - - -
6A TYR* 3.0 47.0 + - + +
8A GLY* 3.7 15.4 - - - -
10A ILE* 3.5 27.0 - - - +
54A LEU* 3.3 26.0 - - + +
55A GLN* 1.3 80.5 + - - +
57A THR* 1.3 59.8 + - - +
58A ASP 3.5 4.9 - - - +
61A PHE* 3.2 50.9 - + + -
62A ARG 4.4 2.2 - - - -
63A THR 3.6 21.3 - - - +
64A THR* 3.5 22.1 - - + +
65A ILE* 3.8 12.5 - - - +
93A LEU* 4.7 6.9 - - + +
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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