Contacts of the strand formed by residues 13 - 19 (chain A) in PDB entry 5I4A
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 LYS 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PRO* 2.9 24.3 + - + +
12A LYS* 1.3 76.1 - - - +
14A ILE* 1.3 73.5 + - - +
53A PRO* 4.2 0.5 - - - +
54A ASP* 3.1 51.3 + - + +
74A ILE* 4.1 28.0 - - + +
75A ILE 3.3 10.3 - - - +
76A LYS* 4.1 9.4 - - + +
77A GLU 4.2 1.1 - - - +
84A PHE* 4.0 2.9 - - - -
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 1.3 86.5 - - - +
15A LYS* 1.3 69.7 + - - +
16A ARG* 5.7 0.4 - - + +
51A GLU* 3.9 16.2 - - + -
52A ILE 3.5 9.9 - - - +
53A PRO* 4.2 6.5 - - + -
73A GLU 3.7 0.3 - - - +
74A ILE* 3.3 6.1 - - - +
75A ILE* 2.7 52.9 + - + +
83A LEU* 4.2 11.9 - - + +
84A PHE* 3.6 42.2 - - + +
87A THR* 3.6 38.4 - - + +
88A LEU 5.4 0.2 - - - +
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Residues in contact with LYS 15 (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 LYS 4.3 0.4 + - - -
14A ILE* 1.3 74.8 - - - +
16A ARG* 1.3 61.7 + - - +
17A LEU* 3.6 36.1 - - + +
50A ILE 3.6 0.2 - - - +
51A GLU* 3.4 1.6 - - - -
52A ILE* 2.8 57.1 + - + +
53A PRO 4.8 4.2 - - - +
54A ASP* 4.6 23.6 + - + +
55A ILE 6.1 0.9 - - - -
72A GLU* 4.0 18.6 + - + +
73A GLU 3.3 8.1 - - - +
74A ILE* 4.6 17.0 - - + +
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Residues in contact with ARG 16 (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 ILE* 4.2 0.9 + - + +
15A LYS* 1.3 73.0 - - - +
17A LEU* 1.3 64.6 + - - +
18A TYR* 3.3 19.1 + - + -
49A TRP* 3.5 25.3 - - + -
50A ILE 3.2 9.4 - - - +
51A GLU* 2.4 48.5 + - + +
72A GLU* 3.5 7.3 - - - +
73A GLU* 2.6 68.1 + - + +
75A ILE* 3.9 24.1 - - + +
83A LEU* 4.2 14.3 - - - +
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Residues in contact with LEU 17 (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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15A LYS* 3.6 27.6 - - + -
16A ARG* 1.3 73.7 - - - +
18A TYR* 1.3 63.5 + - - +
19A PHE* 4.1 15.4 - - + -
49A TRP* 3.1 7.4 - - - +
50A ILE* 2.9 37.4 + - + +
52A ILE* 4.2 21.5 - - + -
57A PHE 6.0 1.3 - - - +
59A ILE* 4.4 19.7 - - + -
68A LYS* 4.5 14.1 - - - +
71A LYS 4.4 2.2 - - - -
72A GLU* 3.5 36.1 - - + +
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Residues in contact with TYR 18 (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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16A ARG* 3.3 25.4 + - + -
17A LEU* 1.3 75.5 - - - +
19A PHE* 1.3 71.9 + - - +
47A LEU* 4.1 23.1 - - + -
48A VAL 3.5 2.0 - - - -
49A TRP* 3.6 32.1 - + + -
68A LYS* 3.7 4.8 - - - +
69A VAL* 2.9 40.1 + - + +
71A LYS* 3.3 57.9 + - + +
73A GLU* 2.5 37.0 + - + -
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Residues in contact with PHE 19 (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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17A LEU* 4.1 14.8 - - + -
18A TYR* 1.3 79.1 - - - +
20A TYR* 1.3 61.7 + - - +
29A PHE* 3.9 21.1 - + + -
33A LEU* 5.1 1.3 - - + -
41A PHE* 4.0 17.5 - + - -
47A LEU* 3.7 4.4 - - - +
48A VAL* 2.7 45.3 + - + +
50A ILE* 4.0 24.2 - - + -
59A ILE* 3.5 24.5 - - + -
64A VAL* 3.9 31.4 - - + -
65A PHE* 5.3 0.7 - - - -
67A TYR 3.2 7.6 - - - +
68A LYS* 3.6 37.2 - - + -
69A VAL* 4.1 3.4 - - - +
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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