Contacts of the strand formed by residues 83 - 90 (chain A) in PDB entry 4ILW
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 GLU 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ARG* 2.5 40.4 + - + +
21A ALA 3.3 6.5 - - - +
22A LYS* 2.9 36.0 + - + -
50A ILE* 3.2 19.2 - - + +
81A LYS 3.6 2.6 + - - +
82A LYS* 1.3 75.9 - - - +
84A TYR* 1.3 62.0 + - - +
106A PRO* 3.3 9.9 - - - +
107A TRP* 2.8 32.8 + - + -
108A ASP* 4.9 9.4 + - - +
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Residues in contact with TYR 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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19A ILE 3.6 0.2 - - - +
20A ARG* 3.2 6.1 - - - +
21A ALA 2.6 39.1 + - - +
23A ALA 5.3 4.0 - - - -
75A SER 4.6 2.8 + - - -
76A LEU* 3.9 25.6 - - + -
77A ASP* 3.0 43.4 + - - +
82A LYS* 3.5 43.5 + - + -
83A GLU* 1.3 73.4 - - - +
85A LEU* 1.3 61.5 + - - +
86A ILE* 3.7 22.6 + - + +
104A ILE* 4.0 15.0 - - + -
105A VAL* 3.2 17.7 - - - +
106A PRO* 3.7 15.3 - - + -
107A TRP* 3.7 6.1 - - - +
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Residues in contact with LEU 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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18A VAL* 3.8 24.5 - - + -
19A ILE 3.4 16.8 - - - +
53A PHE* 4.1 2.9 - - + -
84A TYR* 1.3 71.9 - - - +
86A ILE* 1.3 61.8 + - - +
87A ALA 5.2 0.2 - - - +
103A PHE* 3.4 33.6 - - + +
104A ILE* 3.3 6.9 - - - +
105A VAL* 2.7 33.9 + - + +
107A TRP* 4.0 14.7 - - + +
110A LEU* 4.0 29.2 - - + -
118A LEU* 3.9 33.7 - - + -
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Residues in contact with ILE 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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17A VAL 3.6 1.4 - - - +
18A VAL* 3.3 5.4 - - - -
19A ILE* 2.7 41.5 + - + +
21A ALA* 4.4 16.4 - - + +
47A ILE* 5.6 0.7 - - + -
63A ILE* 3.6 25.4 - - + -
76A LEU* 4.3 16.2 - - + -
84A TYR* 3.7 24.0 - - + +
85A LEU* 1.3 80.7 - - - +
87A ALA* 1.3 61.1 + - - +
88A GLY 4.2 0.2 + - - -
96A MET* 3.8 13.4 - - + +
98A ILE* 3.5 32.1 - - + -
103A PHE 4.0 2.2 - - - -
104A ILE* 4.1 13.0 - - + -
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Residues in contact with ALA 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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11A ALA* 4.2 12.8 - - + +
12A PHE* 4.8 0.9 - - - +
15A ALA* 3.9 17.5 - - + -
17A VAL 3.3 4.9 - - - -
18A VAL* 4.0 15.5 - - + -
85A LEU* 5.9 0.2 - - + -
86A ILE* 1.3 76.8 - - - +
88A GLY* 1.3 58.2 + - - +
98A ILE* 4.5 0.5 - - - +
102A ASP* 3.4 26.6 - - - +
103A PHE* 3.1 31.6 + - + +
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Residues in contact with GLY 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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15A ALA* 3.5 7.3 - - - +
16A ASP 3.0 8.8 + - - -
17A VAL 2.9 29.8 + - - -
87A ALA* 1.3 75.1 - - - +
89A LYS* 1.3 60.4 + - - -
96A MET* 3.6 17.0 - - - +
97A HIS 3.9 6.7 - - - -
98A ILE* 4.5 1.3 - - - -
102A ASP* 4.3 9.9 - - - -
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Residues in contact with LYS 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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15A ALA* 6.2 0.2 - - - -
16A ASP* 2.5 43.3 + - - +
17A VAL* 4.1 0.2 - - - -
88A GLY* 1.3 75.1 - - - -
90A ALA* 1.3 79.1 + - - +
96A MET* 3.1 5.9 - - - +
97A HIS* 2.9 64.6 + - + +
165D LYS* 6.4 2.5 - - - -
166D GLU* 6.0 1.6 - - - -
172D SER* 6.2 2.7 - - - -
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Residues in contact with ALA 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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16A ASP* 3.1 21.4 + - + +
17A VAL* 3.6 19.7 - - + +
56A PRO* 5.1 12.6 - - + -
60A ILE* 5.9 0.4 - - + -
89A LYS* 1.3 95.7 + - - +
91A GLU* 1.3 61.3 + - - +
92A GLY 3.7 4.0 - - - +
95A LYS 3.8 7.0 - - - +
97A HIS* 4.7 0.3 - - - -
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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