Contacts of the strand formed by residues 85 - 93 (chain A) in PDB entry 3I8E
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 ASN 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A MET* 6.1 0.2 - - - +
58A TYR 4.5 0.9 - - - +
79A ILE 3.2 2.3 - - - +
80A LEU* 3.1 8.2 - - - -
81A THR* 2.9 53.2 + - - +
83A LYS 4.2 1.0 - - - +
84A TYR* 1.3 73.5 - - - +
86A ALA* 1.3 64.9 + - - +
87A CYS* 4.9 2.5 - - + -
105A HIS* 6.4 0.2 - - - -
106A GLY 4.0 8.2 + - - -
107A ASN* 3.8 14.7 - - - +
1067A LYS 5.5 0.6 + - - -
1068A ILE* 3.7 38.6 - - + +
1072A PHE* 3.7 22.6 - - - -
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Residues in contact with ALA 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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78A PHE* 4.2 12.3 - - + -
79A ILE 3.5 4.9 - - - -
80A LEU* 3.6 7.1 - - + +
84A TYR 3.9 2.2 + - - -
85A ASN* 1.3 77.1 + - - +
87A CYS* 1.3 65.7 + - - +
105A HIS* 3.6 2.1 - - - +
106A GLY 3.1 31.0 + - - +
108A VAL* 3.9 26.0 - - + +
133A LEU* 5.8 0.2 - - + -
143A ILE* 4.5 3.1 - - + -
152A LEU* 3.7 19.5 - - + -
1066A GLY 4.8 0.9 - - - +
1068A ILE* 6.1 0.3 - - - +
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Residues in contact with CYS 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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57A MET* 3.9 7.9 - - - -
77A LEU 3.9 0.2 - - - +
78A PHE* 3.5 6.5 - - - -
79A ILE* 2.9 52.6 + - - -
85A ASN* 4.9 2.2 - - - -
86A ALA* 1.3 79.1 - - - +
88A ILE* 1.3 63.0 + - - +
89A LEU* 3.6 22.2 - - - -
102A THR* 4.4 1.6 - - + -
104A ALA 3.6 14.4 - - - +
105A HIS* 3.8 3.1 - - + +
152A LEU* 4.1 2.8 - - - +
1066A GLY* 3.7 29.8 - - - +
1068A ILE* 5.8 1.6 - - + -
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Residues in contact with ILE 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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67A PHE* 3.9 31.2 - - + -
76A LEU* 4.2 9.0 - - + -
77A LEU 3.2 6.7 - - - +
78A PHE* 4.2 11.9 - - + -
87A CYS* 1.3 75.3 - - - +
89A LEU* 1.3 66.8 + - - +
102A THR* 3.6 4.7 - - - -
103A ARG* 2.8 50.8 + - + +
104A ALA* 3.2 33.7 + - + +
131A ILE* 4.7 4.3 - - + -
145A LEU* 4.3 15.0 - - + -
152A LEU* 3.8 17.9 - - + -
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Residues in contact with LEU 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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23A PHE* 4.2 1.3 - - + -
39A LEU* 5.1 7.0 - - + -
57A MET* 5.0 4.9 - - - -
76A LEU* 3.3 11.8 - - - +
77A LEU* 2.4 71.7 + - + +
79A ILE* 3.8 14.4 - - + -
87A CYS* 3.6 27.4 - - - -
88A ILE* 1.3 79.4 - - - +
90A GLU* 1.3 60.7 + - - +
100A ILE* 4.2 17.9 - - + -
101A ILE 3.3 15.7 - - - +
102A THR* 4.3 3.4 - - + -
103A ARG* 5.0 0.4 - - - -
1065A VAL* 4.3 28.5 - - + +
1066A GLY* 4.3 1.3 - - - -
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Residues in contact with GLU 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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23A PHE* 3.9 9.9 - - - -
72A GLU* 5.1 3.0 - - - +
74A LYS* 3.2 27.1 + - - +
75A ASP 5.4 1.1 - - - +
76A LEU* 3.6 21.9 - - + +
89A LEU* 1.3 78.0 - - - +
91A TYR* 1.3 64.1 - - - +
92A LYS* 3.7 22.5 - - - +
99A ASP 3.8 0.3 - - - +
100A ILE* 3.4 3.3 - - - -
101A ILE* 2.8 51.6 + - + +
103A ARG* 3.3 31.0 + - + +
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Residues in contact with TYR 91 (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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23A PHE* 3.4 39.6 + + + +
24A THR* 3.7 40.8 - - + +
41A ILE* 4.9 3.6 - - + -
52A VAL* 3.7 27.2 - - + +
53A LYS* 4.5 11.2 - - + -
74A LYS* 3.1 30.5 + - - -
75A ASP 5.5 0.4 + - - -
90A GLU* 1.3 74.2 - - - +
92A LYS* 1.3 65.8 + - - +
93A GLN* 3.2 21.9 + - + -
98A ILE* 3.1 38.0 - - + +
99A ASP 3.7 8.7 - - - -
100A ILE* 4.1 15.3 - - + +
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Residues in contact with LYS 92 (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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74A LYS* 5.9 0.4 - - - +
90A GLU* 3.7 23.6 - - - +
91A TYR* 1.3 78.5 - - - +
93A GLN* 1.3 64.4 + - - +
94A SER* 4.1 3.0 + - - +
97A SER 4.2 0.3 - - - +
98A ILE* 3.9 0.4 - - - -
99A ASP* 2.8 47.7 + - + +
101A ILE* 3.9 31.0 - - + +
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Residues in contact with GLN 93 (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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24A THR* 5.4 2.3 - - - +
91A TYR* 3.2 29.7 + - + -
92A LYS* 1.3 77.5 - - - +
94A SER* 1.3 63.9 + - - +
95A GLY* 2.8 36.7 + - - +
96A GLU* 4.2 3.4 - - - +
97A SER 3.8 3.8 - - - +
98A ILE* 3.4 24.7 - - + +
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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