Contacts of the strand formed by residues 78 - 89 (chain A) in PDB entry 3KJO
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 ILE 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A TYR* 4.3 6.3 - - + -
27A GLY 3.4 12.8 - - - +
28A VAL* 4.4 7.0 - - + -
76A GLY 4.1 2.5 - - - +
77A ASP* 1.3 76.9 - - - +
79A VAL* 1.3 69.1 + - - +
105A THR* 3.3 4.0 - - - +
106A PHE* 2.8 53.6 + - + +
107A GLU 4.2 0.4 - - - +
108A GLY* 4.0 11.9 - - - +
133A VAL* 3.5 24.9 - - + +
136A LEU* 3.7 29.2 - - + -
137A ARG* 3.4 34.5 - - + +
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Residues in contact with VAL 79 (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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25A VAL 5.7 0.2 - - - +
26A TYR* 3.4 11.2 - - - -
27A GLY 2.9 36.9 + - - +
29A VAL* 3.8 19.5 - - + -
49A ILE* 3.8 24.0 - - + -
70A PRO* 5.0 0.2 - - + -
72A ILE* 4.1 13.2 - - + -
78A ILE* 1.3 80.4 - - - +
80A ARG* 1.3 60.6 + - - +
81A PHE* 3.7 36.6 - - + -
104A LEU 3.2 5.4 - - - +
105A THR* 3.6 20.9 - - + +
106A PHE* 4.9 0.7 - - - -
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Residues in contact with ARG 80 (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 TYR* 3.3 15.8 + - + -
25A VAL 3.4 3.4 - - - -
26A TYR* 3.5 33.4 + - + +
79A VAL* 1.3 74.5 - - - +
81A PHE* 1.3 64.6 + - - +
82A HIS* 3.2 41.1 + - - +
102A ALA 3.8 0.6 - - - +
103A SER* 3.1 8.1 - - - +
104A LEU* 2.9 60.6 + - + +
106A PHE* 4.5 0.4 - - + -
123A PHE* 4.8 3.6 - - - +
124A ASN* 2.5 39.4 + - - +
125A PHE* 3.8 0.6 - - - +
129A ASP* 2.7 38.8 + - - -
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Residues in contact with PHE 81 (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 VAL 5.0 0.2 - - - -
24A ASN* 3.2 4.4 - - - -
25A VAL* 2.7 59.2 + - + +
47A VAL* 4.3 11.7 - - + -
49A ILE* 4.5 8.5 - - + -
59A CYS* 4.0 24.2 - - + -
61A LEU* 4.0 9.4 - - + -
70A PRO* 3.5 33.2 - - + -
79A VAL* 3.7 30.9 - - + -
80A ARG* 1.3 80.5 - - - +
82A HIS* 1.3 66.7 + - - +
84A LEU* 4.2 16.2 - - + -
101A PHE* 3.6 17.7 - + + -
102A ALA 3.6 1.8 - - - -
103A SER* 3.5 12.1 - - - -
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Residues in contact with HIS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.7 31.6 + + - -
11A TYR* 2.8 32.7 + + - -
24A ASN* 3.3 15.7 - - - +
80A ARG* 3.2 42.3 + - - -
81A PHE* 1.3 82.9 - - - +
83A ARG* 1.3 96.5 + - - +
84A LEU 3.5 0.2 - - - -
101A PHE* 3.3 5.4 - - - -
102A ALA* 2.8 35.8 + - + +
124A ASN* 5.0 2.0 - - + -
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Residues in contact with ARG 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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9A TYR* 2.7 45.3 + - - -
22A ILE* 3.8 19.7 - - + -
23A VAL 3.7 2.2 - - - -
24A ASN* 3.2 16.2 - - - +
82A HIS* 1.3 92.3 + - - +
84A LEU* 1.3 59.7 + - - +
98A SER* 3.2 23.2 + - - -
99A SER 3.5 19.5 - - - +
100A GLY* 3.0 27.8 + - - -
101A PHE* 3.5 9.7 - - - +
102A ALA* 4.0 9.7 - - - +
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Residues in contact with LEU 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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22A ILE* 3.3 2.0 - - - -
23A VAL* 2.7 44.0 + - + +
25A VAL* 3.8 26.7 - - + -
57A LEU* 4.2 4.3 - - + -
59A CYS* 4.0 22.0 - - - -
61A LEU* 4.0 10.3 - - + -
81A PHE* 4.2 9.9 - - + -
83A ARG* 1.3 77.8 - - - +
85A LYS* 1.3 65.4 + - - +
86A ILE* 4.1 16.6 - - + -
95A GLY* 4.1 3.1 - - - -
96A ILE 3.4 28.9 - - - +
101A PHE* 3.9 23.3 - - + -
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Residues in contact with LYS 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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20A GLY* 5.2 9.6 - - - -
21A THR 3.5 11.2 - - - +
22A ILE* 4.1 12.1 - - + +
83A ARG 3.9 2.4 + - - -
84A LEU* 1.3 72.3 - - - +
86A ILE* 1.3 72.5 + - - +
87A GLN* 3.9 18.2 + - - +
95A GLY* 3.4 5.2 - - - -
96A ILE* 2.9 56.6 + - + +
97A THR 5.4 1.1 - - - +
98A SER* 4.0 18.7 - - - +
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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 LEU* 4.2 24.7 - - + -
18A LYS 3.3 32.5 - - - +
19A GLY* 4.0 0.9 - - - -
20A GLY* 2.8 24.3 + - - -
21A THR* 2.7 23.7 + - - +
23A VAL* 3.8 26.9 - - + -
57A LEU* 4.4 3.1 - - + -
84A LEU* 4.1 17.5 - - + -
85A LYS* 1.3 84.5 - - - +
87A GLN* 1.3 65.7 + - - +
93A THR* 3.7 26.2 - - + -
94A GLN 3.8 0.9 - - - +
95A GLY* 4.3 7.4 - - - -
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Residues in contact with GLN 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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19A GLY* 4.3 6.7 - - - -
20A GLY 4.4 1.8 - - - +
85A LYS* 3.9 21.4 + - - +
86A ILE* 1.3 77.6 - - - +
88A VAL* 1.3 66.1 + - - +
89A TYR* 5.2 2.4 - - - +
93A THR* 3.4 4.0 - - - +
94A GLN* 2.8 69.9 + - + +
96A ILE* 3.7 29.6 - - + +
6B G 3.0 17.2 - - - +
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Residues in contact with VAL 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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19A GLY* 4.6 15.0 - - - +
87A GLN* 1.3 83.7 + - - +
89A TYR* 1.3 64.2 + - - +
90A LYS 4.1 0.8 + - - +
91A LYS* 3.5 39.0 - - - +
92A GLU 3.4 3.6 - - - +
93A THR* 4.4 13.2 - - - +
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Residues in contact with TYR 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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87A GLN* 4.1 0.8 + - - +
88A VAL* 1.3 73.6 - - - +
90A LYS* 1.3 109.6 + - + +
92A GLU* 2.6 25.9 + - - +
94A GLN* 3.5 30.7 - - + +
6B G 3.2 78.0 + + + +
7B G 5.5 0.4 - - - -
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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