Contacts of the strand formed by residues 83 - 89 (chain D) in PDB entry 6EKK
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 GLY 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D LYS 3.6 2.6 + - - -
11D LEU* 3.3 20.2 - - - +
12D LEU 3.1 22.0 + - - -
81D THR* 3.2 6.2 - - - +
82D HIS* 1.3 80.9 - - - +
84D VAL* 1.3 62.7 + - - -
85D ILE 4.4 0.2 - - - -
113D VAL* 3.8 1.1 - - - -
114D CYS* 3.1 13.2 - - - -
164D ILE* 4.3 2.9 - - - -
168D VAL* 3.8 7.4 - - - -
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.4 15.3 - - + +
14D ILE* 3.9 21.8 - - + -
78D TYR* 3.6 32.8 - - + -
81D THR* 4.2 4.7 - - + -
83D GLY* 1.3 78.6 - - - +
85D ILE* 1.3 65.3 + - - +
86D VAL* 3.7 19.1 + - + -
106D ILE* 4.9 1.8 - - + -
113D VAL* 3.7 20.4 - - + -
114D CYS 2.7 11.5 + - - +
115D ARG* 3.2 27.4 - - + +
116D ILE 3.2 6.4 + - - -
164D ILE* 4.0 4.0 - - - +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.6 5.4 - - + -
12D LEU 2.8 14.0 + - - +
13D ILE* 3.4 13.0 - - + +
14D ILE* 3.0 28.1 + - - +
61D ILE* 4.3 17.0 - - + -
84D VAL* 1.3 74.1 - - - +
86D VAL* 1.3 58.0 + - - +
87D VAL* 3.7 12.2 + - + -
116D ILE* 4.1 5.2 - - + -
118D VAL* 3.6 28.3 - - + -
160D MET* 3.9 10.3 - - + -
161D PHE* 3.6 36.3 - - + -
164D ILE* 3.9 28.0 - - + -
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 3.7 22.2 - - + -
84D VAL* 3.8 23.1 - - + +
85D ILE* 1.3 74.2 - - - +
87D VAL* 1.3 60.7 + - - +
99D VAL* 3.6 32.1 - - + +
102D TRP* 4.5 0.9 - - + -
103D LEU* 3.8 38.1 - - + -
106D ILE* 4.7 2.7 - - + -
115D ARG* 4.6 2.7 - - + -
116D ILE 3.0 17.4 + - - +
117D LEU* 3.6 5.4 - - + +
118D VAL 2.8 26.2 + - - +
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 3.8 28.5 - - + -
14D ILE 2.8 19.0 + - - +
15D GLY* 3.3 20.4 - - - -
16D ASP 4.3 1.4 + - - -
19D VAL* 3.7 23.9 - - + +
21D LYS* 4.4 2.7 - - + -
24D LEU* 4.1 12.3 - - + -
85D ILE* 3.9 14.8 - - + +
86D VAL* 1.3 76.4 - - - +
88D TYR* 1.3 73.5 + - - +
95D SER* 5.4 0.2 - - - -
99D VAL* 3.4 10.1 - - - +
118D VAL* 3.4 13.0 - - + +
120D ASN* 4.0 15.5 - - + -
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 4.1 7.4 - - - -
87D VAL* 1.3 81.0 - - - +
89D ASP* 1.3 69.5 + - - +
90D VAL* 3.6 24.5 - - + +
95D SER* 3.5 27.8 - - - +
96D PHE* 3.8 24.0 - + + -
99D VAL* 4.1 2.9 - - + -
117D LEU* 3.7 31.6 - - + -
118D VAL 2.8 13.1 + - - +
119D GLY* 3.3 22.3 - - - -
120D ASN* 2.9 25.6 + - - +
130D VAL* 3.8 18.6 - - + +
135D ALA* 3.1 26.0 - - + +
146D LEU* 3.8 6.6 - - + +
148D GLU* 4.2 6.1 + - - -
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Residues in contact with ASP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLY 4.3 2.3 - - - +
19D VAL* 3.8 21.0 - - + +
88D TYR* 1.3 76.7 - - - +
90D VAL* 1.3 56.1 + - - +
91D THR* 2.6 44.3 + - - +
92D SER* 2.7 45.0 + - - +
95D SER* 2.9 13.0 + - - +
120D ASN 3.6 4.5 - - - -
121D LYS* 3.3 36.4 + - + +
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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