Contacts of the strand formed by residues 84 - 91 (chain D) in PDB entry 2K8M
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 THR 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.3 14.0 - - - +
47D LEU* 3.6 31.7 + - - +
82D GLY 4.0 1.6 - - - -
83D LYS* 1.3 73.9 + - - +
85D LEU* 1.3 64.2 + - - +
86D VAL* 4.9 5.9 - - + +
105D LYS* 5.2 7.0 - - + -
106D VAL 4.0 17.7 - - - +
107D PRO* 4.2 16.8 - - + +
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Residues in contact with LEU 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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10D LEU* 5.8 6.5 - - + -
19D LEU* 5.2 2.9 - - + -
21D VAL* 5.1 19.3 - - + -
44D VAL* 5.9 3.1 - - + -
45D PHE 4.0 0.4 - - - +
46D LEU* 3.7 12.3 - - + -
71D PHE* 5.9 2.7 - - + -
73D PHE* 3.6 35.0 - - + -
83D LYS 3.7 2.6 + - - -
84D THR* 1.3 74.2 - - - +
86D VAL* 1.3 75.4 + - - +
87D MET* 5.1 8.3 - - + +
104D PHE* 5.6 5.4 - - + -
105D LYS* 3.7 0.9 - - - +
106D VAL* 3.4 39.5 + - + -
108D MET* 3.8 37.0 - - + -
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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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44D VAL* 3.9 3.1 - - - +
45D PHE* 2.9 61.3 + - + +
46D LEU* 5.0 3.6 - - - -
84D THR* 4.9 7.9 - - + +
85D LEU* 1.3 86.4 - - - +
87D MET* 1.3 61.9 + - - +
88D ALA* 5.4 0.4 - - + +
103D GLU* 4.4 23.3 - - - +
104D PHE 3.4 8.1 - - - +
105D LYS* 3.5 24.9 - - + -
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Residues in contact with MET 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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6D LEU* 5.1 1.8 - - + -
21D VAL* 4.1 14.8 - - + -
23D ILE* 4.1 32.8 - - + -
42D VAL* 3.4 37.9 - - + -
43D LYS 4.4 0.4 - - - -
44D VAL* 3.6 36.6 - - + -
56D THR* 6.1 0.4 - - + -
71D PHE* 5.7 0.7 - - + -
85D LEU* 5.1 6.3 - - + +
86D VAL* 1.3 72.3 - - - +
88D ALA* 1.3 58.9 + - - +
89D VAL 4.2 0.3 + - - -
103D GLU* 3.2 5.3 - - - -
104D PHE* 2.9 66.6 + - + -
123D LEU* 5.6 0.2 - - - +
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Residues in contact with ALA 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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42D VAL* 3.4 4.0 - - - -
43D LYS* 2.8 46.4 + - + +
45D PHE* 4.3 11.0 - - + -
86D VAL* 4.0 1.9 - - + -
87D MET* 1.3 74.5 - - - +
89D VAL* 1.3 60.8 + - - +
100D ILE* 3.8 34.3 - - + -
103D GLU* 3.6 20.0 - - + +
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Residues in contact with VAL 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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3D LEU* 3.6 24.2 - - + -
29D LEU* 5.0 13.7 - - + -
40D PRO* 3.6 27.6 - - + -
41D TYR* 3.3 16.4 - - - +
42D VAL* 4.0 13.7 - - + +
87D MET 4.2 0.8 + - - -
88D ALA* 1.3 72.8 - - - +
90D TYR* 1.3 62.1 + - - +
100D ILE* 3.2 16.4 - - - +
101D ILE* 3.4 21.7 + - + +
102D GLY 3.1 16.4 + - - +
103D GLU* 5.4 0.4 - - - -
123D LEU* 5.9 1.3 - - + -
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Residues in contact with TYR 90 (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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40D PRO* 3.1 1.7 - - - +
41D TYR* 2.7 72.6 + + + +
43D LYS* 3.7 27.8 - - + -
88D ALA 3.9 0.8 + - - -
89D VAL* 1.3 74.8 - - - +
91D ASP* 1.3 79.6 + - - +
92D PHE* 4.2 22.0 - + + -
97D LYS* 5.5 2.6 - - - +
98D HIS* 2.9 35.5 + - - -
99D ASP* 3.6 26.2 - - - -
100D ILE* 3.9 9.4 - - + -
101D ILE* 4.3 1.3 - - - -
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Residues in contact with ASP 91 (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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32D LEU* 3.6 14.0 - - - +
33D ASP* 4.4 3.9 + - - +
38D SER* 3.2 19.7 - - - -
39D ASP* 2.7 37.5 + - - +
40D PRO* 4.2 3.4 - - + -
90D TYR* 1.3 88.4 - - - +
92D PHE* 1.3 70.4 + - - +
93D ASP 4.0 1.4 + - - -
98D HIS* 2.8 50.2 + - + -
99D ASP 4.8 0.2 + - - -
101D ILE* 3.7 23.0 - - + +
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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