Contacts of the strand formed by residues 84 - 90 (chain A) in PDB entry 2KI6
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.4 11.9 - - - +
47A LEU* 3.6 34.1 + - - +
82A GLY 5.3 0.3 - - - -
83A LYS* 1.3 72.3 + - - +
85A LEU* 1.3 65.8 + - - +
86A VAL* 3.8 6.9 + - + +
105A LYS* 5.0 9.0 - - + -
106A VAL 3.5 24.5 - - - +
107A PRO* 3.6 18.3 - - + +
108A MET 4.6 1.1 - - - +
17B ARG* 4.7 6.8 + - - -
25B ASP* 4.4 21.2 + - - +
27B THR* 5.7 2.6 - - + +
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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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10A LEU* 4.9 10.8 - - + -
21A VAL* 4.1 28.9 - - + -
45A PHE 4.7 0.2 - - - +
46A LEU* 3.8 22.2 - - + -
71A PHE* 4.7 7.6 - - + -
73A PHE* 4.2 13.2 - - + -
83A LYS 3.6 3.8 + - - -
84A THR* 1.3 73.7 - - - +
86A VAL* 1.3 62.2 + - - +
87A MET* 5.4 3.8 - - + +
104A PHE* 5.5 9.6 - - + -
105A LYS* 3.0 22.7 - - - +
106A VAL* 3.2 43.5 + - + +
108A MET* 3.3 17.5 - - + -
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Residues in contact with VAL 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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44A VAL* 4.0 1.2 - - - -
45A PHE* 2.9 62.1 + - + +
46A LEU* 3.8 7.6 - - - +
47A LEU* 5.3 2.7 - - + +
84A THR* 4.0 10.8 - - + +
85A LEU* 1.3 81.4 - - - +
87A MET* 1.3 61.0 + - - +
88A ALA* 3.8 3.7 + - + +
103A GLU* 4.9 4.9 - - - +
104A PHE 3.5 4.0 - - - +
105A LYS* 3.3 35.4 - - + +
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Residues in contact with MET 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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6A LEU* 4.9 0.9 - - + -
21A VAL* 3.8 17.3 - - + -
23A ILE* 3.6 32.3 - - + -
42A VAL* 3.7 36.1 - - + -
43A LYS 4.5 1.3 - - - -
44A VAL* 3.5 31.2 - - + +
71A PHE* 5.1 1.3 - - + -
85A LEU* 5.4 4.7 - - + +
86A VAL* 1.3 70.7 - - - +
88A ALA* 1.3 59.8 + - - +
89A VAL 4.1 0.2 + - - -
103A GLU* 3.0 3.7 - - - -
104A PHE* 2.6 81.7 + - + -
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Residues in contact with ALA 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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42A VAL* 3.4 2.8 - - - -
43A LYS* 2.6 60.9 + - + +
45A PHE* 5.9 3.1 - - + -
86A VAL* 3.8 4.4 + - + +
87A MET* 1.3 73.8 - - - +
89A VAL* 1.3 56.1 + - - +
90A TYR 3.8 0.2 - - - -
100A ILE* 4.3 15.7 - - + -
102A GLY 4.0 2.0 - - - +
103A GLU* 3.3 23.1 - - + +
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Residues in contact with VAL 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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3A LEU* 3.2 29.8 - - + -
29A LEU* 4.7 9.0 - - + -
40A PRO* 3.4 33.9 - - + -
41A TYR 3.6 11.7 - - - +
42A VAL* 3.9 17.3 - - + +
87A MET* 4.1 1.2 + - - +
88A ALA* 1.3 70.5 - - - +
90A TYR* 1.3 59.4 + - - +
100A ILE* 3.7 4.9 - - - +
101A ILE* 3.1 34.9 + - + +
102A GLY 2.7 25.8 + - - +
123A LEU* 6.0 1.3 - - + -
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Residues in contact with TYR 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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40A PRO* 3.2 0.2 - - - +
41A TYR* 2.4 83.3 + + + +
43A LYS* 3.9 27.8 - - + -
88A ALA 3.6 1.0 + - - -
89A VAL* 1.3 73.0 - - - +
91A ASP* 1.3 69.7 + - - +
98A HIS* 2.5 52.9 + + + +
99A ASP 3.7 4.9 - - - -
100A ILE* 3.3 35.4 - - + -
101A ILE* 3.6 2.2 - - - -
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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