Contacts of the strand formed by residues 66 - 73 (chain B) in PDB entry 3IKK
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 SER 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B LYS* 4.0 27.3 - - - +
32B LEU 3.3 11.4 - - - -
33B GLY* 4.6 2.2 - - - -
65B ALA* 1.3 75.9 - - - +
67B ILE* 1.3 72.2 + - - +
68B ASN* 4.2 4.5 + - - -
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU 3.6 0.5 - - - +
31B LYS* 3.3 1.8 - - - +
32B LEU* 2.8 40.7 + - + +
42B PHE* 4.5 10.8 - - + -
56B PRO* 4.4 20.2 - - + -
60B ILE 4.2 13.0 - - - +
61B ILE* 4.0 33.4 - - + -
65B ALA* 5.8 0.9 - - + -
66B SER* 1.3 81.0 - - - +
68B ASN* 1.3 75.1 + - - +
69B VAL* 3.6 7.5 + - + -
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASN* 4.1 26.8 - - + +
30B LEU 3.4 4.7 - - - +
31B LYS* 2.8 28.8 - - - +
55B ARG 4.6 0.2 - - - +
56B PRO* 4.4 4.2 - - - +
66B SER* 4.2 5.7 + - - -
67B ILE* 1.3 78.6 - - - +
69B VAL* 1.3 63.4 + - - +
70B SER* 3.6 5.5 + - - -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASN* 3.2 5.7 - - - -
30B LEU* 2.4 59.6 + - + +
32B LEU* 3.9 28.0 - - + -
42B PHE* 4.6 4.0 - - + -
44B VAL* 4.3 10.5 - - + -
54B VAL* 3.7 29.4 - - + -
55B ARG 4.0 3.6 - - - +
56B PRO* 3.9 21.8 - - + +
67B ILE* 4.6 6.3 - - + -
68B ASN* 1.3 68.4 - - - +
70B SER* 1.3 64.4 + - - +
71B VAL* 3.4 12.0 + - + +
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Residues in contact with SER 70 (chain B).
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* 4.2 3.0 - - - +
74A GLN* 2.7 34.1 + - - -
75A PRO* 4.1 11.6 - - - +
27B THR* 4.1 13.7 - - - -
29B ASN* 3.9 14.8 + - - -
53B CYS 3.9 0.7 - - - +
54B VAL* 3.7 4.0 - - - -
55B ARG 3.0 33.6 + - - +
68B ASN 3.6 4.7 + - - -
69B VAL* 1.3 72.0 - - - +
71B VAL* 1.3 58.8 + - - +
72B MET* 4.0 3.4 + - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.5 12.3 - - + -
18B PHE* 3.6 27.2 - - + -
27B THR* 3.4 1.3 - - - +
28B THR* 2.9 46.9 + - + +
30B LEU* 4.8 7.0 - - + -
44B VAL* 5.2 5.8 - - + -
52B TYR* 4.1 9.4 - - + -
53B CYS 3.6 4.9 - - - +
54B VAL* 4.6 12.8 - - + -
69B VAL* 3.9 20.2 - - + +
70B SER* 1.3 74.3 - - - +
72B MET* 1.3 59.8 + - - +
88B PHE* 4.1 20.9 - - + -
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Residues in contact with MET 72 (chain B).
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* 4.0 13.9 - - - -
53A CYS* 4.0 2.9 - - + -
72A MET* 4.1 17.9 - - - +
74A GLN* 3.2 33.2 - - - +
25B VAL* 3.9 16.4 - - + -
26B VAL 3.4 4.0 - - - -
27B THR* 3.7 20.0 - - + +
51B ARG 3.9 0.2 - - - +
52B TYR* 3.3 9.2 - - - +
53B CYS* 2.9 82.9 + - + +
55B ARG* 3.9 12.6 - - + +
70B SER* 4.2 2.2 - - - +
71B VAL* 1.3 77.4 - - - +
73B LEU* 1.3 61.1 + - - +
74B GLN* 4.7 2.0 + - - -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 4.0 19.1 - - + -
22B PHE* 4.1 18.4 - - + -
24B ASP 4.2 0.2 - - - +
25B VAL* 3.0 9.1 - - - -
26B VAL* 2.6 47.1 + - + +
51B ARG* 3.8 31.6 - - - +
52B TYR* 3.9 20.2 - - + -
71B VAL 4.0 0.6 + - - -
72B MET* 1.3 72.3 - - - +
74B GLN* 1.3 79.3 + - - +
76B PHE* 4.1 4.5 - - + -
123B PHE* 3.3 36.1 - - + -
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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