Contacts of the strand formed by residues 88 - 94 (chain A) 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 PHE 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.6 29.8 - - + -
18A PHE* 3.8 5.8 - + - -
30A LEU* 6.2 1.1 - - + -
44A VAL* 5.7 4.9 - - + -
45A LYS 3.5 8.1 - - - +
46A THR* 3.8 15.9 - - - -
52A TYR* 3.4 54.1 - + - -
54A VAL* 6.0 1.6 - - + -
71A VAL* 4.2 15.9 - - + -
86A HIS* 3.9 6.5 - - + -
87A LYS* 1.3 75.2 - - - +
89A MET* 1.3 62.3 + - - +
118A LYS* 3.3 4.6 - - - +
119A LEU* 2.6 38.6 + - + +
120A ARG 3.5 16.6 - - - -
121A CYS* 3.1 34.3 - - + -
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Residues in contact with MET 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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43A LYS 3.7 0.2 - - - +
44A VAL* 3.4 6.2 - - - +
45A LYS* 2.8 76.1 + - + +
46A THR* 5.0 6.1 - - - +
47A THR* 5.9 1.8 - - - -
87A LYS* 5.5 5.4 - - - +
88A PHE* 1.3 78.4 - - - +
90A VAL* 1.3 68.1 + - - +
91A GLN* 4.1 4.7 - - + +
116A ASP* 5.0 14.4 - - + +
117A SER 3.3 9.9 - - - +
118A LYS* 4.7 8.7 - - + -
119A LEU* 5.0 0.2 - - - -
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Residues in contact with VAL 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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6A GLN* 4.0 5.6 + - - +
8A LEU* 4.2 17.3 - - + -
10A LEU* 4.7 6.5 - - + -
30A LEU* 4.0 26.7 - - + -
32A LEU* 4.1 28.5 - - + -
42A PHE* 4.7 2.5 - - + -
43A LYS 3.4 9.0 - - - +
44A VAL* 4.5 6.7 - - + -
89A MET* 1.3 76.9 - - - +
91A GLN* 1.3 67.8 + - - +
115A MET 3.3 6.1 - - - +
116A ASP* 3.4 2.5 - - - +
117A SER* 2.9 36.1 + - - +
119A LEU* 4.4 12.3 - - + -
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Residues in contact with GLN 91 (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 PHE* 3.1 6.1 - - - +
43A LYS* 2.7 38.1 + - + +
45A LYS* 3.1 41.7 + - + +
89A MET* 4.1 8.5 - - + +
90A VAL* 1.3 72.6 - - - +
92A SER* 1.3 59.7 + - - +
106A TRP* 3.7 12.0 - - + -
114A LEU* 3.1 47.2 - - - +
115A MET 3.4 2.4 - - - +
116A ASP* 3.1 26.8 + - - +
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Residues in contact with SER 92 (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 GLN* 2.5 37.2 + - - -
8A LEU* 3.8 12.3 - - - -
40A VAL* 3.8 12.3 - - - -
41A CYS 3.2 11.0 - - - -
42A PHE* 4.9 0.2 - - - -
91A GLN* 1.3 73.5 - - - +
93A MET* 1.3 69.3 + - - +
106A TRP* 4.7 1.1 - - - -
114A LEU* 3.7 4.3 - - - +
115A MET* 2.8 41.2 + - - +
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Residues in contact with MET 93 (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 VAL* 3.4 4.4 - - - +
41A CYS* 2.7 45.0 + - + +
92A SER* 1.3 80.7 + - - +
94A PHE* 1.3 66.0 + - - +
95A ALA 3.2 0.2 + - - -
96A PRO* 5.4 5.2 - - + -
105A VAL* 4.2 23.8 - - + -
106A TRP* 3.4 43.5 - - + -
109A ALA* 3.9 22.4 - - + -
113A ASP* 2.9 34.1 - - + +
114A LEU* 3.6 7.0 - - + -
115A MET* 3.6 5.6 - - - +
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Residues in contact with PHE 94 (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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4A VAL* 5.5 3.4 - - + -
7A VAL* 3.5 34.8 - - + -
36A THR* 3.4 31.4 - - + -
38A ARG* 3.5 47.4 + - + +
39A ASN 3.5 3.4 - - - -
40A VAL* 3.9 11.9 - - + +
41A CYS* 4.9 0.2 - - - -
93A MET* 1.3 76.1 - - - +
95A ALA* 1.3 58.5 + - - +
96A PRO* 2.8 19.5 - - - +
113A ASP 4.9 0.8 + - - -
115A MET* 3.8 17.0 - - + -
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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