Contacts of the strand formed by residues 33 - 39 (chain A) in PDB entry 2KLL
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 TYR 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA 4.2 3.1 - - - -
28A LEU* 3.7 27.6 - - + -
31A GLU* 3.6 21.1 - - - -
32A SER* 1.3 79.4 + - - +
34A GLU* 1.3 69.2 + - - +
35A ILE* 4.0 7.5 + - + +
82A PHE* 3.2 35.1 - + - -
94A GLU* 4.2 22.4 - - + +
95A LEU* 4.1 43.3 - - + +
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Residues in contact with GLU 34 (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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25A THR 4.3 0.2 - - - +
26A PHE 4.0 0.2 - - - -
27A ALA* 3.0 44.0 + - + +
29A GLU* 3.3 21.0 + - + +
32A SER* 3.6 14.8 + - - +
33A TYR* 1.3 84.2 - - - +
35A ILE* 1.3 61.6 + - - +
36A TYR* 4.5 8.1 - - + -
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Residues in contact with ILE 35 (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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24A ILE* 4.0 21.1 - - + -
25A THR 3.7 11.4 - - - +
26A PHE* 4.4 16.2 - - + -
33A TYR* 4.0 8.2 + - + +
34A GLU* 1.3 81.0 - - - +
36A TYR* 1.3 68.7 + - - +
93A VAL 4.0 21.3 - - - +
94A GLU* 4.1 9.9 - - - +
95A LEU* 4.0 24.0 - - + -
135A ASN* 4.1 2.4 - - - +
136A HIS* 3.1 23.9 + - + +
137A LEU* 4.2 25.6 - - + +
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Residues in contact with TYR 36 (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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25A THR* 2.9 58.5 + - + +
27A ALA* 3.6 28.3 - - + +
34A GLU* 4.4 6.5 - - + -
35A ILE* 1.3 85.7 - - - +
37A VAL* 1.3 62.2 + - - +
38A GLU* 3.2 42.0 - - + +
135A ASN* 3.3 17.9 - - + +
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Residues in contact with VAL 37 (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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18A THR* 3.9 11.0 - - + -
22A GLN* 3.3 37.0 - - + +
23A SER 3.3 20.6 - - - +
24A ILE* 3.4 22.9 - - + -
25A THR 4.4 0.2 - - - +
36A TYR* 1.3 74.7 - - - +
38A GLU* 1.3 69.7 + - - +
39A ASP* 4.9 2.8 - - - +
132A VAL* 3.6 29.4 - - + -
135A ASN* 3.0 16.2 + - - +
136A HIS* 4.5 3.1 - - - +
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Residues in contact with GLU 38 (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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22A GLN* 3.3 4.8 - - - +
23A SER* 2.9 37.0 + - - +
25A THR* 3.1 23.8 - - + +
36A TYR* 3.2 32.7 + - + +
37A VAL* 1.3 91.5 - - - +
39A ASP* 1.3 68.0 + - - +
40A LEU* 5.8 0.9 - - + -
46A LYS* 5.9 5.8 - - - +
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Residues in contact with ASP 39 (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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20A ASN 5.0 0.2 - - - +
21A ASP 5.2 0.2 - - - +
22A GLN* 3.0 40.4 + - + +
37A VAL 4.9 1.9 - - - +
38A GLU* 1.3 80.6 - - - +
40A LEU* 1.3 69.4 + - - +
41A LYS* 5.0 11.6 - - - +
46A LYS* 5.6 0.7 - - - -
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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