Contacts of the helix formed by residues 18 - 28 (chain E) in PDB entry 1KYZ
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 GLU 18 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A LEU* 4.1 12.5 - - + +
11E PRO* 5.9 0.2 - - - +
13E HIS 4.8 0.6 - - - +
14E ILE* 3.4 27.5 - - + +
15E SER* 2.7 53.8 + - - +
17E GLU* 1.3 85.3 + - - +
19E ALA* 1.3 58.5 + - - +
20E ASN 3.4 2.2 - - - -
21E LEU* 3.4 20.7 + - + +
22E PHE* 3.0 27.7 + - - +
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Residues in contact with ALA 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 3.8 23.3 - - + +
111A VAL* 3.8 7.2 - - - +
114A TYR* 4.2 24.0 - - + -
14E ILE* 4.8 3.8 - - - -
15E SER 3.9 1.3 + - - -
16E ASP 3.1 18.1 + - - +
17E GLU 3.3 0.8 - - - -
18E GLU* 1.3 76.5 - - - +
20E ASN* 1.3 60.1 + - - +
22E PHE* 3.3 5.4 + - - +
23E ALA* 2.8 31.2 + - - +
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Residues in contact with ASN 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 2.8 42.5 + - + +
124A ILE* 4.6 7.4 - - - +
186A ILE* 4.7 0.3 - - - +
354A PHE* 3.7 51.8 + - + +
355A ASN* 5.6 0.4 - - - +
17E GLU 4.9 3.4 + - - +
18E GLU* 3.4 0.6 - - - +
19E ALA* 1.3 77.6 - - - +
21E LEU* 1.3 70.3 + - + +
23E ALA* 3.1 1.4 + - - +
24E MET* 2.8 47.0 + - - +
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A LEU* 3.7 27.1 - - + +
309A ALA* 4.1 36.6 - - + +
312A GLY* 6.0 1.1 - - - -
354A PHE* 5.9 0.4 - - - -
355A ASN* 4.4 22.4 - - + +
17E GLU 5.3 2.2 - - - +
18E GLU* 3.4 23.4 + - + +
19E ALA 3.3 0.6 - - - -
20E ASN* 1.3 85.7 - - + +
22E PHE* 1.3 58.3 + - - +
24E MET* 3.5 6.9 + - + +
25E GLN* 3.1 25.8 + - - +
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Residues in contact with PHE 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 4.0 22.9 - - + -
88A ILE* 4.4 6.7 - - + -
89A ILE* 4.8 1.3 - - + -
111A VAL* 3.6 33.0 - - + -
308A LEU* 4.1 4.6 - - + +
10E THR* 4.1 15.9 - - - -
11E PRO* 4.2 11.7 - - + -
14E ILE* 3.2 41.1 - - + -
18E GLU 3.0 10.3 + - - +
19E ALA* 3.7 4.7 - - - +
21E LEU* 1.3 75.8 - - - +
23E ALA* 1.3 63.9 + - - +
25E GLN* 3.3 25.1 + - - -
26E LEU* 3.1 46.0 + - + +
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 3.6 15.2 - - + +
114A TYR* 3.8 24.2 - - + -
115A LEU* 4.1 18.7 - - + +
124A ILE* 4.1 7.9 - - + +
128A ASN* 4.8 2.1 + - - -
19E ALA 2.8 21.2 + - - +
20E ASN 3.5 4.0 - - - +
22E PHE* 1.3 74.5 - - - +
24E MET* 1.3 57.1 + - - +
26E LEU* 3.3 6.5 + - - +
27E ALA* 2.9 28.8 + - - +
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Residues in contact with MET 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 3.8 31.9 - - + -
127A LEU* 3.8 16.8 - - + -
183A HIS* 3.7 28.3 - - + +
312A GLY* 5.7 9.2 - - - -
315A HIS* 4.6 0.2 + - - -
316A ILE* 5.3 11.2 - - + -
354A PHE 5.8 3.1 - - - +
355A ASN* 6.3 2.2 - - + -
20E ASN* 2.8 36.6 + - - +
21E LEU* 3.7 7.6 - - + +
23E ALA* 1.3 78.1 - - + +
25E GLN* 1.3 61.1 + - - +
27E ALA* 3.2 17.1 + - + +
28E SER* 3.6 10.7 + - - -
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Residues in contact with GLN 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A LEU* 3.5 21.5 - - + +
311A LYS* 3.7 20.1 - - + +
312A GLY* 5.9 5.3 - - - +
315A HIS* 3.4 13.5 - - + -
9E ILE 3.5 16.0 + - - -
10E THR* 3.6 16.8 - - + +
11E PRO* 3.7 3.0 - - - +
21E LEU 3.1 14.2 + - - +
22E PHE* 3.3 32.5 + - - +
24E MET* 1.3 74.8 - - - +
26E LEU* 1.3 60.2 + - - +
28E SER 3.3 2.1 + - - -
29E ALA* 3.0 28.8 + - + -
87E TYR* 3.0 27.8 + - - +
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.5 40.6 - - + -
33A PRO* 4.4 9.1 - - + +
36A LEU* 3.8 19.9 - - + +
89A ILE* 3.7 28.7 - - + -
111A VAL* 4.1 15.3 - - + -
115A LEU* 5.2 4.3 - - + -
128A ASN* 3.6 8.5 - - - +
132A GLN* 4.5 1.2 - - - +
10E THR* 4.7 3.4 - - + -
22E PHE* 3.1 46.0 + - + +
23E ALA* 3.7 5.2 - - - +
25E GLN* 1.3 78.0 - - + +
27E ALA* 1.3 62.1 + - - +
28E SER 3.1 1.2 + - - -
29E ALA* 3.4 15.2 + - + +
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 4.0 4.7 - - + -
127A LEU* 3.5 24.8 - - + +
128A ASN* 3.5 25.5 + - - +
131A ASN* 2.8 18.3 - - - +
132A GLN* 3.0 17.0 - - - +
23E ALA 2.9 14.1 + - - +
24E MET* 3.3 17.9 - - + +
25E GLN 3.2 0.4 - - - -
26E LEU* 1.3 78.2 - - - +
28E SER* 1.3 56.4 + - - +
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Residues in contact with SER 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASN* 3.7 12.8 - - - -
132A GLN* 3.6 8.5 - - - +
315A HIS* 2.6 35.1 + - - +
316A ILE* 6.0 0.5 - - - +
319A ILE* 3.8 23.1 - - - -
24E MET 3.6 7.7 + - - -
25E GLN 3.3 2.3 + - - -
27E ALA* 1.3 78.6 - - - +
29E ALA* 1.3 65.3 + - - +
30E SER 3.1 3.4 - - - -
31E VAL* 3.1 23.7 + - - +
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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