Contacts of the helix formed by residues 30 - 42 (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 SER 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A SER* 5.7 1.8 - - - -
33A PRO* 3.7 14.6 - - - +
34A MET* 5.0 1.1 - - - -
131A ASN* 4.4 2.6 + - - +
132A GLN* 2.6 32.3 + - - +
137A MET* 3.6 33.6 - - - -
140A TRP* 4.5 4.2 + - - -
28E SER 4.4 0.5 + - - -
29E ALA* 1.3 77.6 - - - +
31E VAL* 1.3 65.9 + - - +
32E LEU 3.3 0.2 - - - -
33E PRO* 3.2 9.4 - - - +
34E MET* 3.1 27.2 + - - +
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Residues in contact with VAL 31 (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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140A TRP* 4.1 16.6 - - + -
315A HIS* 4.2 12.1 - - + +
318A VAL* 3.3 30.1 - - + -
319A ILE* 3.7 31.9 - - + -
28E SER* 3.1 19.7 - - - +
29E ALA 3.0 1.0 - - - -
30E SER* 1.3 81.2 + - - +
32E LEU* 1.3 57.4 + - - +
34E MET* 4.1 0.4 - - - +
35E ILE* 2.9 29.8 + - - +
83E LEU* 3.4 20.4 - - + -
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Residues in contact with LEU 32 (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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26A LEU* 3.6 13.9 - - + -
29A ALA* 5.1 0.9 - - + -
315A HIS* 5.5 2.5 + - - +
9E ILE* 3.5 37.5 - - + -
29E ALA 3.5 5.4 + - - +
31E VAL* 1.3 79.4 - - - +
33E PRO* 1.3 73.8 - - + +
35E ILE* 3.9 0.7 - - - +
36E LEU* 2.9 26.3 + - + +
83E LEU* 3.9 8.5 - - + +
84E LEU* 4.0 22.7 - - + -
87E TYR* 3.6 48.0 - - + -
89E ILE* 4.1 11.9 - - + -
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Residues in contact with PRO 33 (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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26A LEU* 4.6 2.0 - - + +
29A ALA* 3.7 25.6 - - + -
30A SER* 3.8 26.0 - - - +
29E ALA 3.2 14.4 - - - +
30E SER* 3.2 21.3 - - - +
32E LEU* 1.3 95.0 - - + +
34E MET* 1.3 58.2 + - + +
36E LEU* 3.6 2.6 + - + -
37E LYS* 3.0 26.2 + - - +
128E ASN* 3.5 12.9 + - - +
132E GLN* 3.9 18.3 - - + +
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Residues in contact with MET 34 (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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30A SER* 5.4 0.2 - - - -
137A MET* 4.3 6.7 - - + -
140A TRP* 3.6 57.4 - - + +
141A TYR* 3.9 16.4 - - + -
30E SER* 3.1 21.1 + - - +
31E VAL 4.1 1.6 - - - +
33E PRO* 1.3 76.9 - - - +
35E ILE* 1.3 62.2 + - - +
37E LYS* 3.2 15.1 + - + +
38E SER* 2.9 30.1 + - - -
132E GLN* 3.7 39.5 - - - +
137E MET* 4.1 18.2 - - - -
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Residues in contact with ILE 35 (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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140A TRP* 3.7 7.4 - - + -
143A LEU* 3.7 25.6 - - + -
318A VAL* 3.2 36.3 - - + -
321A LEU* 4.8 1.8 - - + -
31E VAL* 2.9 21.5 + - + +
32E LEU 4.0 0.7 - - - +
34E MET* 1.3 73.6 - - - +
36E LEU* 1.3 62.3 + - - +
38E SER* 3.3 4.0 + - - +
39E ALA* 2.9 27.2 + - - +
80E MET* 3.8 43.1 - - + +
83E LEU* 3.6 16.8 - - + -
84E LEU* 4.2 8.7 - - + -
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Residues in contact with LEU 36 (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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26A LEU* 3.8 39.0 - - + +
32E LEU* 2.9 19.2 + - + +
33E PRO* 3.8 4.5 - - + +
35E ILE* 1.3 77.9 - - - +
37E LYS* 1.3 57.3 + - - +
39E ALA* 3.1 7.8 + - + +
40E LEU* 2.8 45.9 + - + +
45E LEU* 4.3 19.1 - - + -
84E LEU* 4.1 23.8 - - + -
89E ILE* 4.7 7.2 - - + -
115E LEU* 4.8 12.3 - - + -
128E ASN* 3.5 26.5 - - + +
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Residues in contact with LYS 37 (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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140A TRP 5.7 0.6 + - - -
141A TYR* 3.6 24.4 - - - +
33E PRO 3.0 13.6 + - - +
34E MET* 3.2 17.9 + - + +
36E LEU* 1.3 76.0 - - - +
38E SER* 1.3 59.3 + - - +
40E LEU* 2.9 7.7 + - - +
41E GLU* 2.8 53.3 + - - +
128E ASN* 3.1 20.6 + - - +
129E LEU* 3.7 25.7 - - + +
132E GLN* 3.1 44.8 + - + +
133E ASP* 3.8 8.4 + - - +
134E LYS* 4.3 7.7 - - - +
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Residues in contact with SER 38 (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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140A TRP* 3.6 11.4 + - - -
143A LEU* 3.4 42.9 - - - +
144A LYS 4.6 4.0 - - - -
34E MET 2.9 16.5 + - - -
35E ILE 3.8 0.9 - - - -
37E LYS* 1.3 75.9 - - - +
39E ALA* 1.3 58.1 + - - +
41E GLU* 3.2 16.1 + - - +
42E LEU* 2.9 34.6 + - - +
80E MET* 3.7 9.2 - - - -
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Residues in contact with ALA 39 (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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35E ILE 2.9 14.3 + - - +
36E LEU* 3.1 13.9 + - + +
38E SER* 1.3 75.5 - - - +
40E LEU* 1.3 59.0 + - + +
42E LEU 3.3 2.1 + - - -
43E ASP 3.0 6.9 + - - -
44E LEU* 2.9 53.8 + - + +
45E LEU* 5.3 4.5 - - + -
80E MET* 3.9 4.9 - - + +
84E LEU* 3.9 23.6 - - + -
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Residues in contact with LEU 40 (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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36E LEU* 2.8 22.6 + - + +
37E LYS 2.9 6.3 + - - +
39E ALA* 1.3 74.2 - - - +
41E GLU* 1.3 61.1 + - - +
43E ASP* 2.9 22.2 + - - +
44E LEU 4.9 0.2 - - - +
45E LEU* 4.0 28.9 - - + +
115E LEU* 4.4 2.7 - - + +
125E SER* 3.4 54.5 - - - +
128E ASN* 3.7 23.3 - - + +
129E LEU* 3.8 21.2 - - + +
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Residues in contact with GLU 41 (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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140A TRP 4.9 4.3 - - - +
141A TYR* 5.0 6.6 - - - +
144A LYS* 3.8 40.9 + - + +
37E LYS* 2.8 41.2 + - - +
38E SER* 3.2 23.5 + - - +
40E LEU* 1.3 76.8 - - - +
42E LEU* 1.3 61.2 + - - +
43E ASP* 3.1 2.6 + - - +
129E LEU* 3.8 18.1 - - + +
134E LYS* 4.9 6.4 + - - -
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Residues in contact with LEU 42 (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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144A LYS* 3.9 20.6 - - + +
147A VAL* 3.9 33.9 - - + -
148A LEU* 3.6 38.6 - - + -
38E SER* 2.9 21.4 + - - +
39E ALA 3.7 4.5 - - - +
41E GLU* 1.3 75.0 - - - +
43E ASP* 1.3 70.5 + - - +
44E LEU* 3.3 11.2 + - + -
47E ILE* 4.0 0.5 - - - +
66E LEU* 3.2 27.7 - - + +
67E PRO* 5.8 0.3 - - - +
77E LEU* 4.1 9.9 - - + -
80E MET* 4.0 17.5 - - + -
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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