Contacts of the helix formed by residues 27 - 42 (chain E) in PDB entry 1KD1
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 ARG 27 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A G 3.5 10.1 + - - -
657A G 2.3 29.7 + - - -
25E PRO 4.1 3.8 - - - +
26E VAL* 1.3 73.6 - - - +
28E SER* 1.3 64.2 + - - +
29E ASP* 2.7 47.3 + - - +
30E LEU* 3.4 35.5 - - + +
31E ILE* 3.1 24.5 + - - +
109E LEU* 5.3 5.1 - - + +
113E SER* 2.6 17.6 + - - +
4P ASN* 3.1 33.2 + - - +
5P PRO* 3.8 5.2 - - - -
6P ARG* 4.1 17.0 - - - +
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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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26E VAL* 3.8 8.1 + - - +
27E ARG* 1.3 74.0 - - - +
29E ASP* 1.3 60.2 + - - +
31E ILE* 3.7 2.2 - - - +
32E GLY* 2.9 26.0 + - - -
227E GLY 4.5 3.7 - - - +
229E PRO* 3.8 32.3 - - - -
5P PRO* 4.5 12.8 - - - +
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Residues in contact with ASP 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A G 4.3 1.6 - - - +
27E ARG* 2.7 51.8 + - - +
28E SER* 1.3 81.5 + - - +
30E LEU* 1.3 72.4 + - - +
32E GLY* 3.3 2.6 + - - -
33E LYS* 3.0 26.3 + - - +
36E ARG* 4.5 4.9 + - - +
3P THR* 3.3 39.7 - - + +
5P PRO* 3.0 15.2 - - + +
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Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A G 3.2 26.2 - - - +
657A G 3.9 7.9 - - - -
27E ARG* 3.3 44.2 + - + +
29E ASP* 1.3 83.2 - - - +
31E ILE* 1.3 65.3 + - - +
33E LYS* 3.3 11.0 + - + +
34E ALA* 3.0 18.0 + - - +
102E LEU* 5.8 0.2 - - - +
106E GLU* 4.3 17.7 - - + +
109E LEU* 3.7 33.9 - - + -
110E ALA* 3.6 22.0 - - + +
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Residues in contact with ILE 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E VAL* 4.6 1.6 - - + -
27E ARG 3.1 19.3 + - - +
28E SER* 3.7 6.7 - - - +
30E LEU* 1.3 76.0 - - - +
32E GLY* 1.3 65.3 + - - +
34E ALA* 3.0 13.5 + - - +
35E VAL* 3.0 12.6 + - - +
110E ALA* 3.8 21.8 - - - +
113E SER* 3.9 13.9 - - - +
114E ALA* 3.8 26.0 - - + +
220E THR* 3.7 11.0 - - + -
224E ALA* 3.5 28.5 - - + -
227E GLY* 4.0 11.2 - - - +
229E PRO* 3.7 24.7 - - + -
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Residues in contact with GLY 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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28E SER 2.9 15.6 + - - -
29E ASP* 3.7 4.3 - - - -
31E ILE* 1.3 78.3 - - - +
33E LYS* 1.3 55.3 + - - +
35E VAL* 3.3 2.3 + - - +
36E ARG* 2.9 43.5 + - - +
227E GLY* 4.2 18.1 + - - -
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Residues in contact with LYS 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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656A G 4.4 6.2 + - - -
750A A 3.6 39.3 + - - +
751A U 4.1 17.6 + - - -
29E ASP 3.0 12.9 + - - +
30E LEU* 3.7 15.5 - - + +
31E ILE 3.2 0.2 - - - -
32E GLY* 1.3 76.1 - - - +
34E ALA* 1.3 57.8 + - - +
36E ARG* 3.3 23.4 + - + +
37E ALA* 3.0 28.9 + - + +
101E ASP 5.2 1.3 - - - -
102E LEU* 3.8 21.1 - - + -
106E GLU* 2.9 30.5 + - + +
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Residues in contact with ALA 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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30E LEU 3.0 11.6 + - - +
31E ILE 3.0 9.5 + - - +
33E LYS* 1.3 78.7 - - - +
35E VAL* 1.3 61.1 + - - +
37E ALA* 3.5 2.6 + - - +
38E ALA* 3.1 22.7 + - - +
102E LEU* 3.7 20.7 - - + +
107E ARG* 4.6 7.3 - - + +
110E ALA* 3.8 11.2 - - + -
220E THR* 3.7 26.5 - - + +
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Residues in contact with VAL 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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31E ILE* 3.0 14.4 + - + +
32E GLY 3.9 2.0 - - - +
34E ALA* 1.3 73.6 - - - +
36E ARG* 1.3 65.6 + - - +
38E ALA* 3.3 5.0 + - - +
39E GLN* 2.9 41.5 + - - +
220E THR* 3.5 24.0 - - + +
221E GLU* 4.1 13.0 - - + +
224E ALA 3.5 12.1 - - - +
226E GLY 3.9 12.6 - - - +
227E GLY* 3.4 37.5 - - - +
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Residues in contact with ARG 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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751A U 5.5 4.6 + - - -
1348A A 3.0 27.4 + - - +
1349A G 3.6 50.0 + - - +
29E ASP* 4.5 5.3 + - - +
32E GLY* 2.9 38.5 + - - +
33E LYS* 3.5 28.6 - - + +
35E VAL* 1.3 76.9 - - - +
37E ALA* 1.3 56.6 + - - +
39E GLN* 3.1 13.4 + - - +
40E ALA* 2.8 30.3 + - - +
100E LEU* 4.1 12.1 - - + +
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Residues in contact with ALA 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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676A C 5.1 0.2 - - - +
33E LYS* 3.0 17.0 + - + +
34E ALA 3.7 4.9 - - - +
36E ARG* 1.3 76.1 - - - +
38E ALA* 1.3 60.7 + - - +
40E ALA 3.2 0.2 + - - -
41E ASN* 2.5 44.5 + - - +
100E LEU* 4.0 24.8 - - + +
101E ASP 5.0 0.4 - - - +
102E LEU* 4.1 22.2 - - + -
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A U 2.8 24.6 + - - +
676A C 3.5 30.9 + - - +
34E ALA 3.1 15.1 + - - +
35E VAL 3.7 4.5 - - - +
37E ALA* 1.3 81.2 - - - +
39E GLN* 1.3 61.6 + - - +
42E ARG* 3.4 8.6 + - - -
219E ASN* 6.6 0.2 - - - -
220E THR* 6.6 0.2 - - - -
221E GLU* 3.7 26.2 - - + +
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Residues in contact with GLN 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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449A A 5.5 3.2 + - + +
1307A A 2.9 42.2 + - - +
1348A A 6.3 0.8 - - - -
35E VAL* 2.9 32.8 + - - +
36E ARG* 3.6 11.4 - - - +
38E ALA* 1.3 76.7 - - - +
40E ALA* 1.3 55.0 + - - +
42E ARG* 3.6 30.0 + - - +
43E LYS* 2.7 44.8 + - - +
221E GLU* 3.9 12.7 - - - +
226E GLY* 4.6 1.5 + - - -
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Residues in contact with ALA 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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449A A 4.2 17.0 - - - +
36E ARG 2.8 8.7 + - - +
37E ALA 3.7 1.8 - - - +
39E GLN* 1.3 77.4 - - - +
41E ASN* 1.3 64.7 + - - +
42E ARG 3.0 1.9 + - - -
43E LYS* 3.0 26.3 + - - +
98E ARG 3.7 17.9 - - - +
100E LEU* 3.2 39.9 - - + +
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Residues in contact with ASN 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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674A A 4.3 2.8 + - - -
675A U 3.5 28.2 - - - +
676A C 2.7 23.7 + - - +
37E ALA* 2.5 33.0 + - - +
38E ALA 4.0 0.2 - - - +
40E ALA* 1.3 75.8 - - - +
42E ARG* 1.3 58.0 + - - +
43E LYS 3.3 4.4 + - - +
99E SER* 3.5 14.3 - - - +
100E LEU 2.9 42.3 + - - +
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A A 4.4 6.3 + - - +
674A A 4.2 10.0 + - + +
675A U 2.5 64.5 + - - +
1307A A 6.2 1.6 - - - -
38E ALA 3.4 5.6 + - - +
39E GLN* 3.6 29.2 + - - +
40E ALA 3.0 0.2 + - - -
41E ASN* 1.3 77.7 - - - +
43E LYS* 1.3 72.6 + - + +
44E GLN* 3.7 8.7 + - - +
221E GLU* 3.1 37.8 + - - -
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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
------------------------------------------------------------
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