Contacts of the helix formed by residues 33 - 43 (chain B) in PDB entry 1KKC
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 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B GLN* 3.9 11.2 - - - +
30B PRO 6.0 0.2 - - - -
32B ILE* 1.3 77.4 - - - +
34B GLN* 1.3 66.3 + - - +
35B GLN* 3.7 11.2 + - - +
36B ILE* 3.2 31.1 + - - +
37B MET* 3.2 19.5 + - - +
182B LEU* 5.0 0.9 - - - +
183B GLN* 2.7 25.3 + - - +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TYR* 3.3 26.9 - - + +
26B ASP* 3.4 26.9 - - + +
29B GLN* 2.9 23.7 + - - +
33B SER* 1.3 72.7 - - - +
35B GLN* 1.3 62.4 + - - +
37B MET* 3.4 2.4 + - - +
38B GLU* 3.0 51.4 + - - +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 4.4 13.5 - - - +
33B SER* 3.1 9.0 + - - +
34B GLN* 1.3 80.3 - - - +
36B ILE* 1.3 62.2 + - - +
38B GLU* 3.3 12.6 + - - +
39B LEU* 3.1 31.6 + - + +
182B LEU* 3.6 37.9 + - + +
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 4.1 13.5 - - + -
33B SER* 3.2 27.6 + - - +
35B GLN* 1.3 74.8 - - - +
37B MET* 1.3 55.7 + - - +
39B LEU* 3.2 3.4 + - - +
40B HIS* 2.6 47.1 + - + +
178B HIS 3.8 16.2 - - - +
179B ALA* 3.6 19.5 - - - +
180B TYR* 3.9 20.9 - - - +
182B LEU* 3.8 24.0 - - + +
183B GLN* 3.8 30.3 - - + +
184B TYR* 5.5 1.1 - - + -
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Residues in contact with MET 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.1 8.5 - - + +
23B TYR* 3.9 14.6 - - + -
25B TYR* 3.2 38.4 - - + +
28B LEU* 3.7 30.1 - - + -
32B ILE* 3.6 30.5 - - + +
33B SER 3.2 10.9 + - - +
34B GLN 3.7 1.8 - - - +
36B ILE* 1.3 80.5 - - - +
38B GLU* 1.3 57.5 + - - +
40B HIS* 3.9 5.1 - - - +
41B HIS* 2.9 35.0 + - - +
91B PHE* 6.1 0.4 - - - -
92B TRP* 3.6 36.3 - - + -
95B LEU* 4.9 1.6 - - + -
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TYR* 3.6 35.2 - - + -
34B GLN* 3.0 43.7 + - - +
35B GLN* 3.7 12.8 - - - +
36B ILE 3.2 0.2 - - - -
37B MET* 1.3 74.9 - - - +
39B LEU* 1.3 56.7 + - + +
42B LYS* 2.7 56.1 + - + +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A TYR* 4.0 18.6 - - - +
185A LEU* 4.1 26.5 - - + -
186A ASN* 3.5 23.8 - - - +
35B GLN* 3.1 21.6 + - + +
36B ILE* 3.7 3.1 - - - +
38B GLU* 1.3 79.0 - - + +
40B HIS* 1.3 60.0 + - - +
43B LYS* 2.8 47.9 + - + +
44B HIS* 3.1 5.7 + - + -
182B LEU* 3.6 30.7 - - + -
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Residues in contact with HIS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 2.6 32.6 + - + +
37B MET* 3.9 4.7 - - - +
39B LEU* 1.3 73.1 - - - +
41B HIS* 1.3 56.5 + - - +
44B HIS* 3.4 10.8 - - + +
45B HIS* 2.9 26.9 + - - +
88B HIS* 2.9 14.8 + + - -
91B PHE* 3.9 19.0 - + - -
92B TRP* 3.4 18.1 - + + -
174B ASP* 3.0 15.0 - - - -
178B HIS* 3.3 14.3 + + - +
179B ALA* 3.8 23.1 + - + +
2002B MN 2.1 30.9 + - - -
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Residues in contact with HIS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.5 34.3 - - + +
19B PRO 2.7 29.7 + - - -
20B PRO* 4.0 4.2 - - - +
21B LEU* 3.8 27.1 + - + +
25B TYR* 2.9 35.4 - + + -
37B MET 2.9 20.0 + - - +
40B HIS* 1.3 76.3 - - - +
42B LYS* 1.3 64.0 + - - +
43B LYS 3.4 0.2 + - - -
45B HIS* 3.4 5.4 - - - +
46B GLN 3.3 20.6 + - - -
92B TRP* 3.5 29.4 + - + -
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.3 9.2 - - + -
25B TYR* 3.1 43.4 - - + +
38B GLU* 2.7 39.5 + - + +
41B HIS* 1.3 75.3 - - + +
43B LYS* 1.3 65.5 + - + +
46B GLN* 3.0 21.3 - - - +
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASN* 3.4 45.3 - - + +
39B LEU* 2.8 35.2 + - + +
42B LYS* 1.3 82.9 - - + +
44B HIS* 1.3 60.7 + - - +
45B HIS 3.5 0.4 - - - -
46B GLN* 3.4 1.9 + - - +
47B THR* 2.9 37.3 + - - +
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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