Contacts of the helix formed by residues 33 - 43 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.8 12.1 - - - +
30A PRO* 6.0 0.4 - - - -
32A ILE* 1.3 77.3 - - - +
34A GLN* 1.3 63.4 - - - +
35A GLN* 3.7 9.6 + - - +
36A ILE* 3.2 31.1 + - - +
37A MET* 3.0 23.6 + - - +
182A LEU* 5.2 1.2 - - - +
183A GLN* 2.8 22.3 + - - +
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Residues in contact with GLN 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 TYR* 3.2 27.4 - - + +
26A ASP* 3.5 20.2 - - + +
29A GLN* 2.9 24.1 + - - +
33A SER* 1.3 70.2 - - - +
35A GLN* 1.3 62.3 + - - +
37A MET* 3.3 1.0 + - - +
38A GLU* 2.8 64.9 + - - +
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Residues in contact with GLN 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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33A SER* 3.2 8.4 + - - +
34A GLN* 1.3 79.4 - - - +
36A ILE* 1.3 62.0 + - - +
38A GLU* 3.4 12.3 + - - +
39A LEU* 3.0 32.2 + - + +
182A LEU* 3.8 34.3 + - + +
185B LEU* 4.2 14.7 - - - +
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Residues in contact with ILE 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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32A ILE* 3.9 13.0 - - + -
33A SER* 3.2 24.5 + - - +
34A GLN 3.3 0.2 - - - -
35A GLN* 1.3 76.9 - - - +
37A MET* 1.3 55.8 + - - +
39A LEU* 3.2 3.2 + - - +
40A HIS* 2.7 45.3 + - + +
178A HIS 3.9 15.8 - - - +
179A ALA* 3.6 20.2 - - - +
180A TYR* 4.0 18.4 - - - -
182A LEU* 3.9 23.6 - - + +
183A GLN* 3.6 36.3 - - + +
184A TYR* 5.4 1.3 - - + -
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Residues in contact with MET 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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21A LEU* 4.2 7.7 - - + +
23A TYR* 3.9 18.4 - - + +
25A TYR* 3.2 36.1 - - + +
28A LEU* 3.5 30.3 - - + -
32A ILE* 3.3 30.7 - - + +
33A SER 3.0 20.5 + - - +
34A GLN 3.7 0.7 - - - +
36A ILE* 1.3 77.6 - - - +
38A GLU* 1.3 62.8 + - - +
40A HIS* 3.9 5.2 - - - +
41A HIS* 3.0 28.4 + - - +
91A PHE* 6.0 0.4 - - - -
92A TRP* 3.9 31.3 - - + -
95A LEU* 4.9 1.1 - - + -
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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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25A TYR* 3.6 32.9 - - + +
34A GLN* 2.8 53.1 + - - +
35A GLN* 3.8 11.3 - - - +
37A MET* 1.3 75.6 - - - +
39A LEU* 1.3 59.8 + - + +
42A LYS* 2.8 45.6 + - + +
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Residues in contact with LEU 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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35A GLN* 3.0 24.5 + - + +
36A ILE* 3.9 2.7 - - - +
38A GLU* 1.3 76.6 - - + +
40A HIS* 1.3 59.8 + - - +
43A LYS* 2.9 48.4 + - + +
44A HIS* 3.1 5.1 + - - -
182A LEU* 3.5 32.3 - - + -
181B TYR* 3.8 18.4 - - - +
185B LEU* 3.9 26.5 - - + -
186B ASN* 3.4 24.5 - - - +
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Residues in contact with HIS 40 (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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36A ILE* 2.7 31.3 + - + +
37A MET* 3.9 4.9 - - - +
39A LEU* 1.3 73.0 - - - +
41A HIS* 1.3 57.9 + - - +
44A HIS* 3.4 10.1 - - + +
45A HIS* 3.0 26.2 + - - +
88A HIS* 3.1 11.0 + + - -
91A PHE* 3.9 19.7 - + - -
92A TRP* 3.4 20.3 - + + -
174A ASP* 3.1 15.0 - - - -
178A HIS* 3.2 16.9 + + - +
179A ALA* 3.7 22.9 + - + -
2001A MN 2.2 31.1 + - - -
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Residues in contact with HIS 41 (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 LEU* 3.5 35.3 - - + +
19A PRO 2.8 29.6 + - - -
20A PRO* 4.1 4.4 - - - +
21A LEU* 4.0 23.3 + - + +
25A TYR* 2.9 35.6 + + + -
37A MET 3.0 18.1 + - - +
40A HIS* 1.3 75.7 - - - +
42A LYS* 1.3 59.6 - - + +
43A LYS 3.4 0.2 + - - -
45A HIS* 3.3 6.3 - - - +
46A GLN 3.2 24.9 + - - -
92A TRP* 3.3 33.6 + - + -
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Residues in contact with LYS 42 (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 LEU* 4.4 11.0 - - + +
25A TYR* 3.3 37.9 - - + +
38A GLU* 2.8 31.8 + - + +
41A HIS* 1.3 74.3 - - + +
43A LYS* 1.3 66.6 + - + +
46A GLN* 3.2 18.9 + - - +
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Residues in contact with LYS 43 (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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39A LEU* 2.9 33.5 + - + +
41A HIS 3.3 0.2 - - - -
42A LYS* 1.3 89.5 - - + +
44A HIS* 1.3 57.9 + - + +
46A GLN* 3.8 1.3 - - - +
47A THR* 2.6 39.5 + - - -
186B ASN* 3.5 45.7 - - + +
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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