Contacts of the helix formed by residues 33 - 43 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29Y GLN* 3.6 13.5 - - - +
30Y PRO* 5.9 0.7 - - - -
32Y ILE* 1.3 79.9 - - - +
34Y GLN* 1.3 64.3 + - - +
35Y GLN* 3.8 11.6 + - - +
36Y ILE* 3.2 31.7 + - - +
37Y MET* 3.2 19.9 + - - +
182Y LEU* 5.2 0.7 - - - +
183Y GLN* 2.8 23.7 + - - +
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Residues in contact with GLN 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Y TYR* 3.3 25.1 - - + -
26Y ASP* 3.3 25.9 - - + +
29Y GLN* 2.8 22.1 + - - +
32Y ILE 3.8 0.2 + - - -
33Y SER* 1.3 72.3 - - - +
35Y GLN* 1.3 64.8 + - - +
37Y MET* 3.3 2.4 + - - +
38Y GLU* 3.0 54.0 + - - +
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Residues in contact with GLN 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X LEU* 4.2 15.0 - - + +
33Y SER* 4.0 8.9 + - - +
34Y GLN* 1.3 80.6 - - - +
36Y ILE* 1.3 61.6 + - - +
38Y GLU* 3.3 13.5 + - - +
39Y LEU* 3.1 34.9 + - + +
182Y LEU* 3.6 38.3 + - + +
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Residues in contact with ILE 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Y ILE* 3.9 13.7 - - + -
33Y SER* 3.2 24.5 + - - +
35Y GLN* 1.3 74.6 - - - +
37Y MET* 1.3 56.7 + - - +
39Y LEU* 3.2 3.8 + - - +
40Y HIS* 2.7 44.5 + - + +
178Y HIS 3.9 16.3 - - - +
179Y ALA* 3.6 20.0 - - - +
180Y TYR* 3.9 21.1 - - - +
182Y LEU* 3.9 22.9 - - + +
183Y GLN* 3.7 34.8 - - + +
184Y TYR* 5.4 1.3 - - + -
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Residues in contact with MET 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Y LEU* 4.0 9.4 - - + -
23Y TYR* 4.0 13.9 - - + -
25Y TYR* 3.4 33.4 - - + +
28Y LEU* 3.7 29.8 - - + -
32Y ILE* 3.4 31.6 - - + +
33Y SER 3.2 14.2 + - - +
34Y GLN 3.7 1.6 - - - +
36Y ILE* 1.3 76.6 - - - +
38Y GLU* 1.3 57.0 + - - +
40Y HIS* 4.0 5.0 - - - +
41Y HIS* 2.9 34.5 + - - +
91Y PHE* 6.0 0.7 - - - -
92Y TRP* 3.6 36.3 - - + -
95Y LEU* 5.1 1.1 - - + -
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Residues in contact with GLU 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Y TYR* 3.7 32.5 - - + +
34Y GLN* 3.0 51.8 + - - +
35Y GLN* 3.6 14.9 - - - +
36Y ILE 3.2 0.2 - - - -
37Y MET* 1.3 75.6 - - - +
39Y LEU* 1.3 58.3 + - + +
42Y LYS* 2.7 59.1 + - + +
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Residues in contact with LEU 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181X TYR* 3.7 20.2 - - + +
185X LEU* 4.2 24.9 - - + -
186X ASN* 3.6 23.3 - - - +
35Y GLN* 3.1 23.4 + - + +
36Y ILE* 3.9 2.2 - - - +
38Y GLU* 1.3 81.0 - - + +
40Y HIS* 1.3 60.3 + - - +
43Y LYS* 2.9 43.0 + - + +
44Y HIS* 3.0 6.6 + - + -
182Y LEU* 3.5 31.9 - - + -
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Residues in contact with HIS 40 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181X TYR* 5.1 0.2 + - - -
36Y ILE* 2.7 30.5 + - + +
37Y MET* 4.0 4.3 - - - +
39Y LEU* 1.3 73.7 - - - +
41Y HIS* 1.3 57.2 + - - +
44Y HIS* 3.4 11.5 - - + +
45Y HIS* 3.0 27.0 + - - +
88Y HIS* 2.9 16.8 + + - -
91Y PHE* 4.1 11.6 - + - -
92Y TRP* 3.4 22.0 - + + -
174Y ASP* 2.8 20.9 - - - -
178Y HIS* 3.0 16.1 + + - +
179Y ALA* 3.8 20.4 - - + +
2004Y MN 2.0 30.2 + - - -
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Residues in contact with HIS 41 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Y LEU* 3.6 32.1 - - + +
19Y PRO 2.7 29.9 + - - -
20Y PRO* 4.1 3.2 - - - +
21Y LEU* 3.9 26.0 + - + +
25Y TYR* 2.9 33.9 - + + -
37Y MET 2.9 20.5 + - - +
40Y HIS* 1.3 74.8 - - - +
42Y LYS* 1.3 65.1 + - + +
43Y LYS 3.2 1.8 + - - -
45Y HIS* 3.4 5.8 - - - +
46Y GLN 3.3 19.1 + - - -
92Y TRP* 3.4 32.4 + - + -
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Residues in contact with LYS 42 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Y LEU* 4.4 10.3 - - + -
25Y TYR* 3.2 44.1 - - - +
38Y GLU* 2.7 43.2 + - + +
41Y HIS* 1.3 76.5 - - + +
43Y LYS* 1.3 67.2 + - + +
46Y GLN* 3.0 21.2 - - - +
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Residues in contact with LYS 43 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186X ASN* 2.9 44.2 - - + +
39Y LEU* 2.9 28.0 + - + +
42Y LYS* 1.3 90.4 - - + +
44Y HIS* 1.3 61.0 + - - +
45Y HIS 3.5 0.2 - - - -
46Y GLN* 3.4 2.1 + - - +
47Y THR* 2.9 36.7 + - - +
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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