Contacts of the helix formed by residues 33 - 43 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29X GLN* 3.8 12.8 - - - +
30X PRO 5.9 0.4 - - - -
32X ILE* 1.3 79.3 - - - +
34X GLN* 1.3 65.1 - - - +
35X GLN* 3.7 10.5 + - - +
36X ILE* 3.2 32.7 + - - +
37X MET* 3.0 21.8 + - - +
182X LEU* 5.3 0.9 - - - +
183X GLN* 2.9 23.3 + - - +
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Residues in contact with GLN 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X TYR* 3.3 31.8 - - + +
26X ASP* 3.3 23.1 - - + +
29X GLN* 3.0 22.3 + - - +
33X SER* 1.3 71.0 - - - +
35X GLN* 1.3 66.3 + - - +
37X MET* 3.2 1.7 + - - +
38X GLU* 2.9 55.1 + - - +
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Residues in contact with GLN 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X SER* 3.2 8.8 + - - +
34X GLN* 1.3 80.4 - - - +
36X ILE* 1.3 61.4 + - - +
38X GLU* 3.8 12.4 - - - +
39X LEU* 3.1 32.6 + - + +
182X LEU* 3.6 37.8 + - + +
185Y LEU* 4.4 13.7 - - - +
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Residues in contact with ILE 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X ILE* 3.6 18.6 - - + -
33X SER* 3.2 24.5 + - - +
34X GLN 3.2 0.2 - - - -
35X GLN* 1.3 77.3 - - - +
37X MET* 1.3 56.5 - - - +
39X LEU* 3.2 3.5 + - - +
40X HIS* 2.7 45.5 + - + +
178X HIS 4.3 10.5 - - - +
179X ALA* 3.7 19.1 - - - +
180X TYR* 4.1 18.4 - - - -
182X LEU* 4.0 22.7 - - + +
183X GLN* 3.6 36.6 - - + +
184X TYR* 5.3 1.3 - - + -
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Residues in contact with MET 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X LEU* 4.1 18.2 - - + -
23X TYR* 4.1 7.0 - - + -
25X TYR* 3.3 34.8 - - + +
28X LEU* 4.0 27.6 - - + -
32X ILE* 3.3 31.2 - - + +
33X SER 3.0 18.1 + - - +
34X GLN 3.6 1.6 - - - +
36X ILE* 1.3 78.3 - - - +
38X GLU* 1.3 57.9 + - - +
40X HIS* 3.9 3.3 - - - +
41X HIS* 2.9 35.5 + - - +
91X PHE* 6.1 0.2 - - - -
92X TRP* 3.7 36.3 - - + -
95X LEU* 5.2 0.2 - - + -
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Residues in contact with GLU 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X TYR* 3.6 31.8 - - + +
34X GLN* 2.9 49.1 + - - +
35X GLN* 3.8 12.9 - - - +
37X MET* 1.3 75.0 - - - +
39X LEU* 1.3 58.8 + - + +
42X LYS* 2.8 52.9 + - - +
43X LYS* 4.5 1.2 - - - +
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Residues in contact with LEU 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X GLN* 3.1 23.1 + - + +
36X ILE* 3.8 2.9 - - - +
38X GLU* 1.3 77.6 - - + +
40X HIS* 1.3 61.7 + - - +
43X LYS* 2.8 52.6 + - + +
44X HIS* 3.1 6.0 + - + -
182X LEU* 3.4 32.1 - - + -
181Y TYR* 3.8 19.5 - - - +
185Y LEU* 3.9 22.4 - - + -
186Y ASN* 3.6 24.5 - - - +
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Residues in contact with HIS 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X ILE* 2.7 30.2 + - + +
37X MET* 3.9 4.3 - - - +
39X LEU* 1.3 73.6 - - - +
41X HIS* 1.3 56.6 + - - +
44X HIS* 3.3 13.8 - - + +
45X HIS* 2.9 28.1 + - - +
88X HIS* 3.0 10.0 + + - -
91X PHE* 4.0 13.2 - + - -
92X TRP* 3.5 24.6 - + + -
174X ASP* 2.9 16.4 - - - -
178X HIS* 3.0 16.7 + + - +
179X ALA* 3.7 24.3 - - + -
2003X MN 2.2 30.7 + - - -
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Residues in contact with HIS 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X LEU* 3.5 33.3 - - + +
19X PRO 2.7 29.7 + - - -
20X PRO* 4.1 3.6 - - - +
21X LEU* 3.9 25.6 + - + +
25X TYR* 2.9 34.7 + + + -
37X MET 2.9 18.6 + - - +
40X HIS* 1.3 76.3 - - - +
42X LYS* 1.3 65.3 + - + +
45X HIS* 3.3 19.0 - - - +
46X GLN 3.4 6.2 + - - -
92X TRP* 3.5 35.1 + + + -
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Residues in contact with LYS 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X LEU* 4.5 9.0 - - + -
25X TYR* 3.3 31.6 - - + +
38X GLU* 2.8 43.8 + - - +
41X HIS* 1.3 78.4 - - + +
43X LYS* 1.3 79.2 + - + +
46X GLN* 3.1 20.6 - - - +
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Residues in contact with LYS 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X GLU 4.5 0.8 + - - +
39X LEU* 2.8 39.0 + - + +
42X LYS* 1.3 102.3 - - + +
44X HIS* 1.3 60.4 + - + +
45X HIS 3.5 0.2 - - - -
46X GLN* 3.3 2.9 + - - +
47X THR* 2.9 34.9 + - - -
186Y ASN* 3.2 43.3 - - + +
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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