Contacts of the helix formed by residues 30 - 44 (chain B) in PDB entry 5KAL
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 ASP 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B VAL* 1.3 81.0 + - - +
31B ALA* 1.3 66.9 + - - +
33B TYR* 3.0 10.4 + - - +
34B ARG* 2.9 46.2 + - - +
221B LEU* 3.6 22.1 - - + +
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Residues in contact with ALA 31 (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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29B VAL 3.4 3.4 - - - +
30B ASP* 1.3 77.7 - - - +
32B THR* 1.3 58.3 + - - +
34B ARG* 3.4 21.6 + - - +
35B LEU* 2.9 32.5 + - - +
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Residues in contact with THR 32 (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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29B VAL* 3.6 15.6 + - - +
30B ASP 3.2 0.4 - - - -
31B ALA* 1.3 80.3 - - - +
33B TYR* 1.3 61.5 + - - +
35B LEU* 3.3 10.3 + - + +
36B VAL* 2.9 33.6 + - + +
67B VAL* 5.5 8.4 - - + +
69B PHE* 4.5 9.9 - - + -
112B TRP* 6.3 0.7 - - + -
134B ASP 5.7 2.9 - - - +
135B PHE* 3.9 32.8 - - + -
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Residues in contact with TYR 33 (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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29B VAL* 3.3 10.5 + - + +
30B ASP 3.0 9.5 + - - +
32B THR* 1.3 80.0 - - - +
34B ARG* 1.3 67.0 + - + +
36B VAL* 3.5 2.3 + - - +
37B LEU* 2.9 48.4 + - + +
49B LEU* 3.2 46.3 + - + +
51B THR* 3.7 16.6 - - - -
69B PHE* 3.7 28.6 - + + -
220B PRO* 3.8 11.1 - - - +
221B LEU* 4.1 36.1 - - + -
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Residues in contact with ARG 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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30B ASP* 2.9 34.2 + - - +
31B ALA* 3.8 24.8 - - - +
33B TYR* 1.3 83.4 - - + +
35B LEU* 1.3 63.5 + - - +
37B LEU* 3.0 13.3 + - + +
38B ASP* 2.9 29.3 + - - +
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Residues in contact with LEU 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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31B ALA 2.9 18.6 + - - +
32B THR* 3.6 10.1 - - + +
34B ARG* 1.3 77.3 - - - +
36B VAL* 1.3 63.5 + - + +
38B ASP* 3.5 22.5 + - + +
39B CYS* 3.7 12.2 - - - -
109B HIS* 3.6 23.3 - - + +
112B TRP* 3.3 37.2 - - + -
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Residues in contact with VAL 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 THR* 2.9 25.7 + - + +
33B TYR* 3.9 3.1 - - - +
35B LEU* 1.3 74.6 - - + +
37B LEU* 1.3 65.5 + - - +
39B CYS* 3.0 12.9 + - + +
40B VAL* 2.9 33.5 + - + +
49B LEU* 4.2 13.0 - - + -
69B PHE* 4.4 10.8 - - + -
101B LEU* 5.8 1.1 - - + -
105B ILE* 5.9 4.9 - - + -
112B TRP* 5.7 3.4 - - + -
135B PHE* 3.7 39.3 - - + -
137B ILE* 4.5 16.8 - - + -
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Residues in contact with LEU 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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33B TYR* 2.9 40.2 + - + +
34B ARG* 3.0 11.9 + - + +
36B VAL* 1.3 77.5 - - - +
38B ASP* 1.3 64.1 + - - +
40B VAL* 3.3 10.7 + - + +
41B ALA* 2.9 26.3 + - + +
47B MET 5.2 7.0 - - - +
49B LEU* 4.1 26.4 - - + +
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Residues in contact with ASP 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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34B ARG* 2.9 19.4 + - - +
35B LEU* 3.6 16.5 - - + +
36B VAL 3.1 0.2 - - - -
37B LEU* 1.3 78.0 - - - +
39B CYS* 1.3 58.6 + - - +
41B ALA* 3.2 8.3 + - - +
42B ALA* 2.9 26.5 + - - +
108B LYS* 4.3 17.3 + - - +
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Residues in contact with CYS 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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35B LEU 3.7 14.8 - - - -
36B VAL* 3.0 11.7 + - + +
38B ASP* 1.3 75.8 - - - +
40B VAL* 1.3 63.6 + - - +
42B ALA* 2.9 14.9 + - - +
43B VAL* 2.9 16.1 + - - +
101B LEU* 4.0 7.4 - - + -
104B VAL* 4.0 16.1 - - + +
105B ILE* 4.2 30.5 - - + -
108B LYS* 4.1 19.3 - - - -
109B HIS* 4.3 16.8 - - - -
112B TRP* 5.8 2.2 - - - -
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Residues in contact with VAL 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 VAL* 2.9 33.8 + - + +
37B LEU* 3.6 16.8 - - + +
39B CYS* 1.3 74.3 - - - +
41B ALA* 1.3 59.2 + - - +
43B VAL* 3.1 5.7 + - + +
44B ASP* 2.8 29.3 + - - +
47B MET* 4.0 33.0 - - + +
49B LEU* 4.3 18.4 - - + -
71B VAL* 4.7 13.2 - - + -
101B LEU* 3.9 24.9 - - + +
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Residues in contact with ALA 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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37B LEU* 2.9 22.5 + - + +
38B ASP* 3.5 7.4 - - - +
40B VAL* 1.3 75.9 - - - +
42B ALA* 1.3 63.4 + - - +
44B ASP* 3.2 24.3 + - - -
45B PRO* 3.3 19.7 - - + +
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Residues in contact with ALA 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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38B ASP 2.9 12.6 + - - +
39B CYS* 2.9 12.8 + - - +
41B ALA* 1.3 76.9 - - - +
43B VAL* 1.3 61.2 + - - +
104B VAL* 3.8 23.2 - - + +
108B LYS* 4.5 12.3 - - + +
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Residues in contact with VAL 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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39B CYS 2.9 14.1 + - - +
40B VAL* 3.5 6.1 - - + +
42B ALA* 1.3 80.3 - - - +
44B ASP* 1.3 64.2 + - + +
45B PRO* 4.8 1.0 - - - +
47B MET* 6.4 0.2 - - + -
97B ILE* 4.9 14.6 - - + -
100B LYS* 4.3 26.2 - - + +
101B LEU* 3.5 32.1 - - + +
104B VAL* 3.6 24.0 - - + -
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Residues in contact with ASP 44 (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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40B VAL* 2.8 22.1 + - - +
41B ALA* 3.2 5.5 + - - -
43B VAL* 1.3 80.7 - - + +
45B PRO* 1.3 73.9 - - - +
46B LEU* 2.9 24.0 + - - +
47B MET* 3.5 41.9 + - + +
97B ILE* 6.0 1.9 - - + +
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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