Contacts of the helix formed by residues 29 - 44 (chain A) 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 VAL 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A HIS* 1.3 80.7 - - + +
30A ASP* 1.3 68.6 + - - +
31A ALA 3.3 0.2 - - - -
32A THR* 3.2 9.9 + - - -
33A TYR* 2.9 23.0 + - + +
51A THR* 5.3 1.1 - - + -
55A THR* 4.4 17.9 - - + +
61A HIS* 4.4 31.6 - - + +
67A VAL* 4.9 20.2 - - + -
69A PHE* 5.0 4.7 - - + -
221A LEU* 4.0 25.8 - - + -
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 3.3 7.2 + - - -
29A VAL* 1.3 81.2 + - - +
31A ALA* 1.3 58.1 + - - +
33A TYR* 3.3 6.6 + - - +
34A ARG* 2.9 58.1 + - - +
221A LEU* 3.7 20.3 - - + +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 4.0 12.4 + - + +
29A VAL 3.3 0.4 - - - -
30A ASP* 1.3 77.8 - - - +
32A THR* 1.3 58.9 + - - +
34A ARG* 3.3 21.2 + - - +
35A LEU* 2.9 39.1 + - + +
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 4.2 14.0 + - - -
29A VAL* 3.2 14.6 + - - -
31A ALA* 1.3 76.9 - - - +
33A TYR* 1.3 63.3 + - - +
35A LEU* 3.2 12.0 + - + +
36A VAL* 2.9 29.5 + - + +
67A VAL* 5.4 7.9 - - + -
69A PHE* 4.5 12.1 - - + -
112A TRP* 6.5 0.4 - - + -
132A ALA 5.5 2.3 + - - -
133A VAL* 5.3 13.0 - - + +
135A PHE* 4.4 27.6 - - + -
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Residues in contact with TYR 33 (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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29A VAL* 2.9 21.9 + - + +
30A ASP* 3.3 8.0 + - - +
32A THR* 1.3 75.7 - - - +
34A ARG* 1.3 66.7 + - + +
36A VAL 3.4 0.3 + - - -
37A LEU* 2.9 47.8 + - + +
49A LEU* 2.8 54.3 + - + +
51A THR* 3.7 24.0 - - - -
69A PHE* 4.0 13.1 - + - -
220A PRO* 3.9 17.0 - - + +
221A LEU* 4.5 19.7 - - + -
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Residues in contact with ARG 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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30A ASP* 2.9 38.4 + - - +
31A ALA* 3.7 25.5 - - - +
33A TYR* 1.3 81.8 - - + +
35A LEU* 1.3 64.1 + - + +
37A LEU* 3.1 10.3 + - + +
38A ASP* 2.9 31.2 + - - +
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Residues in contact with LEU 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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31A ALA* 2.9 27.5 + - + +
32A THR* 3.5 11.2 - - + +
34A ARG* 1.3 77.9 - - - +
36A VAL* 1.3 63.7 + - + +
38A ASP* 3.4 24.9 + - - +
39A CYS* 3.7 12.2 + - - -
109A HIS* 4.7 18.3 + - + +
112A TRP* 4.6 26.9 - - + -
133A VAL* 5.9 4.9 - - + -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 2.9 18.5 + - + +
33A TYR 3.9 2.9 - - - +
35A LEU* 1.3 74.4 - - + +
37A LEU* 1.3 66.7 + - - +
39A CYS* 3.1 11.6 + - + +
40A VAL* 3.0 30.5 + - + +
49A LEU* 4.0 23.1 - - + -
69A PHE* 4.1 18.2 - - + -
101A LEU* 6.3 0.2 - - + -
105A ILE* 6.0 2.0 - - + -
112A TRP* 5.9 2.0 - - + -
135A PHE* 4.0 31.2 - - + -
137A ILE* 4.4 19.3 - - + -
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Residues in contact with LEU 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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33A TYR* 2.9 37.0 + - + +
34A ARG* 3.1 9.8 + - + +
36A VAL* 1.3 76.6 - - - +
38A ASP* 1.3 64.0 + - - +
40A VAL* 4.2 15.3 - - + -
41A ALA* 2.9 29.2 + - + +
47A MET 4.8 8.7 - - - +
48A ARG* 5.6 0.4 - - - -
49A LEU* 4.0 25.3 - - + +
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Residues in contact with ASP 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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34A ARG* 2.9 20.9 + - - +
35A LEU* 3.5 22.0 - - - +
36A VAL 3.1 0.2 - - - -
37A LEU* 1.3 77.9 - - - +
39A CYS* 1.3 58.8 + - - +
41A ALA* 3.3 6.1 + - - +
42A ALA* 2.9 26.3 + - - +
108A LYS* 4.8 15.3 + - + +
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Residues in contact with CYS 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 LEU 3.8 13.5 - - - -
36A VAL* 3.1 10.5 + - + +
38A ASP* 1.3 75.5 - - - +
40A VAL* 1.3 69.4 + - - +
42A ALA* 2.8 20.6 + - - +
43A VAL* 3.0 14.6 + - - +
101A LEU* 4.0 7.9 - - + -
104A VAL* 4.2 6.9 - - + +
105A ILE* 4.0 38.4 - - + -
108A LYS* 4.4 21.8 - - - -
109A HIS* 4.8 10.3 - - - -
112A TRP* 5.9 2.5 - - - -
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Residues in contact with VAL 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 VAL* 3.0 29.4 + - + +
37A LEU* 3.6 16.8 - - + +
39A CYS* 1.3 73.8 - - - +
41A ALA* 1.3 59.3 + - - +
43A VAL* 3.1 6.6 + - - +
44A ASP 2.9 26.2 + - - +
47A MET* 4.0 38.3 - - + +
48A ARG 5.1 3.8 - - - +
49A LEU* 4.5 6.3 - - + -
71A VAL* 4.3 27.1 - - + -
101A LEU* 3.9 18.8 - - + +
137A ILE* 6.2 0.2 - - + -
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Residues in contact with ALA 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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37A LEU* 2.9 23.7 + - + +
38A ASP* 3.6 5.8 - - - +
40A VAL* 1.3 76.7 - - - +
42A ALA* 1.3 63.4 + - - +
44A ASP* 3.1 25.4 + - - -
45A PRO* 3.4 18.5 - - + +
47A MET 6.0 0.2 - - - -
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Residues in contact with ALA 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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38A ASP 2.9 13.4 + - - +
39A CYS* 2.8 13.5 + - - +
41A ALA* 1.3 76.7 - - - +
43A VAL* 1.3 60.3 + - - +
104A VAL* 3.7 24.5 - - + +
108A LYS* 4.6 13.2 - - - +
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Residues in contact with VAL 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 CYS 3.0 11.4 + - - +
40A VAL 3.5 5.6 - - - +
41A ALA 3.7 0.2 - - - -
42A ALA* 1.3 80.5 - - - +
44A ASP* 1.3 61.5 + - + +
45A PRO* 4.8 0.2 - - - +
47A MET* 4.1 9.6 - - + -
97A ILE* 4.0 26.9 - - + -
100A LYS* 4.4 16.8 - - + -
101A LEU* 3.8 35.0 - - + +
104A VAL* 3.8 17.7 - - + -
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Residues in contact with ASP 44 (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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40A VAL 2.9 15.6 + - - +
41A ALA* 3.1 6.6 + - - -
43A VAL* 1.3 82.0 - - + +
45A PRO* 1.3 74.3 - - - +
46A LEU* 2.8 37.6 + - - +
47A MET* 3.4 40.4 + - + +
73A ASN* 5.5 0.5 - - - +
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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