Contacts of the helix formed by residues 30 - 45 (chain A) in PDB entry 4CAA
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 ASN 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A SER* 3.8 10.3 + - - +
29A ALA* 1.3 75.1 - - - +
31A VAL* 1.3 63.1 + - - +
32A ASP 2.9 0.2 + - - -
33A PHE* 3.1 8.8 + - - +
34A ALA* 2.8 24.2 + - - +
54A PRO* 5.2 1.5 - - - +
55A LEU* 4.8 5.0 - - + +
58A SER* 4.6 14.5 + - - +
80A LEU 5.2 1.5 - - - +
82A PHE* 3.8 25.6 - - - -
95A SER* 5.8 1.8 + - - -
96A PHE* 4.2 20.3 - - - -
99A LEU* 4.7 5.1 - - - +
381B ASN* 2.7 34.5 + - + +
382B ILE 5.6 1.1 - - - +
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Residues in contact with VAL 31 (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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28A SER* 3.9 16.7 + - - +
29A ALA 3.5 0.2 - - - -
30A ASN* 1.3 74.2 - - - +
32A ASP* 1.3 62.5 + - - +
34A ALA* 3.5 10.4 - - - +
35A PHE* 3.3 32.5 + - + -
269A PRO* 3.7 30.1 - - + +
272A LEU* 4.9 6.3 - - + -
380B GLN* 3.8 26.0 - - + +
381B ASN* 3.8 26.7 - - - -
382B ILE* 3.9 21.1 - - + -
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 3.5 12.1 - - - +
29A ALA* 2.8 17.4 + - - +
31A VAL* 1.3 78.8 - - - +
33A PHE* 1.3 63.8 + - - +
35A PHE* 3.1 5.0 + - - +
36A SER* 2.9 26.9 + - - -
81A LYS* 3.7 25.6 + - + +
269A PRO* 3.4 26.7 - - + +
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Residues in contact with PHE 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 ALA 2.7 14.1 + - - +
30A ASN* 3.5 9.4 - - - +
32A ASP* 1.3 72.1 - - - +
34A ALA* 1.3 68.8 + - - +
36A SER* 2.9 19.0 + - - -
37A LEU* 3.1 42.0 + - + +
54A PRO* 4.8 4.7 - - + -
57A ILE* 4.3 21.8 - - + -
58A SER* 3.5 22.7 - - - +
61A LEU* 4.4 5.6 - - + -
79A GLY 3.3 24.2 - - - -
80A LEU* 3.5 39.9 - - + +
81A LYS* 4.0 7.3 - - + +
303A LEU* 4.4 5.6 - - + -
306A LEU* 3.8 19.1 - - + -
308A ILE* 5.4 0.7 - - + -
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Residues in contact with ALA 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 ASN 2.8 16.2 + - - +
31A VAL* 3.5 12.8 - - - +
33A PHE* 1.3 81.2 - - - +
35A PHE* 1.3 62.9 + - + +
37A LEU* 3.4 5.4 + - - +
38A TYR* 3.1 21.5 + - - +
52A PHE* 3.7 7.2 - - - -
54A PRO* 3.6 36.1 - - + -
382B ILE* 4.3 12.8 - - + -
385B MET* 5.9 1.3 - - + -
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Residues in contact with PHE 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 VAL* 3.3 18.1 + - + +
32A ASP 3.1 5.1 + - - +
34A ALA* 1.3 77.3 - - - +
36A SER* 1.3 63.8 + - - +
38A TYR* 3.7 3.5 - - + +
39A LYS* 3.4 30.4 + - - +
267A LEU* 3.5 55.2 - - + +
268A LEU 4.1 14.4 - - - -
269A PRO* 3.9 15.0 - - + -
272A LEU* 4.0 25.6 - - + -
275A TRP* 6.3 0.4 - + - -
373B ILE* 4.3 10.8 - - + -
382B ILE* 3.8 21.8 - - + -
385B MET* 3.8 29.8 - - - -
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Residues in contact with SER 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 ASP* 2.9 20.5 + - - -
33A PHE* 2.9 11.6 + - - -
35A PHE* 1.3 80.4 - - - +
37A LEU* 1.3 60.2 - - - +
39A LYS* 3.7 6.3 + - - +
40A GLN* 3.6 23.3 + - - +
81A LYS* 3.0 30.2 + - - -
306A LEU* 4.2 16.0 - - - +
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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 PHE* 3.1 31.5 + - + +
34A ALA* 3.6 8.7 - - - +
35A PHE 3.4 0.2 - - - -
36A SER* 1.3 74.5 - - - +
38A TYR* 1.3 65.9 + - - +
40A GLN* 3.0 5.2 + - - +
41A LEU* 3.0 31.3 + - + +
52A PHE* 3.8 16.8 - - + -
54A PRO* 5.7 0.4 - - + -
57A ILE* 3.6 31.6 - - + -
299A LEU* 4.7 14.4 - - + -
302A ILE* 3.7 20.2 - - + -
303A LEU* 4.4 8.1 - - + -
306A LEU* 3.6 28.5 - - + -
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Residues in contact with TYR 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 ALA 3.1 13.5 + - - +
35A PHE* 3.7 9.6 - - + +
37A LEU* 1.3 78.2 - - - +
39A LYS* 1.3 71.6 + - + +
41A LEU* 3.1 7.8 + - - +
42A VAL* 3.0 38.7 + - + +
50A VAL* 4.0 24.0 - - + -
52A PHE* 4.0 17.9 - + + -
264A GLU* 2.7 34.5 + - + -
267A LEU* 3.7 28.7 - - + -
371B LEU* 3.4 10.3 - - + +
385B MET* 3.8 31.2 - - + -
387B LYS* 3.3 27.4 - - + +
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Residues in contact with LYS 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 PHE* 3.4 16.7 + - - +
36A SER* 4.1 5.6 - - - +
37A LEU 3.3 0.6 - - - -
38A TYR* 1.3 88.0 - - + +
40A GLN* 1.3 64.1 + - - +
42A VAL* 3.5 7.7 - - - +
43A LEU* 3.1 35.5 + - + +
264A GLU* 2.9 29.6 - - + +
265A ALA* 3.1 23.3 + - - -
267A LEU* 2.9 35.5 + - - -
268A LEU* 3.6 11.7 - - - +
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Residues in contact with GLN 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 SER 3.6 14.2 + - - +
37A LEU 3.0 8.5 + - - +
39A LYS* 1.3 75.8 - - - +
41A LEU* 1.3 64.2 + - - +
42A VAL 2.9 4.6 + - - -
43A LEU* 3.0 23.3 + - - +
44A LYS* 2.7 59.2 + - - +
302A ILE* 3.5 28.9 - - + -
305A GLN* 4.1 14.7 - - + +
306A LEU* 4.9 9.6 - - + -
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Residues in contact with LEU 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* 3.0 23.5 + - + +
38A TYR* 3.4 7.2 - - - +
40A GLN* 1.3 75.4 - - - +
42A VAL* 1.3 60.4 + - - +
44A LYS* 3.9 6.5 + - + +
45A ALA* 3.6 19.6 + - - +
50A VAL* 4.2 23.0 - - + +
52A PHE* 3.8 43.5 - - + -
297A TYR* 3.6 41.5 - - + -
299A LEU* 4.6 6.3 - - + -
302A ILE* 3.5 22.7 - - + -
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Residues in contact with VAL 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 TYR* 3.0 50.5 - - + +
39A LYS* 3.5 9.2 - - - +
40A GLN 2.9 0.2 - - - -
41A LEU* 1.3 76.5 - - - +
43A LEU* 1.3 72.5 + - + +
44A LYS 3.1 1.1 - - - -
45A ALA 2.9 4.0 + - - -
46A PRO* 2.9 42.6 - - + +
50A VAL* 4.8 8.3 - - + -
264A GLU* 4.1 22.4 - - + +
387B LYS* 4.5 4.0 - - - +
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Residues in contact with LEU 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 LYS* 3.1 15.9 + - + +
40A GLN* 3.0 33.7 + - - +
42A VAL* 1.3 82.7 - - + +
44A LYS* 1.3 69.5 + - + +
45A ALA 3.1 1.6 + - - -
46A PRO* 3.8 13.2 - - - +
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Residues in contact with LYS 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 GLN* 2.7 60.0 + - - +
41A LEU* 4.0 9.0 - - + +
43A LEU* 1.3 82.9 - - + +
45A ALA* 1.3 61.9 + - + +
46A PRO* 4.2 0.4 - - - -
301A ASP* 5.0 13.5 - - + -
302A ILE* 4.3 20.2 - - + +
305A GLN* 4.3 15.7 + - - +
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Residues in contact with ALA 45 (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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41A LEU 3.6 10.6 + - - +
42A VAL* 2.9 9.3 + - - +
43A LEU 3.1 1.6 + - - -
44A LYS* 1.3 81.7 - - - +
46A PRO* 1.3 68.7 - - - +
47A ASP 3.4 3.6 + - - -
48A LYS* 3.5 30.8 + - + +
50A VAL* 5.5 2.6 - - - +
387B LYS* 5.3 0.3 + - - -
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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