Contacts of the helix formed by residues 30 - 43 (chain A) in PDB entry 5D0A
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 PHE 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A THR* 5.1 0.7 - - + -
28A ASP 3.9 2.5 - - - -
29A THR* 1.3 69.3 - - - +
31A ASP* 1.3 64.7 + - - +
32A SER 3.5 2.2 - - - -
33A LEU* 3.3 25.2 + - + +
34A LYS* 3.1 17.3 + - - +
57A ARG 4.7 3.4 - - - -
58A VAL* 2.8 34.8 + - + +
60A PRO* 3.8 20.9 - - + -
70A ILE* 4.0 7.6 - - + -
138A LEU* 4.7 4.5 - - + -
142A ALA* 3.6 36.6 - - + -
143A VAL* 3.9 25.6 - - + -
146A ARG* 3.3 48.9 - - + +
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Residues in contact with ASP 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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29A THR* 2.8 31.1 + - - +
30A PHE* 1.3 71.8 - - - +
32A SER* 1.3 64.2 + - - +
34A LYS* 3.0 27.5 + - - +
35A ASP* 3.3 14.6 + - - +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE 5.3 0.2 - - - -
31A ASP* 1.3 78.1 - - - +
33A LEU* 1.3 62.3 + - - +
35A ASP* 3.3 11.0 + - - +
36A ARG* 3.0 20.8 + - - +
503A B12 3.3 23.8 + - - -
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Residues in contact with LEU 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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30A PHE* 3.3 22.5 + - + +
31A ASP 3.2 0.6 - - - -
32A SER* 1.3 80.1 + - - +
34A LYS* 1.3 54.1 + - - +
36A ARG* 3.0 5.5 + - + +
37A LEU* 2.7 55.9 + - + +
57A ARG* 4.1 10.1 - - + +
58A VAL* 3.9 15.9 - - + -
139A SER* 3.7 29.2 - - - +
142A ALA* 3.9 17.0 - - + -
503A B12 3.4 38.3 + - + +
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Residues in contact with LYS 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 PHE 3.1 11.7 + - - +
31A ASP* 3.0 16.5 + - - +
33A LEU* 1.3 76.3 - - - +
35A ASP* 1.3 67.2 + - - +
37A LEU* 3.4 2.9 + - - +
38A ILE* 3.1 35.9 + - + +
54A ILE* 4.1 14.8 - - + +
55A GLU* 3.0 32.6 + - - -
58A VAL* 3.7 23.8 - - + +
353C GLU* 5.9 1.2 + - - -
356C LEU* 5.3 2.6 - - - +
369C GLU* 3.5 18.8 + - - -
372C ILE* 6.3 1.0 - - - +
373C GLU* 5.5 1.6 - - - +
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 3.3 14.7 + - - +
32A SER* 3.7 9.1 - - - +
33A LEU 3.3 0.4 - - - -
34A LYS* 1.3 80.2 - - - +
36A ARG* 1.3 63.7 + - - +
38A ILE* 3.3 3.6 + - - +
39A LEU* 3.0 23.8 + - - +
373C GLU* 2.8 39.6 - - - +
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Residues in contact with ARG 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 SER 3.0 7.0 + - - +
33A LEU* 3.0 9.9 + - + +
35A ASP* 1.3 77.3 - - - +
37A LEU* 1.3 57.3 + - - +
39A LEU* 3.1 26.8 + - - +
40A GLN* 2.8 47.3 + - + +
207A GLY 3.7 4.0 + - - -
208A GLN* 3.4 41.8 - - - +
503A B12 3.5 102.4 - - + +
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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 LEU* 2.7 43.4 + - + +
34A LYS 3.7 4.0 - - - +
36A ARG* 1.3 70.3 - - - +
38A ILE* 1.3 58.2 + - - +
40A GLN* 3.5 4.7 + - - +
41A GLU* 2.9 31.4 + - - +
46A LEU* 4.0 15.1 - - + +
50A GLU* 5.9 0.2 - - + -
54A ILE* 4.1 22.2 - - + +
57A ARG* 3.5 51.8 - - + +
58A VAL* 4.2 8.5 - - + -
503A B12 3.9 26.2 - - + -
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Residues in contact with ILE 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 LYS* 3.1 28.9 + - + +
35A ASP* 3.7 6.7 - - - +
37A LEU* 1.3 71.5 - - - +
39A LEU* 1.3 68.1 + - - +
41A GLU* 3.2 6.0 + - - +
42A SER* 2.9 24.9 + - - -
54A ILE* 3.8 19.3 - - + -
366C LEU* 5.2 2.5 - - + -
369C GLU* 4.1 30.5 - - + +
370C LYS* 4.2 29.1 - - + +
373C GLU* 3.5 34.1 - - + +
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Residues in contact with LEU 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 ASP 3.0 14.2 + - - +
36A ARG* 3.4 39.9 - - - +
38A ILE* 1.3 77.7 - - - +
40A GLN* 1.3 62.8 + - - +
42A SER* 3.1 13.8 + - - +
43A LEU* 3.0 48.1 + - + +
208A GLN* 4.4 4.9 - - - +
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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 ARG* 2.8 37.0 + - - +
37A LEU* 3.8 2.0 - - - +
39A LEU* 1.3 73.4 - - - +
41A GLU* 1.3 63.7 + - - +
43A LEU* 3.2 5.0 + - - +
44A GLY 3.2 3.3 + - - -
45A TYR* 3.0 40.4 + - + +
46A LEU* 3.7 22.1 - - + +
208A GLN* 3.1 35.1 + - - +
209A LEU 3.0 30.3 + - - +
503A B12 3.9 23.2 - - + +
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Residues in contact with GLU 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 19.5 + - - +
38A ILE 3.6 3.8 - - - +
40A GLN* 1.3 77.4 - - - +
42A SER* 1.3 61.6 + - - +
44A GLY* 3.0 14.4 + - - -
45A TYR 5.0 0.4 - - - +
46A LEU* 3.8 23.7 - - + +
54A ILE* 5.7 0.7 - - + -
366C LEU* 3.2 38.6 - - + +
370C LYS* 3.1 29.2 + - - -
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 2.9 18.9 + - - -
39A LEU* 3.1 20.5 + - - +
41A GLU* 1.3 79.1 + - - +
43A LEU* 1.3 65.4 + - - +
44A GLY 3.5 0.5 + - - -
226C PRO* 6.0 0.2 - - - +
227C ASP* 3.0 51.7 + - - +
228C GLU* 4.7 2.4 + - - +
370C LYS* 4.5 7.4 - - - -
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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 LEU* 3.0 39.3 + - + +
40A GLN* 3.7 6.5 - - - +
41A GLU 3.1 0.6 - - - -
42A SER* 1.3 82.7 + - - +
44A GLY* 1.3 60.3 + - - +
45A TYR* 3.3 37.6 - - + +
208A GLN* 3.6 27.6 - - - +
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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