Contacts of the helix formed by residues 30 - 43 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D THR* 4.9 0.9 - - + -
28D ASP 3.9 2.9 - - - -
29D THR* 1.3 71.3 - - - +
31D ASP* 1.3 63.2 + - - +
32D SER 3.4 2.5 - - - -
33D LEU* 3.5 23.2 - - + +
34D LYS* 3.0 21.0 + - - +
57D ARG 4.6 3.6 - - - -
58D VAL* 2.7 31.5 + - + +
60D PRO* 3.7 19.7 - - + -
70D ILE* 4.0 8.1 - - + -
138D LEU* 4.6 4.5 - - + -
142D ALA* 3.5 39.7 - - + -
143D VAL* 3.7 26.7 - - + -
146D ARG* 3.4 45.8 - - - +
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Residues in contact with ASP 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D THR* 3.0 31.7 + - - +
30D PHE* 1.3 69.4 - - - +
32D SER* 1.3 66.4 + - - +
34D LYS* 3.0 26.5 + - - +
35D ASP* 3.2 15.7 + - - +
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Residues in contact with SER 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D PHE 3.4 0.2 - - - -
31D ASP* 1.3 77.6 - - - +
33D LEU* 1.3 65.3 + - - +
34D LYS 3.1 0.5 + - - -
35D ASP* 3.2 10.9 + - - +
36D ARG* 3.0 21.0 + - - +
503D B12 3.0 25.9 + - - -
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 3.4 25.4 + - + +
32D SER* 1.3 78.5 + - - +
34D LYS* 1.3 54.0 + - - +
36D ARG* 3.2 4.1 + - - +
37D LEU* 2.8 67.2 + - + +
57D ARG* 4.0 13.9 - - + +
58D VAL* 3.8 15.9 - - + -
139D SER* 3.7 33.9 - - - +
142D ALA* 4.1 12.6 - - + -
503D B12 3.6 29.1 + - + +
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B GLU* 5.7 2.4 + - - -
356B LEU* 5.8 3.0 - - - +
369B GLU* 4.6 9.4 - - - -
372B ILE* 6.2 2.0 - - - +
373B GLU* 5.8 1.1 - - - +
376B LYS* 5.1 10.7 - - - +
30D PHE 3.0 12.3 + - - +
31D ASP* 3.0 18.2 + - - +
33D LEU* 1.3 74.4 - - - +
35D ASP* 1.3 70.6 + - - +
37D LEU* 3.5 1.9 + - - +
38D ILE* 3.2 40.8 + - + +
54D ILE* 4.1 15.8 - - + +
55D GLU* 3.3 28.4 + - - -
58D VAL* 3.8 18.4 - - + +
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Residues in contact with ASP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLU* 3.0 37.3 - - - +
376B LYS* 5.7 2.6 - - - -
31D ASP* 3.5 16.0 - - - +
32D SER* 3.2 8.4 + - - +
34D LYS* 1.3 81.1 - - - +
36D ARG* 1.3 58.8 + - - +
38D ILE* 3.3 3.8 + - - +
39D LEU* 2.9 29.9 + - - +
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Residues in contact with ARG 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D SER 3.0 13.3 + - - +
33D LEU 3.5 7.2 - - - +
35D ASP* 1.3 76.1 - - - +
37D LEU* 1.3 61.3 + - - +
39D LEU* 3.2 28.8 + - - +
40D GLN* 2.9 43.6 + - + +
207D GLY 3.7 3.4 + - - -
208D GLN* 3.3 41.4 - - - +
503D B12 3.3 99.8 - - + +
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 2.8 52.2 + - + +
34D LYS 3.9 4.3 - - - +
36D ARG* 1.3 72.8 - - - +
38D ILE* 1.3 58.1 + - - +
40D GLN* 3.9 4.4 - - - +
41D GLU* 3.0 30.7 + - - +
46D LEU* 4.2 13.7 - - + +
50D GLU* 5.9 0.2 - - + -
54D ILE* 4.0 24.3 - - + +
57D ARG* 3.5 41.3 - - - +
58D VAL* 4.1 15.0 - - + -
503D B12 4.0 20.9 - - + -
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B LEU* 5.1 1.6 - - + -
369B GLU* 3.9 26.0 - - + +
370B LYS* 3.7 34.4 - - + +
373B GLU* 3.5 32.8 - - + +
34D LYS* 3.2 32.9 + - + +
35D ASP* 3.7 5.2 - - - +
36D ARG 3.2 0.4 - - - -
37D LEU* 1.3 77.2 - - - +
39D LEU* 1.3 63.6 + - - +
41D GLU* 3.3 5.0 + - - +
42D SER* 3.0 22.8 + - - -
54D ILE* 3.9 20.9 - - + -
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ASP 2.9 17.7 + - - +
36D ARG* 3.5 36.1 - - - +
38D ILE* 1.3 76.7 - - - +
40D GLN* 1.3 62.2 + - - +
42D SER* 3.0 14.5 + - - +
43D LEU* 3.0 43.9 + - + +
208D GLN* 4.4 11.0 - - - +
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Residues in contact with GLN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 2.9 37.1 + - + +
37D LEU* 3.9 1.8 - - - +
39D LEU* 1.3 73.7 - - - +
41D GLU* 1.3 60.5 + - - +
43D LEU* 3.3 3.7 + - - +
44D GLY 3.2 3.5 + - - -
45D TYR* 2.8 41.4 + - + +
46D LEU* 3.7 22.1 - - + +
208D GLN* 2.9 37.8 + - - +
209D LEU* 3.0 30.3 + - - +
503D B12 4.0 22.1 - - + +
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B LEU* 3.3 48.4 - - + +
370B LYS* 5.2 2.6 + - - +
37D LEU 3.0 17.2 + - - +
38D ILE 3.7 4.0 - - - +
40D GLN* 1.3 75.8 - - - +
42D SER* 1.3 58.5 + - - +
44D GLY* 2.9 19.5 + - - -
45D TYR 4.9 0.7 - - - +
46D LEU* 3.1 31.0 - - + +
52D PRO* 5.3 5.9 - - - +
54D ILE* 5.0 4.9 - - - +
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Residues in contact with SER 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ASP* 3.0 53.6 + - - +
228B GLU 4.9 1.0 + - - -
370B LYS* 3.9 13.4 - - - +
38D ILE* 3.0 16.1 + - - -
39D LEU* 3.0 19.3 + - - +
41D GLU* 1.3 76.5 - - - +
43D LEU* 1.3 67.1 + - - +
44D GLY 3.2 0.7 + - - -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 3.0 38.9 + - + +
40D GLN* 3.8 6.5 - - - +
41D GLU 3.2 0.2 - - - -
42D SER* 1.3 81.9 - - - +
44D GLY* 1.3 61.6 + - - +
45D TYR* 3.3 36.7 - - + +
208D GLN* 3.6 28.0 - - - +
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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