Contacts of the helix formed by residues 34 - 45 (chain A) in PDB entry 1B0P
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 SER 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A TYR 5.9 0.2 - - - -
29A PRO* 3.8 11.9 - - - +
30A ILE 3.2 32.9 + - - +
31A THR* 3.9 4.3 + - - -
32A PRO* 3.4 2.7 - - - -
33A SER* 1.3 77.9 - - - +
35A THR* 1.3 63.3 + - - +
37A GLY* 3.1 14.4 + - - -
38A GLU* 3.2 25.7 + - - +
997A THR* 4.7 3.9 + - - -
1000A GLN* 4.4 3.2 + - - -
1013A PHE* 5.1 0.9 - - - -
1205B ARG* 3.9 25.7 + - - -
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Residues in contact with THR 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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9A ASP* 5.0 1.6 + - - +
11A ASN* 4.0 24.4 + - + -
12A THR* 4.9 0.2 - - + -
32A PRO 4.7 1.0 + - - -
33A SER 3.3 0.8 - - - -
34A SER* 1.3 76.9 - - - +
36A MET* 1.3 59.5 + - - +
38A GLU* 4.1 2.4 - - - +
39A GLU* 2.9 50.6 + - + +
178A HIS* 4.8 6.2 + - - -
1204B ALA 4.2 5.0 + - - -
1205B ARG* 3.3 28.9 + - - +
1206B PRO* 3.7 25.6 - - + +
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Residues in contact with MET 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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11A ASN* 3.1 47.1 - - + +
14A THR* 3.3 26.5 - - - -
15A ALA* 4.0 8.3 - - + +
33A SER* 3.2 17.4 + - - +
34A SER 3.1 1.4 + - - -
35A THR* 1.3 77.5 - - - +
37A GLY* 1.3 57.5 + - - +
39A GLU* 3.9 7.8 - - - +
40A ALA* 3.3 25.6 + - - +
84A PHE* 3.6 31.2 - - + -
110A HIS* 3.8 19.3 - - - +
112A THR* 3.5 19.3 - - + -
171A PHE* 3.9 7.2 - - + -
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Residues in contact with GLY 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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27A ILE* 4.3 8.7 - - - -
33A SER 4.0 2.4 + - - -
34A SER 3.1 6.5 + - - -
36A MET* 1.3 75.0 - - - +
38A GLU* 1.3 65.2 + - - +
39A GLU 3.3 0.4 - - - -
40A ALA* 3.5 2.4 + - - +
41A ASP* 3.1 16.3 + - - +
58A ILE* 4.7 2.3 - - - +
84A PHE* 3.7 23.2 - - - +
1013A PHE* 3.2 23.4 - - - -
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Residues in contact with GLU 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 SER* 3.2 18.9 + - - +
35A THR* 4.1 4.0 - - - +
37A GLY* 1.3 75.9 - - - +
39A GLU* 1.3 58.0 + - + +
41A ASP* 3.2 4.5 + - - +
42A ASP* 2.9 35.1 + - - +
1000A GLN* 2.7 32.7 - - - +
1012A LYS* 3.4 36.7 - - + +
1013A PHE* 3.7 21.7 - - + -
1197B ARG* 5.1 0.3 + - - -
1205B ARG* 3.0 37.4 + - - +
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Residues in contact with GLU 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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11A ASN 3.9 1.2 - - - +
12A THR* 2.9 38.6 - - - +
15A ALA* 3.3 22.3 - - - +
35A THR* 2.9 42.3 + - + +
36A MET* 3.9 2.4 - - - +
38A GLU* 1.3 74.0 - - + +
40A ALA* 1.3 61.4 + - - +
41A ASP 3.0 1.6 - - - -
42A ASP* 3.1 8.5 + - - +
43A TRP* 2.8 58.3 + - + +
1206B PRO* 3.8 7.6 - - + +
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Residues in contact with ALA 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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15A ALA* 5.7 0.9 - - + -
19A TYR* 3.5 19.3 - - + -
36A MET 3.3 16.5 + - - +
37A GLY 3.9 4.5 - - - +
38A GLU 3.4 0.2 - - - -
39A GLU* 1.3 79.5 - - - +
41A ASP* 1.3 63.4 + - - +
43A TRP* 3.4 5.8 + - + -
44A ALA* 3.0 24.6 + - - +
56A LEU* 3.8 24.0 - - + -
58A ILE* 3.7 7.0 - - + +
84A PHE* 4.4 14.8 - - + -
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Residues in contact with ASP 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 GLY 3.1 13.8 + - - +
38A GLU* 3.4 9.2 - - - +
39A GLU 3.0 0.4 - - - -
40A ALA* 1.3 79.5 - - - +
42A ASP* 1.3 63.5 - - - +
44A ALA* 3.2 4.7 + - - +
45A ALA* 3.1 21.3 + - - +
58A ILE* 3.6 30.2 - - + +
1013A PHE* 3.8 41.2 + - + +
1015A ALA* 4.6 12.1 + - - +
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Residues in contact with ASP 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 GLU* 2.9 24.8 + - - +
39A GLU* 3.1 11.3 + - - +
41A ASP* 1.3 79.0 - - - +
43A TRP* 1.3 58.9 + - + +
45A ALA* 3.2 4.6 + - - +
46A GLN* 2.9 42.9 + - - +
1012A LYS* 4.1 20.3 + - - -
1015A ALA* 4.9 7.3 - - - +
1185B SER* 3.8 19.4 + - - +
1186B VAL 6.1 1.0 - - - -
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Residues in contact with TRP 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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12A THR* 4.3 9.9 - - - -
15A ALA* 3.4 39.7 - - + -
16A HIS* 3.7 21.8 - + + -
19A TYR* 3.9 22.0 - + + -
39A GLU* 2.8 48.9 + - + +
40A ALA* 3.9 4.9 - - - +
41A ASP 3.3 0.2 - - - -
42A ASP* 1.3 76.4 - - + +
44A ALA* 1.3 56.3 + - - +
46A GLN* 3.4 30.5 + - - +
47A GLY 3.2 3.8 + - - -
48A ARG* 2.7 79.5 + - + +
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Residues in contact with ALA 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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19A TYR* 3.4 18.1 + - + +
40A ALA 3.0 18.0 + - - +
41A ASP* 3.5 4.0 - - - +
42A ASP 3.2 0.2 - - - -
43A TRP* 1.3 77.7 - - - +
45A ALA* 1.3 61.2 + - - +
47A GLY* 3.4 9.9 + - - -
55A THR* 4.1 12.7 + - - +
56A LEU 3.9 11.0 - - - +
58A ILE* 3.5 22.7 - - + -
1183B ASP* 4.1 4.0 - - - +
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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 ASP* 3.1 12.6 + - - +
42A ASP 3.6 4.0 - - - +
44A ALA* 1.3 74.9 - - - +
46A GLN* 1.4 56.4 + - - +
47A GLY 3.1 4.9 - - - -
1182B ALA 5.2 2.7 - - - +
1183B ASP* 3.0 16.3 - - - +
1184B GLY* 2.9 33.0 + - - +
1185B SER* 3.3 38.1 - - - +
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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