Contacts of the helix formed by residues 34 - 46 (chain B) in PDB entry 2PDA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1205A ARG* 3.6 15.3 + - - -
29B PRO* 3.7 10.4 - - - +
30B ILE 3.0 34.8 + - - +
31B THR* 3.4 6.8 + - - -
32B PRO 3.3 3.0 - - - -
33B SER* 1.3 75.1 - - - +
35B THR* 1.3 67.9 + - - +
37B GLY* 3.3 7.8 + - - -
38B GLU* 2.9 32.2 + - - +
997B THR* 4.5 4.7 + - - +
1000B GLN* 4.5 5.2 - - - -
1013B PHE* 5.3 0.5 - - - -
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204A ALA 4.5 2.8 + - - -
1205A ARG* 3.4 20.5 + - - +
1206A PRO* 3.5 35.0 - - + +
9B ASP* 5.0 0.4 - - - +
11B ASN* 3.6 20.6 + - + +
12B THR* 4.4 4.3 - - + -
32B PRO 4.4 3.1 + - - -
33B SER 3.3 0.2 - - - -
34B SER* 1.3 74.8 - - - +
36B MET* 1.3 55.1 + - - +
38B GLU* 2.5 40.0 + - + +
39B GLU* 2.9 28.0 + - + +
178B HIS* 4.8 4.9 + - - -
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Residues in contact with MET 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASN* 3.4 30.7 - - - +
14B THR* 3.3 27.1 - - - -
15B ALA* 4.0 13.6 - - + +
33B SER* 3.5 9.6 + - - +
34B SER 3.4 0.2 + - - -
35B THR* 1.3 78.2 - - - +
37B GLY* 1.3 58.4 + - - +
39B GLU* 3.3 3.9 + - - +
40B ALA* 2.9 29.6 + - - +
84B PHE* 3.4 44.4 - - + -
110B HIS* 3.8 20.4 - - + +
112B THR* 3.7 28.3 - - + -
171B PHE* 3.9 7.2 - - + -
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 4.0 13.4 - - - +
33B SER 4.1 1.6 + - - -
34B SER 3.3 6.7 + - - -
35B THR 2.8 2.4 + - - -
36B MET* 1.3 78.1 - - - +
38B GLU* 1.3 57.5 + - - +
40B ALA* 3.4 3.5 + - - +
41B ASP* 3.1 20.4 + - - +
84B PHE* 3.7 23.6 - - - +
1013B PHE* 3.3 20.3 - - - -
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197A ARG* 4.8 0.2 + - - -
1205A ARG* 2.7 43.5 + - - +
29B PRO* 6.2 0.4 - - + -
34B SER* 2.9 30.3 - - - +
35B THR* 2.5 13.3 + - - +
37B GLY* 1.3 69.4 - - - -
39B GLU* 1.3 59.3 + - + +
41B ASP* 3.2 3.6 + - - +
42B ASP* 2.8 34.1 + - - +
1000B GLN* 3.4 11.9 - - - +
1012B LYS* 3.3 36.8 - - - +
1013B PHE* 4.0 21.5 - - + -
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206A PRO* 3.5 13.4 - - + +
11B ASN 4.5 0.2 - - - -
12B THR* 2.8 52.0 + - - +
15B ALA* 3.6 9.8 - - + +
35B THR* 2.9 26.6 + - + +
36B MET* 3.8 5.1 - - - +
38B GLU* 1.3 74.0 - - + +
40B ALA* 1.3 68.0 + - - +
41B ASP 2.9 2.0 - - - -
42B ASP* 4.3 7.4 - - - +
43B TRP* 2.9 56.2 + - + +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA* 5.6 2.2 - - + +
19B TYR* 3.1 36.7 - - + -
27B ILE* 4.9 4.0 - - + -
36B MET 2.9 17.7 + - - +
37B GLY* 3.5 10.3 - - - +
39B GLU* 1.3 77.9 - - - +
41B ASP* 1.3 56.3 + - - +
43B TRP* 4.2 4.4 - - - -
44B ALA* 3.1 10.0 + - - +
56B LEU* 4.2 18.4 - - + -
58B ILE* 4.3 4.6 - - + +
84B PHE* 4.2 15.9 - - + -
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Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLY 3.1 13.5 + - - +
38B GLU* 3.4 8.3 - - - +
39B GLU 2.9 1.4 - - - -
40B ALA* 1.3 75.9 - - - +
42B ASP* 1.3 64.9 + - - +
43B TRP 3.2 1.1 - - - -
44B ALA* 3.5 1.4 + - - +
45B ALA* 3.0 26.5 + - - +
58B ILE* 3.5 26.9 - - + +
1012B LYS* 6.2 0.2 - - - -
1013B PHE* 3.5 47.5 + - + -
1015B ALA* 4.6 8.7 - - - +
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1185A SER* 4.1 11.8 + - - +
38B GLU* 2.8 25.0 + - - +
39B GLU* 4.0 5.4 - - - +
41B ASP* 1.3 76.3 - - - +
43B TRP* 1.3 71.1 + - + +
45B ALA* 3.0 8.6 + - - +
46B GLN* 2.9 42.8 + - - +
1012B LYS* 3.6 25.3 + - - -
1015B ALA* 4.8 7.8 - - - +
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Residues in contact with TRP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 4.5 6.1 - - - -
15B ALA* 2.9 48.7 - - + -
16B HIS* 3.7 6.7 - + + -
19B TYR* 3.5 29.2 - + + -
39B GLU* 2.9 44.9 + - + +
40B ALA* 4.2 0.9 - - - -
42B ASP* 1.3 80.0 - - + +
44B ALA* 1.3 68.5 + - - +
46B GLN* 2.8 28.7 + - - +
48B ARG* 3.3 70.0 + - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183A ASP* 5.1 0.7 - - - +
19B TYR* 3.2 22.4 - - + +
40B ALA 3.1 11.3 + - - +
41B ASP 3.8 1.6 - - - +
43B TRP* 1.3 77.6 - - - +
45B ALA* 1.3 58.9 + - - +
46B GLN 3.0 5.2 + - - -
47B GLY* 3.1 14.4 + - - -
48B ARG 4.7 0.2 - - - -
55B THR* 4.2 9.5 - - - +
56B LEU 3.8 10.8 - - - +
58B ILE* 3.4 34.1 - - + -
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183A ASP* 4.0 7.0 - - - -
1184A GLY* 3.2 33.2 + - - +
1185A SER* 3.6 19.3 - - - -
41B ASP* 3.0 15.5 + - - +
42B ASP* 3.0 12.1 + - - +
44B ALA* 1.3 76.5 - - - +
46B GLN* 1.3 56.0 + - - +
47B GLY 3.4 2.0 + - - -
1015B ALA* 5.2 7.4 - - + -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183A ASP* 4.4 3.8 - - - -
1184A GLY* 5.9 0.4 - - - -
1185A SER* 3.5 24.5 + - - +
42B ASP* 2.9 23.1 + - - +
43B TRP* 2.8 21.8 + - - +
45B ALA* 1.3 80.4 - - - +
47B GLY* 1.3 54.6 + - - +
48B ARG* 3.1 12.2 + - + +
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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