Contacts of the helix formed by residues 34 - 43 (chain A) in PDB entry 1PG3
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 ASP 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN* 2.8 27.0 + - + +
33A ASN* 1.3 78.2 - - + +
35A PRO* 1.3 61.8 - - - +
36A ASP* 3.6 8.5 + - - +
37A THR* 2.5 42.0 + - - +
38A PHE 3.1 9.0 + - - -
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Residues in contact with PRO 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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30A GLN 3.6 0.6 - - - -
31A SER 3.3 19.7 - - - +
32A ILE 3.6 15.7 - - - +
33A ASN 3.6 2.9 - - - +
34A ASP* 1.3 88.0 - - - +
36A ASP* 1.3 61.5 + - - +
38A PHE* 3.8 2.5 - - + -
39A TRP* 2.8 52.2 + - + +
55A VAL* 4.1 1.5 - - - +
56A LYS* 3.9 30.1 - - + -
69A TRP* 4.7 1.6 - - + -
443A GLY* 6.2 0.2 - - - -
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Residues in contact with ASP 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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34A ASP* 3.1 8.3 + - - +
35A PRO* 1.3 82.6 - - - +
37A THR* 1.3 58.2 + - - +
40A GLY* 3.0 25.5 + - - -
55A VAL* 3.0 21.5 + - + +
56A LYS* 2.9 41.6 + - - +
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Residues in contact with THR 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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30A GLN* 3.6 22.4 - - - +
34A ASP* 2.5 32.9 + - - +
36A ASP* 1.3 76.2 - - - +
38A PHE* 1.3 66.3 + - - +
40A GLY* 3.8 0.3 - - - -
41A GLU* 3.1 48.1 + - + +
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Residues in contact with PHE 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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27A LYS* 3.7 41.3 - - + -
30A GLN* 3.5 24.4 - - - +
31A SER* 3.4 28.5 - - - +
34A ASP 3.1 9.5 + - - +
35A PRO* 4.0 2.2 - - + +
37A THR* 1.3 80.9 - - - +
39A TRP* 1.3 91.2 + + - +
41A GLU* 3.2 4.6 + - - +
42A GLN* 2.9 44.1 + - + +
287A THR* 6.0 0.2 - - + -
291A TYR* 6.0 0.4 - + - -
442A PHE* 3.6 42.0 - + + -
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Residues in contact with TRP 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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31A SER 4.6 1.6 + - - -
35A PRO* 2.8 36.2 + - + +
38A PHE* 1.3 97.2 - + - +
40A GLY* 1.3 60.4 + - - +
42A GLN* 3.8 28.0 - - + -
43A GLY 2.9 15.6 + - - -
55A VAL* 3.7 13.2 - - + -
69A TRP* 3.6 23.8 - + + -
70A TYR* 2.8 35.4 + - - +
283A VAL* 4.3 10.8 - - + -
284A TYR* 3.8 22.4 - + - -
287A THR* 4.4 6.7 - - + -
441A PHE* 4.4 10.5 - + - -
442A PHE 3.4 23.8 - - - -
443A GLY* 3.9 14.1 - - - -
471A PRO* 3.5 29.2 - - + +
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Residues in contact with GLY 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 ASP 3.0 23.8 + - - -
37A THR 3.8 0.7 - - - -
39A TRP* 1.3 77.0 - - - +
41A GLU* 1.3 60.1 + - - +
44A LYS* 3.8 8.1 + - - +
52A TYR* 2.6 31.1 + - - -
55A VAL* 3.8 15.6 - - - +
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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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30A GLN* 4.7 10.2 + - - +
37A THR* 3.1 35.7 + - + +
38A PHE* 3.7 2.8 - - - +
40A GLY* 1.3 77.3 - - - +
42A GLN* 1.3 64.2 + - - +
44A LYS* 3.3 24.1 - - - +
802A EDO 3.5 9.0 - - - -
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Residues in contact with GLN 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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27A LYS* 5.0 6.7 - - - +
38A PHE* 2.9 31.8 + - + +
39A TRP* 3.9 19.7 - - + -
41A GLU* 1.3 73.6 - - - +
43A GLY* 1.3 58.4 + - - +
44A LYS 3.0 9.2 + - - -
45A ILE* 3.2 28.6 + - - +
283A VAL* 4.1 0.8 - - - +
287A THR* 3.3 39.8 + - + +
291A TYR* 3.5 24.0 + - - -
802A EDO 3.3 19.7 + - - -
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Residues in contact with GLY 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 TRP 2.9 15.7 + - - -
41A GLU 3.3 0.8 - - - -
42A GLN* 1.3 71.9 - - - +
44A LYS* 1.3 52.6 + - - +
45A ILE* 3.0 10.6 + - - -
46A LEU* 3.4 7.8 + - - +
48A TRP* 2.7 27.4 + - - -
52A TYR* 3.3 16.8 + - - -
70A TYR* 3.6 15.2 + - - -
283A VAL* 3.8 12.0 - - - +
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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