Contacts of the helix formed by residues 34 - 43 (chain B) in PDB entry 1PG4
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLN* 2.8 29.2 + - + +
33B ASN* 1.3 77.6 - - + +
35B PRO* 1.3 63.3 - - - +
36B ASP* 3.6 8.7 + - - +
37B THR* 2.6 39.3 + - - +
38B PHE* 3.0 15.2 + - - +
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Residues in contact with PRO 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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31B SER 3.5 18.1 - - - +
32B ILE 3.6 15.3 - - - +
33B ASN 3.7 3.4 - - - +
34B ASP* 1.3 88.5 - - - +
36B ASP* 1.3 60.6 + - + +
38B PHE* 4.3 2.0 - - + -
39B TRP* 2.7 49.7 + - + +
55B VAL* 4.8 1.6 - - - -
56B LYS* 3.6 33.9 - - + -
69B TRP* 4.6 2.0 - - + -
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Residues in contact with ASP 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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34B ASP* 3.3 7.9 + - - +
35B PRO* 1.3 80.3 - - - +
37B THR* 1.3 59.3 + - - +
40B GLY* 2.8 28.1 + - - -
55B VAL* 3.6 19.5 - - + +
56B LYS* 2.9 42.2 + - - +
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Residues in contact with THR 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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30B GLN* 3.5 19.3 - - - +
34B ASP* 2.6 32.1 + - - +
36B ASP* 1.3 76.1 - - - +
38B PHE* 1.3 67.1 + - - +
40B GLY* 3.9 0.8 - - - -
41B GLU* 3.1 42.4 + - + +
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Residues in contact with PHE 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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27B LYS* 3.7 35.9 - - + -
30B GLN* 3.5 28.2 + - - +
31B SER* 3.6 21.3 - - - -
34B ASP 3.0 17.2 + - - +
35B PRO* 3.9 2.2 - - + +
37B THR* 1.3 79.7 - - - +
39B TRP* 1.3 94.1 + + - +
41B GLU* 3.7 5.6 - - - +
42B GLN* 3.0 39.3 + - + +
287B THR* 6.0 0.9 - - + -
291B TYR* 6.4 0.4 - + - -
442B PHE* 3.6 37.9 - + + -
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Residues in contact with TRP 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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31B SER 4.6 1.6 + - - -
35B PRO* 2.7 34.2 + - + +
38B PHE* 1.3 94.7 - + - +
40B GLY* 1.3 60.3 + - - +
41B GLU 3.1 1.6 - - - -
42B GLN* 3.8 28.5 - - + +
43B GLY 2.9 16.5 + - - -
55B VAL* 3.7 12.1 - - + -
69B TRP* 3.6 24.3 - + + -
70B TYR* 2.8 38.6 + - - +
283B VAL* 4.2 10.5 - - + -
284B TYR* 3.7 24.0 - + - -
287B THR* 4.3 13.2 - - + -
441B PHE* 4.6 2.9 - + - -
442B PHE 3.4 22.7 - - - -
443B GLY* 4.0 14.3 - - - -
471B PRO* 3.5 25.8 - - + +
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Residues in contact with GLY 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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36B ASP 2.8 22.3 + - - -
37B THR* 3.9 1.1 - - - -
39B TRP* 1.3 76.2 - - - +
41B GLU* 1.3 59.3 + - - +
44B LYS* 3.9 9.4 - - - -
52B TYR* 2.6 30.6 + - - -
55B VAL* 3.8 16.7 - - - +
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Residues in contact with GLU 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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30B GLN* 4.4 10.6 + - - +
37B THR* 3.1 33.6 + - + +
38B PHE* 3.7 3.8 - - - +
39B TRP 3.1 0.2 - - - -
40B GLY* 1.3 76.3 - - - +
42B GLN* 1.3 63.3 + - - +
43B GLY 3.1 1.6 - - - -
44B LYS* 3.1 26.7 + - - +
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Residues in contact with GLN 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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38B PHE* 3.0 30.1 + - + +
39B TRP* 3.8 25.4 - - + -
41B GLU* 1.3 72.8 - - - +
43B GLY* 1.3 60.8 + - - +
44B LYS 3.0 6.6 + - - -
45B ILE* 3.0 36.2 + - - +
283B VAL* 4.4 0.9 - - + -
287B THR* 3.0 38.9 + - + +
291B TYR* 3.9 24.8 + - - -
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Residues in contact with GLY 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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39B TRP 2.9 15.1 + - - -
41B GLU 3.1 1.0 - - - -
42B GLN* 1.3 76.5 - - - +
44B LYS* 1.3 57.0 + - - +
45B ILE* 3.0 7.3 + - - +
46B LEU* 3.2 7.8 + - - +
48B TRP* 3.0 21.8 + - - -
52B TYR* 3.4 18.6 + - - -
70B TYR* 3.6 15.0 + - - -
283B VAL* 3.9 11.4 - - - +
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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