Contacts of the helix formed by residues 36 - 45 (chain A) in PDB entry 4PDG
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 GLY 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.1 13.4 + - - +
34A LEU 3.3 2.0 + - - -
35A THR* 1.3 82.9 + - - +
37A PHE* 1.3 65.5 + - - -
38A GLU 3.5 2.0 - - - -
39A GLN* 3.5 17.9 + - - +
40A LEU* 3.1 21.8 + - - +
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Residues in contact with PHE 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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25A ILE* 3.7 42.8 - - + -
26A GLU* 4.1 0.4 - - - -
27A ALA* 3.4 36.8 - - + -
30A PRO* 3.6 35.6 + - + +
33A VAL* 3.9 24.8 + - + +
36A GLY* 1.3 73.6 - - - -
38A GLU* 1.3 63.5 + - + +
39A GLN* 4.0 0.4 + - - -
40A LEU* 3.1 7.5 + - + +
41A LYS* 2.8 50.3 + - + +
94A LEU* 4.3 4.0 - - + -
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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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36A GLY 3.5 0.2 - - - -
37A PHE* 1.3 82.2 - - + +
39A GLN* 1.3 61.9 + - - +
41A LYS* 3.3 10.8 + - - +
42A LYS* 2.7 37.9 + - - +
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Residues in contact with GLN 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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35A THR 4.0 15.2 + - - +
36A GLY* 3.5 24.8 - - - +
37A PHE 4.0 0.2 + - - -
38A GLU* 1.3 85.3 + - + +
40A LEU* 1.3 56.5 + - - +
42A LYS* 3.7 4.8 - - - +
43A GLU* 2.8 40.8 + - + +
116A LEU* 4.7 3.1 - - + -
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Residues in contact with LEU 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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25A ILE* 3.8 35.2 - - + -
33A VAL* 4.0 16.8 - - + -
36A GLY 3.1 10.3 + - - +
37A PHE* 3.1 14.6 + - + +
39A GLN* 1.3 78.1 - - - +
41A LYS* 1.3 59.6 + - - +
44A LEU* 2.9 50.1 + - + +
69A LEU* 3.7 30.3 - - + -
114A TRP* 3.9 20.0 - - + -
116A LEU* 3.9 25.7 - - + +
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Residues in contact with LYS 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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24A SER* 5.2 4.0 - - - -
25A ILE* 2.6 39.9 + - + +
26A GLU* 4.5 8.3 - - - +
37A PHE* 2.8 46.0 + - + +
38A GLU* 3.5 7.4 - - - +
40A LEU* 1.3 81.4 - - - +
42A LYS* 1.3 62.2 + - - +
45A THR* 2.5 36.7 + - - +
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Residues in contact with LYS 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 2.7 21.9 + - - +
39A GLN* 3.8 6.1 - - - +
41A LYS* 1.3 75.4 - - - +
43A GLU* 1.3 70.3 + - + +
45A THR* 4.4 7.6 + - - +
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Residues in contact with GLU 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 GLN* 2.8 23.4 + - + +
42A LYS* 1.3 85.7 - - + +
44A LEU* 1.3 64.6 + - + +
45A THR 3.6 3.5 + - - +
47A LYS* 3.9 13.2 - - - +
67A PHE* 3.2 41.6 - - + -
116A LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 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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22A ILE* 3.8 14.7 - - + +
25A ILE* 3.8 15.5 - - + -
40A LEU* 2.9 50.2 + - + +
43A GLU* 1.3 75.2 - - - +
45A THR* 1.3 65.8 + - - +
46A GLY 3.2 0.3 + - - -
47A LYS* 3.0 24.0 + - + +
63A ILE* 3.6 39.3 - - + -
67A PHE* 4.1 15.7 - - + -
69A LEU* 4.1 10.3 - - + -
96A MET* 4.7 0.4 - - + -
116A LEU* 3.8 26.0 - - + -
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Residues in contact with THR 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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22A ILE* 4.1 7.6 - - - -
23A ILE 3.4 26.9 - - - +
24A SER* 4.4 2.9 - - - -
25A ILE* 4.5 11.6 + - - +
41A LYS* 2.5 33.4 + - - +
42A LYS* 4.6 5.8 - - - +
43A GLU 3.4 5.2 - - - +
44A LEU* 1.3 76.7 - - - +
46A GLY* 1.3 61.4 + - - +
47A LYS* 3.3 1.3 + - - +
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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