Contacts of the helix formed by residues 35 - 47 (chain H) in PDB entry 1GZ0
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 ARG 35 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ILE* 3.0 37.9 - - + +
33H ASP* 2.8 13.1 + - - +
34H LYS* 1.3 77.6 - - + +
36H LEU* 1.3 63.8 + - - +
38H PRO* 3.5 10.4 - - - +
39H LEU* 4.1 12.1 + - - +
68H GLN* 3.1 28.6 - - - +
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Residues in contact with LEU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ILE* 4.0 19.5 - - + -
27H ILE* 5.3 0.7 - - + -
28H LEU* 4.0 24.2 - - + -
33H ASP* 2.6 44.5 + - + +
35H ARG* 1.3 73.1 - - - +
37H LEU* 1.3 55.1 + - + +
39H LEU* 3.1 11.1 + - + +
40H ILE* 2.6 51.5 + - + +
68H GLN 4.0 11.2 - - - +
69H GLY 4.1 9.0 - - - +
70H ILE* 3.9 35.9 - - + -
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H GLU* 4.1 21.5 - - + +
33H ASP* 2.9 51.0 + - + +
34H LYS* 4.0 5.4 - - - +
36H LEU* 1.3 75.1 - - + +
38H PRO* 1.3 73.5 - - + +
40H ILE* 3.0 12.1 + - + +
41H HIS* 3.0 36.3 + - + +
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Residues in contact with PRO 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H LYS 2.9 28.3 - - - +
35H ARG* 3.5 8.5 - - - +
36H LEU 3.5 3.4 - - - -
37H LEU* 1.3 90.4 - - + +
39H LEU* 1.3 60.3 + - - +
41H HIS* 3.6 4.8 + - + +
42H ALA* 3.4 17.5 + - - +
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Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 4.0 26.9 - - + +
11H VAL* 4.1 9.9 - - + -
12H GLN* 3.9 40.2 - - + +
15H LEU* 4.9 4.5 - - + -
35H ARG 4.1 8.5 + - - +
36H LEU* 3.1 13.3 + - + +
38H PRO* 1.3 78.5 - - - +
40H ILE* 1.3 60.7 + - - +
42H ALA* 2.8 29.8 + - - +
43H LEU* 3.1 31.9 + - + -
70H ILE* 4.0 17.9 - - + -
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Residues in contact with ILE 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ILE* 3.7 38.1 - - + -
28H LEU* 5.6 2.7 - - + -
36H LEU* 2.6 41.9 + - + +
37H LEU* 3.0 11.2 + - + +
39H LEU* 1.3 79.2 - - + +
41H HIS* 1.3 59.9 + - + +
43H LEU* 3.3 10.1 + - + +
44H GLU* 3.1 42.8 + - - +
50H ILE* 3.7 16.6 - - + +
70H ILE* 5.0 4.9 - - + -
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Residues in contact with HIS 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H LEU* 3.0 28.1 + - + +
38H PRO* 4.0 5.4 - - + +
40H ILE* 1.3 79.3 - - + +
42H ALA* 1.3 56.7 + - - +
44H GLU* 3.1 31.7 + - + +
45H SER* 2.8 38.6 + - - +
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Residues in contact with ALA 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LEU* 3.5 21.1 - - + +
38H PRO 3.4 11.3 + - - +
39H LEU* 2.8 15.8 + - - +
41H HIS* 1.3 80.3 - - - +
43H LEU* 1.3 57.7 + - - +
45H SER* 3.4 10.7 - - - -
46H GLN* 3.3 21.8 + - - +
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H VAL* 4.6 1.6 - - + -
15H LEU* 3.5 31.9 - - + -
22H PHE* 4.0 20.0 - - + -
25H VAL* 3.8 33.9 - - + -
39H LEU* 3.1 34.4 + - + +
40H ILE* 3.5 9.6 - - + +
41H HIS 3.1 0.2 - - - -
42H ALA* 1.3 73.6 - - - +
44H GLU* 1.3 59.6 + - - +
45H SER 3.1 1.6 - - - -
46H GLN* 2.9 4.6 + - - +
47H GLY 2.9 23.6 + - - -
48H VAL* 2.9 29.1 + - + +
50H ILE* 4.1 12.6 - - + -
70H ILE* 4.4 4.5 - - + -
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Residues in contact with GLU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ILE* 3.1 31.3 + - - +
41H HIS* 3.1 38.9 + - - +
43H LEU* 1.3 79.6 - - - +
45H SER* 1.3 63.6 + - - +
47H GLY* 3.0 13.8 + - - +
48H VAL 4.7 6.1 - - - +
50H ILE* 3.8 13.8 - - + +
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Residues in contact with SER 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H HIS 2.8 21.4 + - - -
42H ALA* 3.4 13.7 - - - -
44H GLU* 1.3 79.0 - - - +
46H GLN* 1.3 61.2 + - - +
47H GLY* 3.3 1.4 + - - -
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Residues in contact with GLN 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LEU* 3.9 20.9 - - + +
19H PRO* 3.8 27.2 - - + +
20H GLU* 5.9 0.2 - - - -
42H ALA 3.3 7.9 + - - +
43H LEU 2.9 8.9 + - - +
45H SER* 1.3 79.7 - - - +
47H GLY* 1.3 61.4 + - - +
48H VAL* 3.7 14.2 + - + +
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Residues in contact with GLY 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LEU 2.9 2.6 + - - -
44H GLU* 3.0 14.6 + - - -
45H SER 3.1 1.8 + - - -
46H GLN* 1.3 80.7 - - - +
48H VAL* 1.3 62.4 + - - +
49H VAL* 3.6 5.4 + - - +
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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