Contacts of the helix formed by residues 34 - 41 (chain H) in PDB entry 6ALG
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 34 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ARG* 3.1 41.8 + - - +
49G SER* 6.2 2.7 - - - -
32H GLU 3.0 0.8 + - - -
33H ARG* 1.3 76.2 - - - +
35H PHE* 1.3 61.7 + - - +
36H GLY 3.2 6.6 + - - -
37H HIS* 3.7 2.5 + - - -
38H THR* 3.9 2.8 + - - +
199H ASP* 3.1 11.0 + - - -
1081I PRO* 5.4 5.4 - - - -
1083I GLU* 5.1 6.5 - - - -
1084I ASP* 5.5 0.7 - - - -
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Residues in contact with PHE 35 (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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46G ILE* 3.5 29.2 - - + -
49G SER* 4.6 4.7 - - - -
50G SER* 4.2 17.3 - - - -
223G ILE* 3.7 18.8 - - + -
224G LEU* 5.5 1.6 - - + -
227G GLN* 3.7 34.3 - - + +
8H PHE* 4.5 8.7 - + - -
31H LEU* 3.3 29.0 - - + +
32H GLU* 2.8 47.1 + - + +
33H ARG 4.8 3.1 - - - -
34H GLY* 1.3 77.3 - - - +
36H GLY* 1.3 64.5 + - - +
37H HIS 3.3 0.7 - - - -
38H THR* 3.7 19.5 - - + +
39H LEU* 3.6 16.8 + - + +
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Residues in contact with GLY 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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31H LEU* 4.5 5.8 - - - -
34H GLY 3.2 0.4 - - - -
35H PHE* 1.3 79.1 - - - +
37H HIS* 1.3 57.0 + - - +
39H LEU* 4.5 0.2 - - - +
40H GLY* 2.9 25.5 + - - -
187H VAL* 3.7 23.7 - - - +
199H ASP* 2.9 25.5 + - - +
201H LEU* 3.5 12.9 - - - +
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Residues in contact with HIS 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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41G ASN* 5.6 0.3 + - - -
45G ARG* 3.6 32.7 - - - +
34H GLY* 3.7 2.5 + - - -
35H PHE 3.3 0.2 - - - -
36H GLY* 1.3 73.7 - - - +
38H THR* 1.3 60.7 + - - +
39H LEU 3.2 2.0 - - - -
40H GLY 3.8 1.6 - - - +
41H ASN* 3.1 30.7 + - - +
185H TYR* 3.3 33.7 + + - +
187H VAL* 4.0 23.3 - - + +
199H ASP* 5.7 0.9 - - - -
1084I ASP* 4.2 3.8 - - - -
1216I ARG* 3.6 58.0 + - + +
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Residues in contact with THR 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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42G ALA* 3.6 32.2 + - - +
45G ARG* 3.8 23.8 - - + +
46G ILE* 4.2 13.5 - - + +
224G LEU* 4.4 5.6 - - + +
34H GLY 3.9 0.8 + - - +
35H PHE* 3.7 40.8 - - + +
37H HIS* 1.3 78.4 - - - +
39H LEU* 1.3 69.0 + - + +
41H ASN* 5.3 0.4 - - - -
42H ALA* 3.4 20.6 - - - +
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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
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224G LEU* 4.7 9.9 - - + -
227G GLN* 4.6 27.6 - - + +
228G LEU* 3.7 27.8 - - + -
231G PHE* 5.5 5.8 - - + -
11H PRO* 6.3 0.9 - - + -
28H LEU* 5.0 7.6 - - + -
31H LEU* 3.8 24.0 - - + -
35H PHE* 3.6 14.3 + - + +
37H HIS 3.2 0.2 - - - -
38H THR* 1.3 91.3 - - + +
40H GLY* 1.3 59.9 + - - +
41H ASN 3.2 2.2 - - - -
42H ALA* 3.8 4.3 - - + +
43H LEU* 2.9 44.3 + - + +
201H LEU* 4.1 16.3 - - + +
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Residues in contact with GLY 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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36H GLY 2.9 19.9 + - - -
37H HIS 3.7 0.2 + - - -
39H LEU* 1.3 77.8 - - - +
41H ASN* 1.3 56.8 + - - +
43H LEU* 4.4 0.5 - - - +
44H ARG* 3.2 22.3 + - - +
185H TYR* 3.2 36.5 - - - -
201H LEU* 3.9 9.3 - - - +
203H ILE* 4.6 5.6 - - - +
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Residues in contact with ASN 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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37G HIS 5.5 1.0 + - - -
38G THR* 6.0 1.9 - - - +
41G ASN* 3.2 19.9 - - - +
37H HIS 3.1 18.5 + - - +
38H THR* 5.3 0.4 - - - -
40H GLY* 1.3 75.9 - - - +
42H ALA* 1.3 59.5 + - - +
43H LEU 3.2 2.0 - - - -
44H ARG* 2.8 30.2 + - - -
45H ARG* 2.9 37.4 + - - +
185H TYR* 4.1 11.1 - - - +
1216I ARG 4.4 2.9 - - - +
1217I THR* 2.6 37.9 + - - +
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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