Contacts of the helix formed by residues 35 - 43 (chain A) in PDB entry 4GAT
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 ALA 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A CYS* 3.8 3.1 - - - -
34A ASN* 1.3 85.1 + - - +
36A CYS* 1.3 58.4 + - - +
38A LEU* 4.3 5.6 - - - -
39A PHE* 2.6 39.0 + - - +
52A LYS* 6.2 4.0 - - + -
119C T 4.2 33.9 - - + +
120C A 3.6 15.7 + - - +
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Residues in contact with CYS 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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12A CYS* 3.7 10.1 - - - -
14A ASN* 3.9 17.9 - - + +
15A CYS* 3.8 14.8 - - - -
32A LEU* 4.2 8.5 - - + -
33A CYS* 3.7 2.8 - - - -
34A ASN 3.4 1.0 - - - -
35A ALA* 1.3 77.3 - - - +
37A GLY* 1.3 60.9 + - - +
39A PHE* 4.8 2.0 - - - -
40A LEU* 2.8 37.3 + - - +
49A LEU* 5.2 7.9 - - - -
52A LYS* 5.8 1.6 - - - -
67A ZN 2.3 36.3 - - - -
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Residues in contact with GLY 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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24A ARG* 3.9 20.0 - - - -
25A ARG 5.0 2.5 - - - -
32A LEU* 3.6 24.9 - - - +
33A CYS 4.0 1.6 + - - -
34A ASN 3.7 2.4 + - - -
35A ALA 3.4 0.2 - - - -
36A CYS* 1.3 79.8 - - - +
38A LEU* 1.3 62.9 + - - +
40A LEU* 5.0 0.4 - - - -
41A LYS* 3.1 29.3 + - - +
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Residues in contact with LEU 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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24A ARG* 3.6 34.8 - - - +
34A ASN* 3.0 31.8 + - + +
35A ALA* 3.8 5.6 - - - +
37A GLY* 1.3 78.9 - - - +
39A PHE* 1.3 60.0 + - - +
41A LYS* 4.4 1.7 - - - +
42A LEU* 3.0 37.3 + - + +
105B G 5.3 0.2 - - + -
106B A 3.1 32.5 - - + +
119C T 4.7 8.5 - - + -
120C A 3.2 39.3 - - + +
121C T 4.3 1.3 - - + +
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Residues in contact with PHE 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 ALA 2.6 22.5 + - - +
36A CYS* 4.2 1.6 - - - +
38A LEU* 1.3 74.4 - - - +
40A LEU* 1.3 65.1 + - + +
42A LEU 3.2 0.3 + - - -
43A HIS* 2.7 93.9 + + + -
45A VAL* 4.9 2.9 - - + -
47A ARG* 2.6 55.4 - - + -
118C C 3.6 21.3 - - - -
119C T 3.1 35.4 - - + +
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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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14A ASN* 4.2 18.6 - - - +
26A ASN* 3.4 29.4 - - - +
32A LEU* 4.8 3.1 - - + -
36A CYS* 2.8 23.3 + - - +
37A GLY* 4.7 1.1 - - - +
39A PHE* 1.3 79.1 - - + +
41A LYS* 1.3 56.2 + - - +
44A GLY* 2.6 38.1 + - - +
45A VAL 4.1 24.7 - - - +
46A VAL* 5.1 4.5 - - - -
47A ARG* 5.7 3.4 - - + +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PRO* 5.8 15.9 - - + -
37A GLY 3.1 20.5 + - - +
38A LEU* 4.4 1.8 - - - +
39A PHE 3.2 0.2 - - - -
40A LEU* 1.3 82.8 - - - +
42A LEU* 1.3 68.7 + - + +
43A HIS 4.5 0.2 - - - -
44A GLY* 4.0 4.5 + - - -
105B G 5.7 7.0 - - - +
106B A 4.0 20.0 + - - +
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Residues in contact with LEU 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 LEU* 3.0 32.9 + - + +
39A PHE 3.2 1.8 + - - -
41A LYS* 1.3 87.1 - - + +
43A HIS* 1.3 74.2 + - + +
106B A 5.8 5.4 - - + +
107B T 4.4 28.0 - - + +
108B A 5.8 0.2 - - - +
119C T 4.2 26.0 - - + +
120C A 5.2 0.4 - - - +
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Residues in contact with HIS 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 PHE* 2.7 80.7 + + + +
40A LEU* 4.5 0.4 - - - +
42A LEU* 1.3 87.2 - - + +
44A GLY* 1.3 65.2 + - - +
45A VAL* 3.2 22.7 + - + +
47A ARG* 5.0 2.9 - - - -
118C C 2.9 28.8 + + - -
119C T 4.6 8.3 - - + -
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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