Contacts of the helix formed by residues 35 - 47 (chain R) in PDB entry 1T9G
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 PRO 35 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R LEU 3.5 7.2 - - - +
34R ALA* 1.3 84.2 - - + +
36R ILE* 1.3 53.4 + - + +
37R THR 2.6 14.4 + - - -
38R LEU* 2.7 36.4 + - + +
39R ASN* 2.9 9.5 + - - +
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Residues in contact with ILE 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27R GLU* 3.6 25.6 - - + +
34R ALA* 4.2 12.8 - - + -
35R PRO* 1.3 72.9 - - + +
37R THR* 1.3 52.1 + - - +
39R ASN* 2.8 20.9 + - - +
40R THR* 2.6 29.6 + - - -
111R GLY* 3.6 18.4 - - - -
112R ALA* 4.0 6.3 - - + +
113R SER* 3.9 32.3 - - - +
168R VAL 4.6 0.8 - - - +
170R GLY* 4.4 23.5 - - - +
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Residues in contact with THR 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R VAL* 4.4 9.6 - - + -
25R ILE 4.8 0.8 + - - +
26R ALA* 3.9 18.6 - - + -
27R GLU* 3.3 28.6 + - - +
33R LEU* 3.6 20.6 - - + -
34R ALA 3.0 15.5 + - - -
35R PRO 2.6 5.9 + - - -
36R ILE* 1.3 74.0 - - - +
38R LEU* 1.3 57.9 + - - -
40R THR* 3.2 8.2 + - - -
41R ILE* 3.0 43.8 + - + +
53R CYS* 5.1 0.2 - - - -
67R LEU* 4.7 0.4 - - + -
111R GLY* 5.6 1.4 + - - +
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Residues in contact with LEU 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R LEU* 4.2 20.2 - - + -
35R PRO* 2.7 30.1 + - + +
37R THR* 1.3 67.6 - - - +
39R ASN* 1.3 59.2 + - - +
41R ILE* 2.8 24.7 + - + +
42R THR* 3.0 14.4 + - - -
70R VAL* 4.1 31.6 - - + -
175R ALA* 3.9 15.5 - - + -
176R ALA 3.7 31.7 + - - +
178R THR* 4.5 18.2 - - + -
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Residues in contact with ASN 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R PRO* 2.9 15.8 + - - +
36R ILE* 2.8 38.7 - - - +
38R LEU* 1.3 73.5 - - - +
40R THR* 1.3 61.5 + - - +
41R ILE 3.1 0.9 + - - -
42R THR* 3.3 4.9 + - - -
43R ALA* 3.2 17.8 + - - +
168R VAL* 4.9 2.2 - - + -
169R ARG 5.1 0.9 - - - +
170R GLY* 3.5 31.4 - - - +
173R PHE* 3.6 22.1 - - + +
174R ASP 3.5 11.8 + - - -
175R ALA* 3.9 13.5 + - - +
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Residues in contact with THR 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R VAL* 3.8 15.7 - - + -
36R ILE 2.6 23.2 + - - -
37R THR* 3.2 13.0 + - - -
39R ASN* 1.3 77.2 - - - +
41R ILE* 1.3 57.4 + - - +
43R ALA* 3.4 7.5 - - - +
44R ALA* 2.8 25.7 + - - +
109R CYS* 3.7 26.0 - - + -
110R ALA* 3.9 18.4 - - - +
111R GLY* 3.3 16.7 + - - -
168R VAL* 4.4 12.9 + - + +
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Residues in contact with ILE 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R VAL* 4.2 18.2 - - + -
37R THR* 3.0 33.4 + - + +
38R LEU* 2.8 13.6 + - + +
40R THR* 1.3 75.7 - - - +
42R THR* 1.3 66.7 + - - +
44R ALA* 3.1 7.0 + - - +
45R THR* 2.9 25.0 + - + +
51R VAL* 4.9 2.9 - - + -
53R CYS* 4.8 3.6 - - - -
67R LEU* 4.5 13.7 - - + -
70R VAL* 4.4 8.3 - - + -
71R ALA 4.0 17.3 - - - +
72R GLY* 4.8 4.7 - - - -
73R ILE* 3.4 38.1 - - + -
176R ALA* 4.1 9.0 - - + -
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Residues in contact with THR 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R LEU 3.0 3.4 + - - -
39R ASN 3.4 4.9 - - - -
41R ILE* 1.3 75.4 - - - +
43R ALA* 1.3 62.5 + - - +
45R THR* 2.8 23.8 + - - -
46R ARG* 3.2 44.6 + - - +
173R PHE* 4.0 3.1 - - + -
174R ASP* 2.4 43.1 + - + +
175R ALA 3.8 0.3 - - - -
176R ALA* 3.4 20.4 + - - +
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Residues in contact with ALA 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R ASN 3.2 7.3 + - - +
40R THR 3.4 9.4 - - - +
42R THR* 1.3 79.5 - - - +
44R ALA* 1.3 63.5 + - - +
46R ARG* 3.4 11.0 - - - +
47R LEU* 4.0 3.9 - - - +
109R CYS* 6.0 0.4 - - - -
138R ILE* 3.2 27.1 - - + +
166R PHE* 5.8 0.9 - - + -
168R VAL* 3.8 23.3 - - + -
173R PHE* 3.6 31.4 - - + -
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Residues in contact with ALA 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R THR* 4.3 7.8 + - + -
24R VAL* 4.0 12.3 - - + -
40R THR 2.8 14.8 + - - +
41R ILE* 3.2 15.9 - - - +
42R THR 3.1 0.2 - - - -
43R ALA* 1.3 78.0 - - - +
45R THR* 1.3 57.0 + - - +
47R LEU* 3.2 36.8 + - - +
48R GLY 4.3 1.0 + - - -
49R GLY 5.1 0.9 - - - +
51R VAL* 3.8 30.8 - - + +
109R CYS* 4.6 4.0 - - - -
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Residues in contact with THR 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R ILE* 2.9 13.1 + - + +
42R THR* 2.8 18.4 + - - -
44R ALA* 1.3 68.4 - - - +
46R ARG* 1.3 58.2 + - - +
47R LEU 3.1 1.8 - - - -
48R GLY* 2.9 24.3 + - - +
49R GLY 5.4 1.3 - - - +
51R VAL* 3.9 18.4 - - + -
71R ALA 5.3 0.2 - - - +
72R GLY* 3.7 32.1 - - - +
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Residues in contact with ARG 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R THR* 3.2 33.7 + - - +
43R ALA* 3.4 17.0 - - - +
45R THR* 1.3 75.8 + - - +
47R LEU* 1.3 59.1 + - - +
48R GLY* 3.2 1.6 + - - -
138R ILE* 4.5 20.8 - - + +
141R PRO* 5.8 1.0 - - - +
172R SER 5.5 0.8 + - - -
173R PHE* 3.9 22.9 - - + +
174R ASP* 3.7 20.8 + - - -
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Residues in contact with LEU 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R GLN* 2.9 33.9 - - - +
22R THR* 3.2 30.1 - - + +
43R ALA 4.0 11.0 - - - +
44R ALA* 3.2 16.1 + - - +
45R THR 3.1 1.2 - - - -
46R ARG* 1.3 74.1 - - - +
48R GLY* 1.3 60.3 + - - +
49R GLY 5.1 0.9 - - - +
107R HIS* 3.7 24.2 - - + +
138R ILE* 4.0 22.9 - - + -
140R SER 4.5 0.4 - - - +
141R PRO* 3.7 38.8 - - + +
144R PHE* 4.8 4.9 - - + -
166R PHE* 4.3 10.8 - - + -
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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