Contacts of the helix formed by residues 32 - 45 (chain R) in PDB entry 5XS0
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 THR 32 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208P CYS* 5.0 1.1 - - - -
203Q ALA 4.5 0.2 + - - -
207Q SER* 2.4 37.7 + - - +
30R GLN 3.4 6.3 + - - +
31R TYR* 1.3 78.0 - - - +
33R ALA* 1.3 61.7 + - - +
34R GLU* 3.8 15.8 + - - +
35R GLU* 3.2 14.9 + - - +
36R TYR* 2.8 29.2 + - - +
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Residues in contact with ALA 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205P TYR* 3.3 36.9 - - + +
208P CYS* 3.7 33.4 - - + +
32R THR* 1.3 73.5 - - - +
34R GLU* 1.3 67.6 + - - +
36R TYR* 3.9 0.7 - - - +
37R GLN* 2.9 32.6 + - - +
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Residues in contact with GLU 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205P TYR* 4.6 9.4 + - - +
203Q ALA* 3.6 25.1 - - + +
206Q ASN* 5.0 9.9 - - - +
207Q SER* 4.7 1.0 + - - -
32R THR* 3.8 17.7 + - - +
33R ALA* 1.3 87.1 + - - +
35R GLU* 1.3 56.0 + - - +
37R GLN* 3.3 10.6 + - - +
38R ALA* 2.9 30.3 + - - +
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Residues in contact with GLU 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200Q VAL* 5.0 2.7 - - + +
203Q ALA* 3.7 16.3 + - - +
204Q ARG* 3.2 34.1 + - + +
207Q SER* 3.5 15.6 + - - -
31R TYR* 3.6 20.7 - - + -
32R THR* 3.2 17.0 + - - +
34R GLU* 1.3 75.7 - - - +
36R TYR* 1.3 67.8 + - - +
38R ALA* 3.4 1.5 + - - +
39R ILE* 2.9 38.9 + - + +
79R PHE 4.8 1.0 - - - +
116R LYS* 3.1 35.6 + - - -
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Residues in contact with TYR 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201P GLU* 3.1 27.0 + - - -
204P ARG* 2.6 53.5 + - + -
205P TYR* 4.5 9.9 - - + -
208P CYS* 4.2 20.2 - - - -
80Q GLY* 4.6 1.1 - - - -
81Q TYR* 3.4 31.9 - + - -
82Q ASN* 3.6 23.3 - - - -
31R TYR* 4.1 13.8 - - + +
32R THR 2.8 23.2 + - - +
33R ALA 3.9 3.4 - - - +
35R GLU* 1.3 74.0 - - - +
37R GLN* 1.3 62.3 + - + +
39R ILE* 3.9 0.2 - - - -
40R GLN* 2.9 42.7 + - + +
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Residues in contact with GLN 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201P GLU* 4.8 8.7 - - - +
205P TYR* 3.1 37.8 + - + +
33R ALA 2.9 17.6 + - - +
34R GLU* 3.7 6.3 - - - +
36R TYR* 1.3 83.1 - - - +
38R ALA* 1.3 64.0 + - - +
40R GLN* 3.9 2.0 - - - +
41R LYS* 3.0 59.6 + - + +
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Residues in contact with ALA 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199Q SER* 4.2 10.5 - - - +
200Q VAL* 3.6 35.8 - - + +
203Q ALA* 4.2 8.1 - - + -
34R GLU 2.9 17.0 + - - +
35R GLU* 3.7 4.9 - - - +
37R GLN* 1.3 78.0 - - - +
39R ILE* 1.3 58.5 + - - +
41R LYS* 3.4 5.7 + - - +
42R ALA* 2.9 30.3 + - - +
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Residues in contact with ILE 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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81Q TYR* 3.3 42.2 - - + +
200Q VAL* 3.6 20.4 - - + -
204Q ARG* 4.8 0.4 - - - +
31R TYR* 3.8 17.5 - - + -
35R GLU* 2.9 31.9 + - + +
38R ALA* 1.3 72.6 - - - +
40R GLN* 1.3 60.9 + - - +
42R ALA* 3.9 0.3 - - - +
43R LEU* 2.9 38.4 + - + +
78R MET* 3.7 35.2 - - + +
79R PHE* 4.1 12.1 - - + -
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Residues in contact with GLN 40 (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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201P GLU* 3.6 20.5 + - - +
204P ARG* 3.5 12.3 - - - +
76Q ASN* 3.1 29.1 + - - +
77Q GLU* 4.5 10.3 + - - +
80Q GLY* 3.4 14.3 - - - -
81Q TYR* 3.9 23.1 + - + +
36R TYR* 2.9 33.3 + - + +
37R GLN* 4.0 3.4 - - - +
39R ILE* 1.3 77.1 - - - +
41R LYS* 1.3 64.4 + - + +
43R LEU* 3.6 9.9 + - - +
44R ARG* 3.8 29.1 + - - +
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Residues in contact with LYS 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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201P GLU* 5.8 7.9 + - - +
37R GLN* 3.0 55.2 + - + +
38R ALA* 3.7 4.7 - - - +
40R GLN* 1.3 77.2 - - + +
42R ALA* 1.3 62.7 + - - +
44R ARG* 3.2 43.3 + - - +
45R GLN* 4.1 4.9 + - - +
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Residues in contact with ALA 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197Q GLU* 3.7 25.8 - - - +
200Q VAL* 4.0 4.9 - - + -
38R ALA 2.9 17.5 + - - +
39R ILE 3.3 3.6 + - - +
41R LYS* 1.3 77.3 - - - +
43R LEU* 1.3 61.8 + - - +
45R GLN* 3.1 35.1 + - - +
78R MET* 4.0 19.5 - - + +
161R ALA* 3.6 6.3 - - - +
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Residues in contact with LEU 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81Q TYR* 3.6 31.4 - - + -
39R ILE* 2.9 26.7 + - + +
40R GLN* 4.1 7.6 - - - +
41R LYS 3.3 0.6 - - - -
42R ALA* 1.3 75.8 - - - +
44R ARG* 1.3 58.8 + - - +
45R GLN 3.2 0.2 - - - -
78R MET* 3.6 20.4 - - + -
79R PHE* 4.6 3.6 - - + -
158R PHE* 3.3 32.8 - - + +
159R GLY* 4.0 2.3 - - - -
160R ASN 3.1 9.4 + - - -
161R ALA* 3.0 40.3 + - + -
162R LEU* 4.2 24.9 - - + +
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Residues in contact with ARG 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196P LEU* 3.7 21.5 - - - +
201P GLU* 4.8 9.7 + - - +
77Q GLU* 2.8 47.6 + - - +
40R GLN* 3.8 26.1 + - - +
41R LYS* 3.2 46.0 + - - +
42R ALA 3.1 0.8 - - - -
43R LEU* 1.3 76.6 - - - +
45R GLN* 1.3 66.3 + - - +
46R ARG* 3.3 7.1 + - - +
160R ASN* 3.4 22.0 + - - +
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Residues in contact with GLN 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Q LYS 4.8 10.7 + - - +
192Q LYS* 3.3 35.1 - - + +
197Q GLU* 3.0 31.6 + - - +
41R LYS 4.4 3.3 - - - +
42R ALA* 3.1 25.4 + - - +
44R ARG* 1.3 76.4 - - - +
46R ARG* 1.3 61.0 + - - +
160R ASN* 3.5 0.7 - - - +
161R ALA* 3.1 30.4 + - + -
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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