Contacts of the helix formed by residues 32 - 45 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208S CYS* 4.5 1.1 - - - -
203T ALA 4.6 0.3 + - - -
207T SER* 3.6 32.3 + - - +
30U GLN 3.3 6.2 + - - +
31U TYR* 1.3 76.0 - - - +
33U ALA* 1.3 57.3 + - - +
34U GLU* 3.2 23.8 + - - +
35U GLU* 3.3 15.4 + - - +
36U TYR* 2.7 34.6 + - - +
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Residues in contact with ALA 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205S TYR* 3.5 36.0 - - + +
208S CYS* 3.8 35.6 - - + +
32U THR* 1.3 73.6 - - - +
34U GLU* 1.3 66.2 + - - +
36U TYR* 3.8 1.4 - - - +
37U GLN* 2.9 32.1 + - - +
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Residues in contact with GLU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205S TYR* 4.8 11.2 + - - +
203T ALA* 3.7 23.6 - - + +
206T ASN* 5.3 9.2 - - + +
207T SER* 5.6 0.3 - - - -
32U THR* 3.5 22.1 + - - +
33U ALA* 1.3 86.8 + - - +
35U GLU* 1.3 56.8 + - - +
37U GLN* 3.3 7.4 + - - +
38U ALA* 3.0 28.4 + - - +
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Residues in contact with GLU 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200T VAL* 5.0 3.4 - - + +
203T ALA* 3.8 16.5 + - + +
204T ARG* 3.1 33.3 + - + +
207T SER* 3.7 19.1 + - - -
31U TYR* 3.6 22.4 - - + -
32U THR* 3.3 16.8 + - - +
34U GLU* 1.3 75.7 - - - +
36U TYR* 1.3 66.9 + - - +
38U ALA* 3.4 1.8 + - - +
39U ILE* 2.9 39.6 + - + +
79U PHE 4.9 0.2 - - - +
116U LYS* 3.0 31.0 + - - -
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Residues in contact with TYR 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201S GLU* 3.2 27.8 + - - -
204S ARG* 2.9 49.9 + - + -
205S TYR* 4.6 11.4 - + + -
208S CYS* 3.9 20.9 - - - -
80T GLY* 4.6 2.0 - - - -
81T TYR* 3.4 31.8 - + - -
82T ASN* 3.6 21.3 - - - +
31U TYR* 4.2 13.7 - - + -
32U THR 2.7 25.1 + - - +
33U ALA* 3.8 4.7 - - - +
35U GLU* 1.3 72.1 - - - +
37U GLN* 1.3 62.0 + - + +
40U GLN* 2.9 41.2 + - + +
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Residues in contact with GLN 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201S GLU* 5.3 5.8 - - - +
205S TYR* 3.2 35.8 + - + -
33U ALA 2.9 17.8 + - - +
34U GLU* 3.7 6.1 - - - +
36U TYR* 1.3 82.7 - - + +
38U ALA* 1.3 64.2 + - - +
40U GLN* 3.8 3.5 - - - +
41U LYS* 2.9 61.2 + - + +
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Residues in contact with ALA 38 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199T SER* 4.2 11.2 - - - +
200T VAL* 3.5 37.2 - - + +
203T ALA* 4.3 4.7 - - + -
34U GLU 3.0 17.4 + - - +
35U GLU* 3.7 5.2 - - - +
37U GLN* 1.3 76.4 - - - +
39U ILE* 1.3 57.1 + - - +
41U LYS* 3.5 5.2 + - - +
42U ALA* 2.9 30.5 + - - +
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Residues in contact with ILE 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T TYR* 3.4 33.4 - - + +
200T VAL* 3.7 12.6 - - + -
204T ARG* 4.6 0.2 - - - +
31U TYR* 3.6 37.0 - - + +
35U GLU* 2.9 28.6 + - + +
38U ALA* 1.3 72.0 - - - +
40U GLN* 1.3 60.3 + - - +
42U ALA* 3.3 0.6 + - - -
43U LEU* 2.9 34.7 + - + +
78U MET* 3.6 42.7 - - + +
79U PHE* 4.1 7.6 - - + -
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Residues in contact with GLN 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201S GLU* 3.3 26.6 + - - +
204S ARG* 3.7 2.8 - - - +
76T ASN* 3.5 22.9 + - - +
77T GLU* 4.3 11.6 + - - +
80T GLY* 3.7 5.9 - - - -
81T TYR* 3.7 26.3 + - + +
36U TYR* 2.9 40.0 + - + +
37U GLN* 3.8 4.9 - - - +
39U ILE* 1.3 79.4 - - - +
41U LYS* 1.3 62.2 + - - +
43U LEU* 3.7 9.9 + - - +
44U ARG* 3.8 32.4 + - - +
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Residues in contact with LYS 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201S GLU* 6.3 0.6 - - - +
37U GLN* 2.9 55.3 + - + +
38U ALA* 3.8 4.3 - - - +
40U GLN* 1.3 76.9 - - + +
42U ALA* 1.3 63.8 + - - +
44U ARG* 3.1 43.5 + - - +
45U GLN* 4.1 5.0 + - - +
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Residues in contact with ALA 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197T GLU* 3.3 33.2 - - - +
200T VAL* 4.0 4.5 - - + -
38U ALA 2.9 19.0 + - - +
39U ILE 3.3 1.8 + - - +
41U LYS* 1.3 76.7 - - - +
43U LEU* 1.3 62.1 + - - +
44U ARG 3.2 1.0 + - - -
45U GLN* 3.1 30.6 + - - +
78U MET* 3.8 15.0 - - + -
161U ALA* 3.5 9.4 - - - +
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Residues in contact with LEU 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T TYR* 3.6 32.5 - - + -
39U ILE* 2.9 25.5 + - + +
40U GLN* 4.1 7.2 - - - +
41U LYS 3.2 0.4 - - - -
42U ALA* 1.3 77.1 - - - +
44U ARG* 1.3 57.3 + - - +
45U GLN 3.2 0.2 - - - -
78U MET* 3.6 17.7 - - + -
79U PHE* 4.6 3.4 - - + -
158U PHE* 3.3 32.5 - - + +
159U GLY* 4.0 1.9 - - - +
160U ASN* 3.2 10.2 + - - -
161U ALA* 3.0 34.4 + - + -
162U LEU* 3.9 33.0 - - + +
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Residues in contact with ARG 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196S LEU* 3.9 18.1 - - - +
201S GLU* 4.6 10.5 + - - +
77T GLU* 3.0 44.2 + - - +
40U GLN* 3.8 31.1 + - - +
41U LYS* 3.1 48.0 + - - +
43U LEU* 1.3 77.2 - - + +
45U GLN* 1.3 66.0 + - - +
46U ARG* 3.3 6.9 + - - +
160U ASN* 3.5 20.8 + - - +
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Residues in contact with GLN 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190T LYS 4.9 9.8 - - - +
191T ALA 5.1 0.2 - - - -
192T LYS* 3.8 36.1 + - + +
197T GLU* 2.7 32.6 + - - +
41U LYS 4.4 3.8 - - - +
42U ALA* 3.1 28.4 + - - +
43U LEU 3.2 1.0 - - - -
44U ARG* 1.3 76.1 - - - +
46U ARG* 1.3 61.4 + - - +
160U ASN* 3.5 0.6 - - - -
161U ALA* 3.0 30.7 + - - -
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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