Contacts of the helix formed by residues 32 - 45 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208R CYS* 5.1 1.6 - - - -
203S ALA 4.3 0.3 + - - -
206S ASN 5.5 0.4 - - - +
207S SER* 3.1 39.8 + - - +
30T GLN 3.4 5.8 + - - +
31T TYR* 1.3 75.6 - - - +
33T ALA* 1.3 58.1 + - - +
34T GLU* 3.7 16.0 + - - +
35T GLU* 3.2 18.9 + - - +
36T TYR* 2.7 34.9 + - - +
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Residues in contact with ALA 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205R TYR* 3.6 35.8 - - + +
208R CYS* 3.7 33.8 - - + +
32T THR* 1.3 72.9 - - - +
34T GLU* 1.3 63.4 + - - +
36T TYR* 3.7 0.9 - - - +
37T GLN* 2.9 32.7 + - - +
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Residues in contact with GLU 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205R TYR* 4.8 11.2 + - - +
203S ALA* 3.6 22.5 - - + +
206S ASN* 5.1 10.0 - - + +
32T THR* 3.7 17.3 + - - +
33T ALA* 1.3 86.3 + - - +
35T GLU* 1.3 55.9 + - - +
37T GLN* 3.9 4.9 - - - +
38T ALA* 2.9 31.2 + - - +
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Residues in contact with GLU 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81S TYR* 4.5 0.2 - - - -
200S VAL* 4.9 2.9 - - + +
203S ALA* 3.6 15.2 - - + +
204S ARG* 3.0 40.1 + - + +
207S SER* 3.0 24.3 + - - -
31T TYR* 3.3 29.5 - - + -
32T THR* 3.2 17.0 + - - +
34T GLU* 1.3 75.7 - - - +
36T TYR* 1.3 67.1 + - - +
38T ALA* 3.5 2.3 + - - +
39T ILE* 2.9 33.9 + - + +
79T PHE 4.9 0.2 - - - +
116T LYS* 3.1 21.4 + - - -
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Residues in contact with TYR 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201R GLU* 3.0 28.3 + - - -
204R ARG* 2.3 55.9 + - + +
205R TYR* 4.3 16.6 - - + -
208R CYS* 3.8 22.4 - - - -
80S GLY* 4.6 1.3 - - - -
81S TYR* 3.4 34.6 + + - +
82S ASN* 3.8 13.0 - - - -
31T TYR* 4.2 10.2 - - + +
32T THR 2.7 21.4 + - - +
33T ALA 3.7 4.9 - - - +
35T GLU* 1.3 73.3 - - - +
37T GLN* 1.3 69.2 + - + +
40T GLN* 2.9 37.6 + - + +
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Residues in contact with GLN 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201R GLU* 4.4 12.6 + - - +
205R TYR* 3.1 35.7 + - + -
33T ALA 2.9 17.6 + - - +
34T GLU* 3.9 4.2 - - - +
36T TYR* 1.3 81.5 - - + +
38T ALA* 1.3 67.2 + - - +
40T GLN* 3.4 3.2 + - - +
41T LYS* 2.9 58.4 + - + +
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Residues in contact with ALA 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199S SER* 4.2 14.1 - - - +
200S VAL* 3.5 36.7 - - + +
203S ALA* 4.5 1.3 - - + -
34T GLU 2.9 17.9 + - - +
35T GLU* 3.8 5.4 - - - +
37T GLN* 1.3 78.0 - - - +
39T ILE* 1.3 57.2 + - - +
41T LYS* 3.8 6.0 - - - +
42T ALA* 2.9 31.0 + - - +
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Residues in contact with ILE 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81S TYR* 3.4 34.1 - - + +
200S VAL* 3.5 20.4 - - + -
204S ARG* 4.3 0.4 - - - +
31T TYR* 3.6 36.6 - - + +
35T GLU* 2.9 28.3 + - + +
38T ALA* 1.3 75.3 - - - +
40T GLN* 1.3 63.7 + - - +
42T ALA* 3.8 0.2 - - - -
43T LEU* 2.9 29.5 + - + +
78T MET* 3.6 36.1 - - + +
79T PHE* 4.1 6.1 - - + -
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Residues in contact with GLN 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201R GLU* 3.8 18.1 + - - +
204R ARG* 3.5 13.5 - - - +
76S ASN* 3.1 27.9 + - - +
77S GLU* 4.6 8.7 + - - +
80S GLY* 3.2 16.6 - - - -
81S TYR* 3.7 24.5 + - + +
36T TYR* 2.9 29.1 + - + +
37T GLN* 3.8 4.5 - - - +
39T ILE* 1.3 80.5 - - - +
41T LYS* 1.3 64.1 + - - +
43T LEU* 3.6 8.9 + - - +
44T ARG* 3.8 30.2 + - - +
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Residues in contact with LYS 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201R GLU* 6.1 3.9 - - - +
37T GLN* 2.9 54.7 + - + +
38T ALA* 3.8 4.7 - - - +
40T GLN* 1.3 77.5 - - - +
42T ALA* 1.3 64.1 + - - +
44T ARG* 3.0 46.6 + - - +
45T GLN* 4.0 5.0 + - - +
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Residues in contact with ALA 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197S GLU* 3.4 30.8 - - - +
200S VAL* 4.0 6.5 - - + -
38T ALA 2.9 19.0 + - - +
39T ILE 3.3 3.3 + - - +
41T LYS* 1.3 76.6 - - - +
43T LEU* 1.3 62.5 + - - +
45T GLN* 3.2 30.0 + - - +
78T MET* 4.0 13.1 - - - +
161T ALA* 3.5 9.3 - - - +
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Residues in contact with LEU 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81S TYR* 3.6 26.2 - - + -
39T ILE* 2.9 31.7 + - + +
40T GLN* 4.1 7.4 - - - +
41T LYS 3.2 0.4 - - - -
42T ALA* 1.3 77.1 - - - +
44T ARG* 1.3 58.2 + - - +
45T GLN 3.3 0.2 - - - -
78T MET* 3.6 17.7 - - + -
79T PHE* 4.5 3.4 - - + -
158T PHE* 3.3 32.5 - - + +
159T GLY* 4.0 1.9 - - - +
160T ASN 3.2 9.2 + - - -
161T ALA* 3.0 35.1 + - + -
162T LEU* 3.9 33.7 - - + +
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Residues in contact with ARG 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196R LEU* 3.7 20.3 - - - +
201R GLU* 4.8 10.5 + - - +
77S GLU* 2.8 49.5 + - - +
40T GLN* 3.8 25.1 + - - +
41T LYS* 3.0 54.1 + - - +
43T LEU* 1.3 77.6 - - - +
45T GLN* 1.3 64.6 + - - +
46T ARG* 3.3 9.7 + - - +
160T ASN* 3.5 22.1 + - - +
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Residues in contact with GLN 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190S LYS 4.3 11.8 - - - +
192S LYS* 3.6 29.1 + - + +
197S GLU* 3.0 34.9 + - - +
41T LYS 4.3 3.4 - - - +
42T ALA* 3.2 27.0 + - - +
44T ARG* 1.3 76.0 - - - +
46T ARG* 1.3 65.8 + - - +
47T LEU* 4.7 0.2 - - - +
160T ASN* 3.7 0.4 - - - -
161T ALA* 3.2 31.7 + - + -
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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