Contacts of the helix formed by residues 32 - 44 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30L GLN 3.3 5.7 + - - +
31L TYR* 1.3 74.5 - - - +
33L ALA* 1.3 57.4 + - - +
34L GLU* 3.3 25.2 + - - +
35L GLU* 3.2 16.2 + - - +
36L TYR* 2.8 33.0 + - - +
208U CYS* 5.4 0.7 - - - -
207V SER* 3.2 36.7 + - - +
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Residues in contact with ALA 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L TYR 3.9 0.6 + - - -
32L THR* 1.3 73.6 - - - +
34L GLU* 1.3 70.7 + - + +
36L TYR* 3.8 0.7 - - - +
37L GLN 2.9 19.2 + - - -
205U TYR* 3.1 42.0 - - + +
208U CYS* 4.0 32.4 - - + +
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Residues in contact with GLU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L THR* 3.3 26.4 + - - +
33L ALA* 1.3 84.4 + - + +
35L GLU* 1.3 55.6 + - - +
37L GLN* 3.8 4.1 + - - +
38L ALA* 2.9 30.3 + - - +
205U TYR* 4.6 12.6 - - - +
203V ALA* 3.5 26.5 - - + +
206V ASN* 4.6 13.6 - - + +
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Residues in contact with GLU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L TYR* 3.5 29.6 - - + -
32L THR* 3.2 15.4 + - - +
34L GLU* 1.3 76.5 - - - +
36L TYR* 1.3 66.1 + - - +
38L ALA* 3.4 2.5 + - - +
39L ILE* 2.9 36.5 + - + +
79L PHE 4.7 0.9 - - - +
116L LYS* 3.0 27.3 + - - -
81V TYR* 4.5 0.2 - - - -
200V VAL* 5.0 2.9 - - + +
203V ALA* 3.5 15.2 - - + +
204V ARG* 3.2 31.5 + - + +
207V SER* 3.3 21.3 + - - -
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Residues in contact with TYR 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L TYR* 4.3 12.9 - - + +
32L THR 2.8 21.4 + - - +
33L ALA* 3.8 6.5 - - - +
35L GLU* 1.3 74.5 - - - +
37L GLN* 1.3 62.5 + - + +
40L GLN* 2.9 40.5 + - + +
201U GLU* 3.1 26.8 + - - -
204U ARG* 2.3 57.0 + - + -
205U TYR* 4.5 9.6 - + - -
208U CYS* 4.1 20.6 - - - -
80V GLY* 4.5 2.5 - - - -
81V TYR* 3.4 33.2 - + - -
82V ASN* 3.7 17.0 - - - +
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Residues in contact with GLN 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ALA 2.9 18.1 + - - +
34L GLU* 3.8 4.6 + - - +
36L TYR* 1.3 84.0 - - + +
38L ALA* 1.3 65.8 + - - +
40L GLN* 3.8 2.5 - - - +
41L LYS* 2.9 54.0 + - + +
201U GLU* 4.4 10.5 - - - +
205U TYR* 3.7 40.2 + - + +
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Residues in contact with ALA 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L GLU 2.9 17.5 + - - +
35L GLU 3.8 4.5 - - - +
37L GLN* 1.3 77.6 - - - +
39L ILE* 1.3 58.4 + - - +
41L LYS* 3.8 5.1 - - - +
42L ALA* 2.9 30.1 + - - +
199V SER* 4.0 15.5 - - - +
200V VAL* 3.6 35.8 - - + +
203V ALA* 4.4 3.1 - - + -
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Residues in contact with ILE 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L TYR* 3.7 25.4 - - + +
35L GLU* 2.9 29.2 + - + +
38L ALA* 1.3 75.5 - - - +
40L GLN* 1.3 58.0 + - - +
43L LEU* 2.9 39.5 + - + +
78L MET* 3.4 44.1 - - + +
79L PHE* 4.1 8.3 - - + -
81V TYR* 3.4 39.7 - - + +
200V VAL* 3.5 14.1 - - + -
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Residues in contact with GLN 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L TYR* 2.9 39.5 + - + +
37L GLN* 3.8 4.3 - - - +
39L ILE* 1.3 79.5 - - - +
41L LYS* 1.3 63.3 + - + +
43L LEU* 3.7 8.9 + - - +
44L ARG* 3.8 30.5 + - - +
201U GLU* 3.8 18.0 + - - +
204U ARG* 3.6 6.1 - - - +
76V ASN* 3.2 28.4 + - - +
77V GLU* 4.6 8.6 + - - +
80V GLY* 3.3 15.5 - - - -
81V TYR* 3.7 24.5 + - + +
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Residues in contact with LYS 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L GLN* 2.9 50.9 + - + +
38L ALA* 3.8 4.5 - - - +
40L GLN* 1.3 77.9 - - + +
42L ALA* 1.3 63.3 + - - +
44L ARG* 3.2 43.4 + - - +
45L GLN* 4.1 4.7 + - - +
201U GLU* 5.6 7.6 - - - +
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Residues in contact with ALA 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ALA 2.9 18.5 + - - +
41L LYS* 1.3 76.4 - - - +
43L LEU* 1.3 62.6 + - - +
45L GLN* 2.9 34.5 + - - +
78L MET* 3.9 18.3 - - + +
161L ALA* 3.7 5.6 - - - +
197V GLU* 3.4 32.8 - - - +
200V VAL* 4.0 3.6 - - + -
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Residues in contact with LEU 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ILE* 2.9 32.7 + - + +
40L GLN* 4.2 7.0 - - - +
41L LYS 3.3 0.6 - - - -
42L ALA* 1.3 74.1 - - - +
44L ARG* 1.3 61.1 + - - +
45L GLN 3.2 0.2 - - - -
78L MET* 3.5 19.7 - - + -
79L PHE* 4.4 3.4 - - + -
158L PHE* 3.3 33.0 - - + +
159L GLY* 4.5 1.3 - - - -
160L ASN 3.1 8.7 + - - -
161L ALA* 2.9 37.1 + - + -
162L LEU* 4.0 33.4 - - + +
81V TYR* 3.7 23.8 - - + -
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Residues in contact with ARG 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L GLN* 3.8 28.7 + - - +
41L LYS* 3.2 47.8 + - - +
43L LEU* 1.3 77.4 - - - +
45L GLN* 1.3 65.1 + - - +
46L ARG* 3.3 6.9 + - - +
160L ASN* 3.5 21.3 - - - +
196U LEU* 3.8 19.2 - - - +
201U GLU* 4.7 10.5 + - - +
77V GLU* 2.6 51.5 + - - +
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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