Contacts of the helix formed by residues 30 - 41 (chain L) in PDB entry 5OXV
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 30 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222I A 3.4 9.0 - - - +
223I C 3.4 29.6 - - - +
63K ARG* 2.8 40.0 + - - +
27L GLN 4.3 5.4 - - - +
28L GLY* 2.5 23.4 + - - +
29L ILE* 1.3 76.6 - - - +
31L LYS* 1.3 62.5 + - - +
32L PRO* 3.6 15.4 - - - +
33L ALA* 3.5 5.8 + - - +
34L ILE* 3.0 18.8 + - - +
55L ARG* 4.6 2.7 - - - +
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Residues in contact with LYS 31 (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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223I C 3.7 7.5 + - - +
-226J T 6.1 3.7 - - - +
30L THR* 1.3 68.0 - - - +
32L PRO* 1.4 73.2 - - + +
33L ALA 3.2 2.0 - - - -
34L ILE* 3.6 10.7 + - - -
35L ARG* 3.0 42.9 + - - +
51L TYR* 3.5 41.7 - - + -
55L ARG* 4.5 8.2 - - - +
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Residues in contact with PRO 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222I A 3.3 46.9 - - + +
223I C 3.5 14.8 - - - +
30L THR* 3.6 6.3 - - - +
31L LYS* 1.4 95.5 - - + +
33L ALA* 1.3 56.9 + - - +
35L ARG* 2.9 18.6 - - + +
36L ARG* 2.8 35.8 + - - +
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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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61K LEU 3.7 9.4 - - - +
62K ILE* 4.2 18.8 - - + -
63K ARG* 4.3 2.2 - - - +
29L ILE* 5.3 2.2 - - + -
30L THR* 3.5 19.0 + - - +
31L LYS 3.2 0.6 - - - -
32L PRO* 1.3 76.5 - - - +
34L ILE* 1.3 56.1 + - + +
35L ARG 2.4 15.9 + - - -
36L ARG* 2.7 40.1 + - - +
37L LEU* 2.9 17.2 + - - +
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Residues in contact with ILE 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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104K PHE* 3.8 8.3 - - + -
29L ILE* 3.0 43.5 - - + +
30L THR 3.0 15.0 + - - +
31L LYS* 3.8 5.2 - - - +
33L ALA* 1.3 73.5 - - - +
35L ARG* 1.3 59.8 + - - +
37L LEU* 4.3 12.9 - - + +
38L ALA* 3.7 16.3 + - - +
46L ILE* 4.8 1.7 - - - +
50L ILE* 5.1 1.7 - - + +
51L TYR* 3.9 30.9 - - + +
54L THR* 3.5 38.8 - - + +
55L ARG* 3.8 22.0 - - + +
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Residues in contact with ARG 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-227J G 3.8 24.5 + - - +
-226J T 5.5 9.6 + - - +
50K GLU* 4.4 12.9 + - - +
31L LYS* 3.0 30.3 + - - +
32L PRO* 2.9 23.6 - - - +
33L ALA 2.4 12.5 + - - -
34L ILE* 1.3 67.4 - - - +
36L ARG* 1.3 61.5 + - + +
37L LEU 3.2 0.7 - - - -
38L ALA* 2.7 27.7 + - - +
39L ARG* 3.1 51.4 + - + +
46L ILE* 4.3 13.0 - - + +
51L TYR* 2.8 31.2 + - + -
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Residues in contact with ARG 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I A 5.1 2.2 - - - -
222I A 3.1 40.1 + - - -
54K TYR* 3.3 42.0 - - + +
61K LEU* 2.4 55.6 + - + +
62K ILE 4.7 0.2 - - - -
63K ARG* 4.2 10.5 - - - +
32L PRO* 2.8 40.5 + - - +
33L ALA* 2.7 18.7 + - - +
35L ARG* 1.3 73.4 - - + +
37L LEU* 1.3 63.4 + - - +
39L ARG* 3.0 18.4 + - - +
40L ARG 3.2 9.4 + - - -
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Residues in contact with LEU 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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61K LEU* 3.5 14.5 - - + +
62K ILE* 3.8 20.2 - - + -
97K GLU* 3.3 46.0 - - + +
100K LEU* 3.7 28.3 - - + -
101K VAL* 3.6 22.1 - - + +
104K PHE* 3.8 16.8 - - + -
29L ILE* 6.0 0.9 - - + -
33L ALA 2.9 19.4 + - - +
34L ILE* 4.4 12.1 - - + +
36L ARG* 1.3 73.4 - - - +
38L ALA* 1.3 64.3 + - - +
39L ARG 2.9 1.6 + - - -
40L ARG* 3.3 4.3 + - - +
41L GLY* 3.0 16.5 + - - -
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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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104K PHE* 3.4 30.6 - - + -
119K ILE* 5.0 0.9 - - + -
34L ILE 3.7 8.7 + - - +
35L ARG 2.7 17.1 + - - +
37L LEU* 1.3 73.7 - - - +
39L ARG* 1.3 55.6 + - - -
41L GLY 3.2 1.6 + - - -
42L GLY 3.2 4.3 + - - -
43L VAL* 2.9 38.3 + - + +
46L ILE* 3.7 26.0 - - + -
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Residues in contact with ARG 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-227J G 4.8 5.9 + - - -
-226J T 4.9 4.9 + - - -
47K ALA* 3.7 23.1 - - - +
50K GLU* 2.9 39.8 + - + +
51K ILE* 3.5 31.8 - - - +
54K TYR* 4.0 11.4 - - + -
55K GLN* 3.8 0.2 + - - -
35L ARG* 3.1 49.2 + - + +
36L ARG* 3.0 10.0 + - - +
37L LEU 2.9 0.8 + - - -
38L ALA* 1.3 74.3 - - - +
40L ARG* 1.3 59.8 + - - +
41L GLY 2.7 3.8 - - - -
42L GLY* 2.8 16.5 + - - -
43L VAL 2.7 34.2 + - - -
44L LYS* 3.0 28.2 + - - +
46L ILE* 4.4 13.5 - - - +
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Residues in contact with ARG 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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54K TYR* 2.7 28.7 + - + +
55K GLN* 3.3 24.0 + - - -
57K SER* 3.0 34.7 + - - -
58K THR* 3.7 14.3 + - - +
59K GLU* 3.2 27.5 + - - -
60K LEU* 5.0 1.6 - - - +
61K LEU* 3.7 28.8 - - + +
97K GLU* 5.2 1.6 + - - +
101K VAL* 3.4 23.4 - - + +
105K GLU* 4.5 1.9 - - - +
36L ARG 3.2 8.2 + - - +
37L LEU 3.6 7.9 - - - +
39L ARG* 1.3 77.7 - - - +
41L GLY* 1.3 55.8 + - - +
42L GLY 3.3 0.2 - - - -
106Q GLY* 4.8 4.4 - - - -
107Q VAL* 3.4 37.2 - - + +
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Residues in contact with GLY 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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55K GLN* 4.4 1.6 - - - -
101K VAL* 3.8 19.7 - - - -
104K PHE* 4.1 6.8 - - - -
105K GLU* 3.5 29.4 + - - +
108K ASN* 4.5 2.4 + - - +
37L LEU 3.0 11.7 + - - -
38L ALA 3.2 6.5 + - - -
39L ARG 2.7 1.8 - - - -
40L ARG* 1.3 81.8 - - - +
42L GLY* 1.3 59.4 + - - +
43L VAL* 3.3 5.0 + - - +
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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