Contacts of the helix formed by residues 31 - 38 (chain u) in PDB entry 4IL6
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 ASN 31 (chain u).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386b ALA* 5.8 0.7 - - + -
21u TYR* 5.5 1.4 + - - -
29u ASN 3.6 2.6 + - - -
30u THR* 1.3 78.5 - - + +
32u ILE* 1.3 64.6 + - - +
33u ALA* 3.0 36.1 + - - +
34u ALA* 3.1 21.0 + - + +
35u PHE* 4.6 1.9 - - - -
96u ASP 3.0 24.7 + - - +
97u ARG* 3.3 17.8 + - - +
98u TYR 4.0 1.8 + - - -
99u ASN* 3.8 5.1 - - - +
100u ASN* 3.4 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324c LEU* 3.9 37.7 - - + +
30u THR 3.7 0.8 + - - -
31u ASN* 1.3 73.9 - - - +
33u ALA* 1.3 68.3 + - + +
34u ALA 3.1 1.4 + - - -
35u PHE* 3.2 25.7 + - - +
42u TYR* 3.9 10.6 - - + -
46u ALA* 3.6 42.6 - - + +
47u LYS* 3.7 11.0 - - - +
50u VAL* 3.9 12.3 - - + +
97u ARG 2.7 22.2 + - - +
98u TYR* 3.9 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387b GLU* 6.0 1.6 - - - +
31u ASN* 3.0 16.9 + - - +
32u ILE* 1.3 82.1 - - + +
34u ALA* 1.3 61.5 + - - +
35u PHE 3.2 0.2 - - - -
36u ILE* 3.2 31.1 + - + +
37u GLN* 4.7 0.3 + - - +
42u TYR* 4.5 2.7 - - - -
51v SER* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629b DMS 6.2 0.4 - - + -
25u ILE* 3.5 12.9 - - + +
30u THR* 3.6 22.7 - - + -
31u ASN* 3.1 16.1 + - + +
33u ALA* 1.3 79.0 - - - +
35u PHE* 1.3 55.6 + - - +
36u ILE 3.0 6.0 + - - -
37u GLN* 2.8 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25u ILE* 3.6 35.2 - - + -
27u LEU* 4.1 5.8 - - + -
30u THR 4.9 0.9 - - - -
31u ASN 4.6 3.6 - - - -
32u ILE* 3.2 29.3 + - - +
33u ALA 3.2 1.0 - - - -
34u ALA* 1.3 75.0 - - - +
36u ILE* 1.3 61.6 + - - +
37u GLN 3.2 1.1 + - - -
38u TYR 3.5 10.0 + - - +
41u LEU* 3.4 43.3 - - + +
42u TYR* 4.0 5.9 - - + +
46u ALA* 3.8 26.2 - - + -
49u ILE* 3.7 39.5 - - + -
50u VAL* 4.3 20.4 - - + -
82u PHE* 4.0 10.8 - + - -
97u ARG* 4.6 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33u ALA* 3.4 19.5 - - + +
34u ALA 3.0 1.0 - - - -
35u PHE* 1.3 75.1 - - - +
37u GLN* 1.3 64.6 + - - +
38u TYR* 3.2 3.8 + - - -
42u TYR* 3.4 44.2 - - + -
51v SER* 3.3 44.9 - - - +
52v LEU* 4.1 12.6 - - + -
58v THR* 4.7 7.9 - - + -
61v LEU* 4.7 2.6 - - - +
82v TYR* 3.7 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25u ILE* 3.7 20.0 - - - +
33u ALA 5.6 0.4 - - - +
34u ALA* 2.8 37.8 + - - +
35u PHE 3.2 0.2 - - - -
36u ILE* 1.3 77.5 - - - +
38u TYR* 1.3 87.5 + - + +
61v LEU* 3.3 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 38 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24u LYS* 6.1 0.9 - - - -
25u ILE* 3.7 28.8 - - + +
35u PHE 3.5 13.3 + - - +
36u ILE 3.2 5.6 + - - +
37u GLN* 1.3 102.7 + - + +
39u ARG* 1.3 66.4 + - - +
40u GLY 3.5 1.9 + - - -
41u LEU* 3.8 17.5 + - + +
78u ASN* 3.5 20.0 - - - +
81u HIS* 3.4 59.2 + + + +
61v LEU* 4.6 7.4 - - + -
82v TYR* 4.7 4.0 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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