Contacts of the helix formed by residues 97 - 105 (chain D) in PDB entry 1SL0
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 GLY 97 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D SER* 2.7 4.9 + - - -
96D LYS* 1.3 81.2 - - - +
98D GLN* 1.3 62.4 + - - +
99D LEU 3.2 1.3 - - - -
100D LYS* 3.3 7.8 + - - +
101D GLU* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C VAL* 3.6 11.2 - - + +
322C ALA 3.0 27.7 + - - +
324C ALA* 5.1 3.8 + - - +
93D ALA 4.2 3.1 - - - +
94D LEU* 3.8 15.9 - - + +
95D SER* 2.6 45.3 + - - +
97D GLY* 1.3 75.8 - - - +
99D LEU* 1.3 58.0 + - - +
101D GLU* 3.1 8.7 + - - +
102D PHE* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 6.5 0.4 - - + -
38D ILE* 6.4 1.3 - - + -
41D ILE* 4.2 17.0 - - + -
42D LEU* 6.4 1.8 - - + -
45D ILE* 4.5 13.5 - - + -
78D LEU* 6.2 1.6 - - + -
94D LEU* 3.9 18.3 - - + +
95D SER 2.8 14.9 + - - +
98D GLN* 1.3 72.1 - - - +
100D LYS* 1.3 59.5 + - - +
101D GLU 2.9 5.2 - - - -
102D PHE* 3.1 6.0 + - - +
103D LEU* 2.8 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 4.8 10.2 - - + +
96D LYS 3.9 14.4 + - - +
97D GLY* 3.3 12.8 + - - +
99D LEU* 1.3 78.3 - - - +
101D GLU* 1.3 57.0 + - - +
103D LEU* 4.1 5.6 - - - -
104D ASP* 3.4 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLY 3.2 11.0 + - - +
98D GLN* 3.1 12.3 + - - +
99D LEU 2.9 0.6 - - - -
100D LYS* 1.3 76.9 - - - +
102D PHE* 1.3 63.9 + - - +
103D LEU 3.2 1.3 - - - -
104D ASP* 4.6 1.5 - - - +
105D ALA* 3.2 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C VAL* 6.3 2.5 - - + -
94D LEU* 4.5 16.6 - - + -
98D GLN 2.9 15.4 + - - +
99D LEU* 3.8 7.2 - - - +
101D GLU* 1.3 77.8 - - - +
103D LEU* 1.3 57.3 + - - +
105D ALA* 4.3 1.3 - - - +
106D ASN* 2.3 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 6.3 2.7 - - + -
45D ILE* 5.9 4.9 - - + -
53D LEU* 5.4 13.2 - - + -
99D LEU 2.8 18.2 + - - +
100D LYS* 4.3 5.4 - - - +
102D PHE* 1.3 75.9 - - - +
104D ASP* 1.3 53.9 + - - +
106D ASN* 2.4 35.3 + - - +
107D LEU* 2.6 21.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LYS 3.4 19.2 + - - +
101D GLU* 4.6 2.5 - - - +
103D LEU* 1.3 76.6 - - - +
105D ALA* 1.3 57.2 + - - +
106D ASN 2.8 6.2 + - - -
107D LEU* 3.1 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLU 3.2 18.8 + - - +
102D PHE* 4.3 5.4 - - - +
103D LEU 2.8 3.2 + - - -
104D ASP* 1.3 74.3 - - - +
106D ASN* 1.3 65.7 + - - +
----------------------------------------------------------
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