Contacts of the helix formed by residues 106 - 110 (chain G) in PDB entry 1KD1
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 106 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G PHE* 3.8 21.7 - - - +
92G PRO* 3.4 28.8 - - - +
93G MET* 4.4 2.8 - - - -
94G GLN* 4.5 12.2 + - - +
105G GLU* 1.3 78.4 - - + +
107G PHE* 1.3 67.2 + - - +
108G LEU 3.2 2.9 + - - -
109G GLY* 3.2 32.5 + - - -
110G GLU* 3.3 18.1 + - - +
111G LYS 5.7 0.4 + - - -
112G ALA 5.5 2.0 + - - -
113G PRO* 5.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G MET* 3.3 42.8 - - + -
104G ILE* 4.3 12.5 + - + +
105G GLU 3.2 3.3 - - - -
106G ASN* 1.3 72.1 - - - +
108G LEU* 1.3 91.5 + - + +
109G GLY 2.9 3.4 - - - -
110G GLU* 2.7 44.7 + - - +
114G ARG* 3.7 46.2 - - + +
152G THR* 3.5 41.5 - - + -
153G ARG 5.2 0.7 - - - -
154G ILE* 5.5 6.7 - - + -
164G ASP 3.8 7.4 - - - -
165G GLY 3.8 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2694A A 5.1 8.0 + - - +
2702A A 4.8 8.2 + - + +
2703A A 3.8 14.5 - - + +
91G PHE* 3.6 27.3 + - + +
93G MET* 5.6 0.8 - - - +
106G ASN 3.2 2.6 + - - -
107G PHE* 1.3 114.6 - - + +
109G GLY* 1.3 56.2 + - - +
110G GLU* 3.3 7.1 + - + +
154G ILE* 4.4 11.2 - - + -
157G LYS* 4.2 22.2 - - - +
162G PHE* 4.2 24.0 - - + +
164G ASP* 3.6 28.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2690A U 4.8 2.9 + - - -
2703A A 3.8 12.1 + - - +
91G PHE* 3.4 24.5 - - - -
106G ASN* 3.2 25.7 + - - -
107G PHE 2.7 4.6 + - - -
108G LEU* 1.3 73.4 - - - +
110G GLU* 1.3 65.5 + - - +
111G LYS* 3.5 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2703A A 3.8 20.3 + - + +
2704A C 3.4 37.1 + - + +
106G ASN* 3.3 22.7 + - - -
107G PHE* 2.7 32.6 + - - +
108G LEU* 3.3 5.3 + - + +
109G GLY* 1.3 73.2 - - - +
111G LYS* 1.3 63.0 + - - +
112G ALA 3.6 17.1 - - - +
114G ARG* 2.7 49.6 + - - +
----------------------------------------------------------
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