Contacts of the helix formed by residues 102 - 112 (chain Q) in PDB entry 3K9Q
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 ASP 102 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100Q TYR 2.9 2.2 + - - -
101Q THR* 1.3 80.2 - - - +
103Q LYS* 1.3 67.5 + - - +
104Q ASP* 3.0 30.5 + - - +
105Q LYS* 3.1 35.2 + - + +
106Q ALA* 2.9 25.3 + - - +
119Q ILE* 4.4 3.6 - - - +
123Q ALA* 3.9 2.4 - - - +
124Q THR* 2.6 34.1 + - - +
125Q GLY* 4.1 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q ASP* 1.3 71.5 - - - +
104Q ASP* 1.3 70.4 + - - +
106Q ALA* 3.8 2.1 - - - +
107Q GLN* 3.1 27.8 + - - +
124Q THR 2.8 13.7 + - - +
125Q GLY* 4.2 10.1 - - - -
126Q ASP* 3.1 42.0 + - + +
127Q LEU* 3.7 23.3 - - + +
144Q THR* 4.6 9.4 + - - -
145Q VAL* 4.2 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q ASP* 3.0 13.6 + - - +
103Q LYS* 1.3 85.0 - - - +
105Q LYS* 1.3 63.5 + - + +
107Q GLN* 3.1 21.2 - - - +
108Q ALA 4.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Q PHE 3.7 23.1 + - - +
100Q TYR* 3.5 22.8 - - + -
101Q THR* 4.7 9.9 + - - +
102Q ASP* 3.1 35.1 + - + +
104Q ASP* 1.3 76.2 - - + +
106Q ALA* 1.3 62.7 + - - +
107Q GLN 3.0 2.0 + - - -
108Q ALA* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Q GLU* 5.3 0.2 - - + -
100Q TYR* 3.7 22.6 + - + +
102Q ASP 2.9 17.0 + - - +
103Q LYS 3.8 3.8 - - - +
105Q LYS* 1.3 72.3 - - - +
107Q GLN* 1.3 63.9 + - - +
108Q ALA 3.0 2.7 - - - -
109Q HIS* 3.0 26.8 + - + +
110Q ILE 4.1 0.2 + - - -
117Q VAL* 3.7 17.6 - - + +
119Q ILE* 3.9 17.0 - - + -
145Q VAL* 3.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Q LYS* 3.1 16.9 + - - +
104Q ASP* 3.1 21.3 - - - +
105Q LYS 3.0 0.2 - - - -
106Q ALA* 1.3 76.4 - - - +
108Q ALA* 1.3 61.8 + - - +
110Q ILE* 2.9 49.0 + - - +
111Q GLU* 3.1 32.4 + - - +
144Q THR* 4.7 4.3 + - - -
145Q VAL* 4.2 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q ASP* 5.3 0.9 - - - +
80Q ALA* 4.3 9.0 - - + -
81Q SER* 3.6 33.4 - - - +
100Q TYR* 4.5 5.4 - - + -
104Q ASP 4.3 0.8 + - - -
105Q LYS 3.1 16.5 + - - +
106Q ALA 4.7 0.2 - - - -
107Q GLN* 1.3 77.2 - - - +
109Q HIS* 1.3 55.6 + - - +
111Q GLU* 3.5 14.5 + - - +
112Q ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 109 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q ASN* 3.3 29.1 + - + -
80Q ALA* 3.5 20.8 - - + +
83Q LEU* 4.3 1.1 - - + -
85Q TRP* 3.0 29.8 + - - -
93Q VAL* 3.6 28.4 - - + +
95Q GLU* 2.9 24.0 + - + -
100Q TYR* 4.6 2.9 - + - -
106Q ALA* 3.0 22.2 + - - -
108Q ALA* 1.3 73.4 - - - +
110Q ILE* 1.3 63.4 + - - +
112Q ALA* 3.3 2.0 + - - -
113Q GLY 3.1 6.6 + - - -
114Q ALA* 3.0 23.7 + - + +
117Q VAL* 3.4 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107Q GLN* 2.9 43.3 + - - +
109Q HIS* 1.3 73.1 - - - +
111Q GLU* 1.3 62.6 + - - +
113Q GLY* 3.0 19.9 + - - -
114Q ALA 3.4 15.0 - - - +
115Q LYS 3.7 18.8 - - - +
116Q LYS* 4.0 5.8 - - - -
117Q VAL* 4.0 11.9 - - + -
144Q THR* 3.7 36.1 - - + +
145Q VAL* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81Q SER* 4.2 13.9 - - - +
107Q GLN* 3.1 40.1 + - + +
108Q ALA* 3.7 15.7 + - - +
110Q ILE* 1.3 77.8 - - - +
112Q ALA* 1.3 60.2 + - - +
113Q GLY* 3.2 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q ALA 3.6 16.8 - - - +
81Q SER 3.7 12.5 + - - +
83Q LEU 3.3 21.0 - - - +
84Q PRO* 4.9 0.2 - - - +
85Q TRP* 3.4 14.7 + - + -
86Q LYS* 2.9 23.0 + - - +
108Q ALA 3.0 17.2 + - - +
109Q HIS 3.6 6.3 - - - +
110Q ILE 3.2 0.4 - - - -
111Q GLU* 1.3 74.7 - - - +
113Q GLY* 1.3 56.2 + - - +
----------------------------------------------------------
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