Contacts of the helix formed by residues 104 - 114 (chain B) in PDB entry 3CJD
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 HIS 104 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG* 3.4 31.2 + - - -
100B PHE* 2.7 58.3 + + + +
101B ALA 3.9 0.2 - - - -
103B GLU* 1.3 97.5 + - + +
105B PRO* 1.3 59.1 - - - +
106B LYS 3.3 2.6 + - - -
107B LEU* 3.4 10.5 + - + +
108B TRP* 2.9 27.7 + - - +
202B CL 3.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA 3.3 17.0 - - - +
102B ARG 3.6 10.1 - - - +
103B GLU 3.4 10.1 - - - +
104B HIS* 1.3 87.8 - - - +
106B LYS* 1.3 70.9 + - + +
108B TRP* 3.8 5.8 - - + +
109B ARG* 3.0 36.5 + - + +
202B CL 3.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.3 32.5 - - - +
25B GLU 3.6 11.3 + - - +
26B ALA 2.7 27.1 + - - -
27B GLU* 4.0 5.4 - - - +
28B GLY* 3.6 16.2 - - - +
29B LEU 5.2 2.4 + - - -
105B PRO* 1.3 84.9 - - + +
107B LEU* 1.3 64.2 + - - +
109B ARG* 3.5 5.8 + - - +
110B ALA* 3.1 23.0 + - - +
202B CL 3.2 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 4.0 12.3 - - + +
24B ILE* 3.8 21.1 - - + -
25B GLU* 3.7 26.7 - - + +
62B VAL* 3.8 24.2 - - + -
63B ASN* 4.5 0.3 - - - +
66B THR* 3.7 22.7 + - + +
69B ARG* 3.7 31.4 - - - +
104B HIS* 4.0 14.8 - - + +
106B LYS* 1.3 71.7 - - - +
108B TRP* 1.3 65.6 + - - +
110B ALA* 3.4 14.8 + - + +
111B LEU* 3.5 11.8 + - - +
202B CL 3.3 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 3.0 30.3 + + - -
100B PHE* 4.0 28.2 - + + -
101B ALA* 3.5 35.2 - - + +
104B HIS 2.9 19.2 + - - +
105B PRO* 3.8 5.8 - - + +
107B LEU* 1.3 76.3 - - - +
109B ARG* 1.3 89.8 + - + +
111B LEU* 3.1 27.4 + - + +
112B PHE* 3.6 19.0 - + - -
165B HIS* 3.7 23.1 - + - -
168B VAL* 4.0 15.7 - - + -
169B LEU* 4.1 31.2 - - + -
172B LEU* 4.2 12.8 - - + -
173B GLU* 6.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 6.2 0.2 - - - +
105B PRO* 3.0 24.0 + - + +
106B LYS* 4.0 5.6 - - - +
107B LEU 3.4 0.2 - - - -
108B TRP* 1.3 100.2 - - + +
110B ALA* 1.3 50.8 + - - +
112B PHE* 3.0 31.6 + - - +
113B ASP* 2.7 75.6 + - - +
165B HIS* 4.9 2.6 + - - -
169B LEU* 3.6 29.9 - - - +
173B GLU* 4.5 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.2 20.6 - - + -
29B LEU* 4.2 28.9 - - + +
59B THR* 4.8 0.2 - - + -
62B VAL* 6.0 0.2 - - + -
63B ASN* 3.2 26.1 + - - +
106B LYS 3.1 13.6 + - - +
107B LEU* 3.5 12.1 - - + +
109B ARG* 1.3 74.8 - - - +
111B LEU* 1.3 62.0 + - - +
114B VAL* 3.2 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 3.2 16.6 + - - -
201A STE 3.3 32.3 - - + +
63B ASN* 3.6 36.1 + - + +
66B THR* 3.9 15.3 - - + -
67B PHE* 3.6 22.7 - - + -
70B LEU* 3.7 30.1 - - + -
97B TYR* 5.8 0.2 - - + -
100B PHE* 5.0 0.2 - - + -
107B LEU 3.5 6.7 + - - +
108B TRP* 3.1 21.9 + - + +
110B ALA* 1.3 78.1 - - - +
112B PHE* 1.3 71.3 + - + +
114B VAL* 3.7 5.0 - - - +
126B TYR* 4.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.8 22.4 - - + -
173A GLU* 5.0 4.8 - - - +
175A ARG* 3.0 30.5 + - + +
177A SER* 4.1 3.6 - - - -
201A STE 3.7 38.1 - - + -
97B TYR* 3.2 27.6 - + - -
108B TRP* 3.6 28.3 - + - -
109B ARG* 3.0 23.5 + - - +
111B LEU* 1.3 86.9 - - + +
113B ASP* 1.3 59.9 + - - +
114B VAL 3.6 0.7 - - - -
161B PHE* 4.0 6.7 - + - -
165B HIS* 3.3 32.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 4.7 0.4 + - - -
29B LEU* 4.0 20.2 - - + +
109B ARG* 2.7 63.3 + - - +
110B ALA* 4.5 0.2 - - - -
112B PHE* 1.3 77.9 - - - +
114B VAL* 1.3 65.6 + - - +
115B GLU* 3.8 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 3.1 26.8 + - - +
29B LEU* 3.8 8.8 - - + +
56B ASN* 3.1 25.1 - - - +
59B THR* 3.8 25.8 - - + -
60B LEU* 4.1 14.6 - - + -
63B ASN* 3.3 15.3 - - - +
110B ALA 3.2 21.1 + - - +
111B LEU 3.7 12.8 - - - +
113B ASP* 1.3 77.0 - - - +
115B GLU* 1.3 57.2 - - - +
116B MSE 3.0 18.6 + - + -
126B TYR* 4.2 4.7 - - - +
----------------------------------------------------------
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