Contacts of the helix formed by residues 106 - 123 (chain C) in PDB entry 1CX2
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 PRO 106 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ASN 5.5 0.9 - - - +
105C ILE* 1.3 93.6 - - - +
107C PHE* 1.3 63.2 + - + +
108C LEU 2.7 16.2 + - - -
109C ARG* 3.3 13.6 + - + +
110C SER* 2.9 20.8 + - - -
360C LYS* 4.8 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ILE* 3.3 38.4 - - + -
106C PRO* 1.3 84.7 - - + +
108C LEU* 1.3 61.7 + - + +
110C SER* 3.6 9.0 - - - -
111C LEU* 4.0 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ILE* 5.7 2.7 - - + -
103C VAL* 4.3 25.8 - - + +
105C ILE* 3.2 46.7 - - + +
106C PRO 2.7 6.3 + - - -
107C PHE* 1.3 83.4 - - + +
109C ARG* 1.3 66.8 + - - +
110C SER 3.2 1.3 - - - -
111C LEU* 3.1 21.9 + - + +
112C ILE* 3.0 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 4.0 11.2 + - - +
104C ASN* 4.5 13.0 + - - +
105C ILE 3.0 11.1 + - - +
106C PRO* 4.0 7.9 - - + +
108C LEU* 1.3 77.3 - - - +
110C SER* 1.3 51.6 + - - +
112C ILE* 2.9 9.2 + - - +
113C MET* 2.7 31.5 + - - -
346C GLU* 3.3 10.9 + - - -
357C PHE* 3.1 30.3 - - + -
358C LYS* 2.7 48.0 + - - +
359C LEU 2.4 26.2 + - - -
360C LYS* 2.8 40.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PRO 2.9 16.4 + - - -
107C PHE* 3.6 11.4 - - - -
109C ARG* 1.3 72.4 - - - +
111C LEU* 1.3 66.1 + - - +
113C MET* 3.7 3.5 - - - +
114C LYS* 2.7 37.6 + - - +
360C LYS* 3.4 31.4 - - - +
365C LEU* 4.0 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE 4.0 18.4 - - - +
108C LEU* 3.1 25.3 + - + +
110C SER* 1.3 82.2 + - - +
112C ILE* 1.3 60.2 + - + +
114C LYS* 3.4 26.7 - - + +
115C TYR* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 5.5 2.0 - - + -
100C TRP* 4.2 19.3 - - + -
103C VAL* 4.4 18.2 - - + -
108C LEU* 3.0 22.0 - - + +
109C ARG 2.9 10.3 + - - +
111C LEU* 1.3 74.8 - - + +
113C MET* 1.3 52.9 + - - +
115C TYR* 2.8 27.3 + - + +
116C VAL* 2.9 21.1 + - + +
357C PHE* 3.5 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG 2.7 18.3 + - - +
110C SER* 3.7 6.7 - - - +
112C ILE* 1.3 72.1 - - - +
114C LYS* 1.3 63.9 + - - +
116C VAL* 2.8 40.3 - - + +
117C LEU* 2.9 43.4 + - + +
345C ILE* 4.5 10.8 - - + -
357C PHE* 3.6 8.0 - - + -
359C LEU* 3.6 18.8 - - + -
360C LYS* 2.8 54.3 - - + +
365C LEU* 3.5 16.8 - - + -
701C S58 5.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C SER 2.7 22.3 + - - +
111C LEU* 3.4 24.3 - - + +
113C MET* 1.3 72.8 - - - +
115C TYR* 1.3 58.4 + - - +
117C LEU* 3.2 5.5 - - - +
118C THR* 2.9 38.0 + - + +
365C LEU* 3.2 47.5 - - + +
366C LEU* 5.9 0.2 - - + -
368C ASN* 4.4 6.0 + - - +
369C GLN* 3.7 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU 3.0 12.4 + - - +
112C ILE* 2.8 14.2 + - - +
114C LYS* 1.3 76.5 - - - +
116C VAL* 1.3 70.6 + - + +
118C THR* 2.9 20.5 + - - -
119C SER* 2.7 50.5 + - - -
120C ARG* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 5.5 11.7 - - + -
112C ILE* 2.9 30.4 + - + +
113C MET* 2.8 51.3 + - + +
115C TYR* 1.3 77.5 - - + +
117C LEU* 1.3 66.3 + - + +
119C SER* 3.6 3.4 + - - -
120C ARG* 2.9 43.6 + - - +
355C TYR* 5.6 0.9 - - + -
357C PHE* 4.8 7.0 - - + -
359C LEU* 4.8 7.6 - - + -
531C LEU* 4.8 0.9 - - - -
701C S58 4.4 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C MET* 3.3 46.4 - - + +
114C LYS* 3.2 9.2 - - - +
115C TYR 3.0 0.2 - - - -
116C VAL* 1.3 85.9 - - + +
118C THR* 1.3 66.6 + - - +
120C ARG* 3.6 5.9 + - - +
121C SER* 3.6 14.0 + - - -
345C ILE* 5.5 1.6 - - + -
360C LYS 4.9 0.7 - - - +
365C LEU* 4.6 12.6 - - + -
366C LEU* 4.2 27.4 - - + -
531C LEU* 4.0 30.3 - - + +
535C MET* 3.8 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LYS* 2.9 21.3 + - + +
115C TYR* 2.9 28.1 + - - -
117C LEU* 1.3 78.4 - - - +
119C SER* 1.3 64.3 + - - +
121C SER* 3.5 7.4 + - - -
122C TYR* 3.8 8.1 + - - +
366C LEU* 3.8 23.1 - - + +
369C GLN* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 2.7 55.4 + - - -
116C VAL* 3.6 2.9 + - - -
118C THR* 1.3 79.5 + - - +
120C ARG* 1.3 72.5 + - - +
121C SER 2.9 1.9 + - - -
122C TYR* 3.0 33.3 + - - -
123C LEU* 4.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 4.7 17.8 - - - +
93C LEU* 5.4 2.6 - - - +
115C TYR* 6.3 1.2 - - - -
116C VAL* 2.9 31.6 + - - +
117C LEU 3.8 3.6 - - - +
119C SER* 1.3 83.4 + - - +
121C SER* 1.3 57.7 + - - +
123C LEU* 2.9 23.3 - - - +
355C TYR* 4.0 12.3 + - - -
524C GLU* 5.1 13.7 + - - -
527C ALA* 3.3 22.8 - - - +
528C PRO* 3.3 32.9 - - + +
531C LEU* 3.8 15.5 - - + -
701C S58 3.2 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU 3.6 7.8 + - - -
118C THR 3.5 5.7 + - - -
119C SER 2.9 3.0 + - - -
120C ARG* 1.3 75.4 - - - +
122C TYR* 1.3 62.7 + - - +
123C LEU 2.9 6.7 + - - -
124C ILE* 3.1 27.2 + - - +
371C PHE* 5.7 4.5 - - - -
528C PRO* 3.3 18.9 + - - +
531C LEU* 3.9 16.1 - - - +
532C LYS* 3.7 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 6.4 0.9 - - - -
118C THR 3.8 6.6 + - - +
119C SER* 3.0 31.0 + - - +
121C SER* 1.3 77.1 - - - +
123C LEU* 1.3 86.9 + - + +
124C ILE 3.1 9.1 + - - +
471C SER* 2.5 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 5.3 2.0 - - - +
119C SER 4.0 0.2 - - - +
120C ARG* 2.9 29.4 - - - +
121C SER 2.9 1.2 - - - -
122C TYR* 1.3 128.4 - - + +
124C ILE* 1.3 63.6 + - + +
125C ASP* 5.6 0.2 - - - -
469C ARG* 2.4 50.7 + - - +
470C PHE* 4.0 32.3 - - + -
471C SER* 3.7 10.8 - - - +
528C PRO* 4.3 4.3 - - + -
529C PHE* 4.9 0.9 - - - -
----------------------------------------------------------
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