Contacts of the helix formed by residues 106 - 121 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN 5.6 0.4 - - - +
105B ILE* 1.4 89.7 - - - +
107B PHE* 1.3 62.3 + - + +
108B LEU 2.6 17.6 + - - -
109B ARG* 3.2 13.2 + - + +
110B SER* 2.8 20.5 + - - -
360B LYS* 5.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 3.3 38.6 - - + -
106B PRO* 1.3 84.5 - - + +
108B LEU* 1.3 59.9 + - + +
110B SER* 3.6 9.6 - - - -
111B LEU* 4.0 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 5.7 2.5 - - + -
103B VAL* 4.3 25.6 - - + +
105B ILE* 3.2 45.3 - - + +
106B PRO 2.6 6.5 + - - -
107B PHE* 1.3 82.2 - - + +
109B ARG* 1.3 67.1 + - - +
110B SER 3.1 0.9 - - - -
111B LEU* 3.1 22.0 + - + +
112B ILE* 3.0 32.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
103B VAL* 4.0 11.8 + - + +
104B ASN* 4.5 12.1 + - - +
105B ILE 3.0 12.4 + - - +
106B PRO* 4.0 8.1 - - + +
108B LEU* 1.3 76.5 - - - +
110B SER* 1.3 52.5 + - - +
112B ILE* 2.9 8.5 + - - +
113B MET* 2.7 31.1 + - - +
346B GLU* 3.3 14.8 + - - -
357B PHE* 3.1 30.2 - - + -
358B LYS* 2.7 47.9 + - - +
359B LEU 2.6 25.4 + - - -
360B LYS* 3.1 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO 2.8 17.5 + - - -
107B PHE* 3.6 11.1 - - - -
109B ARG* 1.3 74.0 - - - +
111B LEU* 1.3 63.9 + - - +
113B MET* 3.7 2.1 - - - +
114B LYS* 2.7 36.1 + - - +
360B LYS* 3.2 33.6 - - - +
365B LEU* 4.0 13.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
107B PHE 4.0 18.2 - - - +
108B LEU* 3.1 25.0 + - + +
110B SER* 1.3 81.8 + - - +
112B ILE* 1.3 67.7 + - + +
114B LYS* 3.3 25.0 - - + +
115B TYR* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 5.5 2.5 - - + -
100B TRP* 4.2 20.0 - - + -
103B VAL* 4.4 17.5 - - + -
108B LEU* 3.1 20.9 - - + +
109B ARG 2.9 10.6 + - - +
111B LEU* 1.3 76.1 - - + +
113B MET* 1.3 63.3 + - - +
115B TYR* 2.8 18.3 + - - +
116B VAL* 2.9 19.0 + - + +
357B PHE* 3.5 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ARG 2.7 18.3 + - - +
110B SER* 3.7 4.0 - - - +
112B ILE* 1.3 69.6 - - - +
114B LYS* 1.3 62.7 + - - +
116B VAL* 2.8 43.1 - - + +
117B LEU* 2.9 42.4 + - + +
345B ILE* 4.6 13.9 - - + -
357B PHE* 3.7 8.2 - - + -
359B LEU* 3.6 15.5 - - + -
360B LYS* 2.6 57.9 - - + +
365B LEU* 3.4 21.8 - - + -
531B LEU* 5.9 0.7 - - + -
701B S58 5.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B SER 2.7 22.9 + - - +
111B LEU* 3.3 24.3 - - + +
113B MET* 1.3 72.5 - - - +
115B TYR* 1.3 59.5 + - - +
117B LEU* 3.2 5.0 - - - +
118B THR* 2.9 37.9 + - + +
365B LEU* 3.3 44.1 - - + +
366B LEU* 5.8 0.2 - - + -
368B ASN* 4.3 10.7 + - - +
369B GLN* 3.7 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU 3.0 12.0 + - - +
112B ILE* 2.8 12.4 + - - +
114B LYS* 1.3 76.9 - - - +
116B VAL* 1.3 64.6 + - + +
118B THR* 3.0 19.4 + - - -
119B SER* 2.7 60.4 + - - -
120B ARG* 6.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 5.4 11.9 - - + -
112B ILE* 2.9 26.2 + - + +
113B MET* 2.8 51.3 + - + +
115B TYR* 1.3 82.5 - - + +
117B LEU* 1.3 70.8 + - + +
119B SER* 3.5 0.8 + - - -
120B ARG* 3.0 37.4 + - - +
355B TYR* 5.6 0.4 - - + -
357B PHE* 4.8 7.2 - - + -
359B LEU* 4.8 8.3 - - + -
531B LEU* 4.8 1.3 - - - -
701B S58 4.4 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 3.3 48.0 - - + +
114B LYS* 3.2 9.4 - - - +
115B TYR 3.0 0.4 - - - -
116B VAL* 1.3 86.0 - - + +
118B THR* 1.3 68.0 + - - +
120B ARG* 3.4 6.2 + - - +
121B SER* 3.6 13.2 + - - -
345B ILE* 5.5 1.8 - - + -
360B LYS 4.9 0.9 - - - +
365B LEU* 4.5 12.3 - - + -
366B LEU* 4.3 26.5 - - + -
531B LEU* 3.9 26.9 - - + +
535B MET* 3.9 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 2.9 29.3 + - + +
115B TYR* 3.0 23.7 + - - -
117B LEU* 1.3 76.5 - - - +
119B SER* 1.3 62.5 + - - +
121B SER* 3.4 8.3 + - - -
122B TYR* 3.8 7.8 + - - +
366B LEU* 3.7 20.6 - - + +
369B GLN* 3.4 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR* 2.7 54.9 + - - -
116B VAL* 3.5 2.6 + - - -
118B THR* 1.3 77.9 + - - +
120B ARG* 1.3 72.8 + - - +
121B SER 2.9 1.9 + - - -
122B TYR* 3.0 34.1 + - - -
123B LEU* 4.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 4.6 18.0 - - - +
93B LEU* 5.4 2.8 - - - +
115B TYR* 6.3 1.0 - - - -
116B VAL* 3.0 29.6 + - - +
117B LEU 3.7 2.9 - - - +
118B THR 3.4 0.2 - - - -
119B SER* 1.3 82.4 + - - +
121B SER* 1.3 57.8 + - - +
123B LEU* 3.1 20.9 - - - +
355B TYR* 3.9 8.3 + - - -
524B GLU* 5.0 13.7 + - - -
527B ALA* 3.2 18.0 - - + +
528B PRO* 3.2 37.4 - - + +
531B LEU* 3.8 14.1 - - + -
701B S58 2.6 53.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU 3.6 7.9 + - - -
118B THR 3.4 6.4 + - - -
119B SER 3.1 1.4 - - - -
120B ARG* 1.3 78.0 - - - +
122B TYR* 1.3 65.1 + - - +
123B LEU 2.9 2.9 + - - -
124B ILE* 3.2 25.9 + - - +
371B PHE* 5.6 5.4 - - - -
528B PRO* 3.3 19.2 + - - +
531B LEU* 3.9 15.4 - - - +
532B LYS* 3.6 21.8 - - - +
----------------------------------------------------------
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