Contacts of the helix formed by residues 123 - 145 (chain P) in PDB entry 6F0X
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 LYS 123 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ASP* 3.5 49.0 + - - +
239E LEU* 6.2 2.5 - - - -
241E ASP* 5.7 4.6 + - - +
122P ARG* 1.3 82.4 - - + +
124P CYS* 1.3 64.1 + - - +
126P GLN* 4.7 4.0 - - + -
127P ALA* 2.9 30.7 + - + +
270P LYS* 5.3 12.3 - - + +
272P PHE* 4.4 17.0 - - + -
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Residues in contact with CYS 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P PRO* 6.0 0.4 - - - -
97P PHE* 3.7 21.1 - - - -
122P ARG 3.1 6.4 - - - +
123P LYS* 1.3 79.2 - - - +
125P GLN* 1.3 81.4 + - + +
128P LEU* 3.0 26.8 + - - +
272P PHE* 3.3 43.2 - - + -
274P GLU* 5.3 7.4 - - - +
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Residues in contact with GLN 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P PHE* 2.6 45.4 + - - +
98P TYR* 2.9 33.5 + - + +
122P ARG* 3.6 6.4 + - - +
124P CYS* 1.3 86.9 - - + +
126P GLN* 1.3 58.0 + - - +
128P LEU* 3.3 12.9 + - - +
129P ALA* 2.9 30.5 + - - +
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Residues in contact with GLN 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P ARG* 3.3 26.5 + - + +
123P LYS* 4.1 4.3 - - + +
124P CYS 3.3 1.0 - - - -
125P GLN* 1.3 79.0 - - - +
127P ALA* 1.3 58.3 + - - +
129P ALA* 3.2 12.0 + - - +
130P GLU* 2.9 26.9 + - - +
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Residues in contact with ALA 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P LYS* 2.9 20.6 + - + +
126P GLN* 1.3 74.3 - - - +
128P LEU* 1.3 65.3 + - - +
130P GLU* 3.1 10.4 - - - +
131P LEU 3.0 17.8 + - - -
269P PHE* 3.5 10.5 - - + -
270P LYS* 3.7 21.8 - - + +
272P PHE* 3.6 23.1 - - + -
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Residues in contact with LEU 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P LEU* 5.9 4.0 - - + -
91P TYR* 3.5 19.1 - - + -
94P LEU* 3.9 40.2 - - + +
97P PHE* 4.1 17.5 - - + -
98P TYR 4.8 5.2 - - - +
124P CYS* 3.0 18.1 + - - +
125P GLN* 3.3 15.4 + - - +
127P ALA* 1.3 76.9 - - - +
129P ALA* 1.3 57.8 + - - +
131P LEU* 3.2 10.5 + - + +
132P GLU* 2.8 60.6 + - - +
269P PHE* 5.3 0.4 - - - -
272P PHE* 4.6 6.4 - - + -
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Residues in contact with ALA 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P GLN 2.9 16.5 + - - +
126P GLN* 3.7 14.6 - - - +
127P ALA 3.2 0.2 - - - -
128P LEU* 1.3 74.5 - - + +
130P GLU* 1.3 66.3 + - - +
132P GLU* 3.6 14.1 - - - +
133P SER* 2.9 24.9 + - - -
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Residues in contact with GLU 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P GLN* 2.9 15.2 + - - +
127P ALA* 3.1 13.7 - - - +
129P ALA* 1.3 76.1 - - - +
131P LEU* 1.3 64.3 + - - +
133P SER* 3.2 6.4 + - - -
134P VAL* 3.0 26.5 + - + +
267P VAL* 2.9 50.3 - - - +
268P THR 3.1 13.9 - - - +
269P PHE* 3.7 24.1 + - + -
270P LYS 4.7 2.0 - - - +
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Residues in contact with LEU 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P LEU* 4.3 12.3 - - + -
78P LYS* 5.4 0.4 - - + -
81P MET* 3.5 43.7 - - + -
87P LEU* 3.8 22.0 - - + -
91P TYR* 4.1 25.8 - - + -
127P ALA 3.0 6.9 + - - +
128P LEU* 3.2 11.4 + - - +
130P GLU* 1.3 76.2 - - - +
132P GLU* 1.3 58.8 + - - +
134P VAL* 3.1 13.1 - - + +
135P LEU* 2.9 35.9 + - + +
269P PHE* 3.5 21.8 - - + -
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Residues in contact with GLU 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P TYR* 2.8 30.9 + - + +
95P LYS* 5.7 2.6 + - - -
128P LEU* 2.8 37.2 + - + +
129P ALA* 3.1 12.6 + - - +
131P LEU* 1.3 72.3 - - - +
133P SER* 1.3 62.5 + - - +
135P LEU* 3.2 10.3 + - - +
136P SER* 2.8 30.7 + - - -
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Residues in contact with SER 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P ALA 2.9 12.3 + - - -
130P GLU* 3.6 9.9 - - - -
132P GLU* 1.3 75.3 - - - +
134P VAL* 1.3 63.0 + - - +
136P SER* 3.3 4.0 + - - -
137P HIS* 2.6 55.8 + - - -
225P TRP* 3.2 14.5 + - - -
267P VAL* 6.1 1.3 - - - -
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Residues in contact with VAL 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P LEU* 4.4 14.8 - - + -
130P GLU* 3.0 31.6 + - + +
131P LEU* 3.1 15.0 - - + +
133P SER* 1.3 77.0 - - - +
135P LEU* 1.3 65.0 + - - +
137P HIS* 3.8 1.7 - - - +
138P LEU* 2.9 44.8 + - + +
213P VAL* 4.8 12.6 - - + -
225P TRP* 4.1 20.2 - - + -
226P PHE* 6.3 0.9 - - + -
265P ALA* 5.6 3.8 - - + -
267P VAL 4.8 6.7 - - - +
269P PHE* 5.2 7.2 - - + -
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Residues in contact with LEU 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P CYS* 4.6 15.1 - - + +
77P LEU* 4.0 25.1 - - + -
78P LYS* 3.6 39.0 - - + +
91P TYR* 3.7 25.6 - - + +
131P LEU* 2.9 31.3 + - + +
132P GLU* 3.2 10.1 + - - +
134P VAL* 1.3 71.7 - - - +
136P SER* 1.3 63.5 + - - +
138P LEU* 3.1 12.5 + - + +
139P GLU* 2.9 31.1 + - - +
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Residues in contact with SER 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P GLU 2.8 16.5 + - - -
133P SER* 3.7 7.2 - - - -
135P LEU* 1.3 77.1 - - - +
137P HIS* 1.3 63.3 + - - +
139P GLU* 3.0 15.2 + - - +
140P ASP* 2.9 36.8 + - - +
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Residues in contact with HIS 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P SER* 2.6 49.1 + - - +
134P VAL 4.0 0.2 - - - +
136P SER* 1.3 79.3 - - - +
138P LEU* 1.3 57.8 + - - +
140P ASP* 3.1 22.8 - - + +
141P PHE* 2.8 29.1 + - - +
223P GLU* 5.1 2.5 - - - +
225P TRP* 3.1 67.1 - + + -
226P PHE* 3.9 6.1 - - + -
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Residues in contact with LEU 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P THR* 5.0 11.9 - - + -
74P CYS* 5.0 8.7 - - - -
77P LEU* 4.1 16.4 - - + -
134P VAL* 2.9 43.6 + - + +
135P LEU* 3.2 18.2 - - + +
137P HIS* 1.3 76.2 - - - +
139P GLU* 1.3 62.6 + - - +
141P PHE* 3.0 3.1 + - + +
142P PHE* 2.8 49.5 + - + -
150P VAL* 5.9 1.3 - - + -
213P VAL* 4.5 19.7 - - + -
226P PHE* 3.7 24.9 - - + -
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Residues in contact with GLU 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P CYS* 3.4 28.7 - - - -
71P GLN* 5.3 7.1 + - - +
74P CYS* 4.1 13.6 - - - -
135P LEU* 2.9 22.4 + - - +
136P SER* 3.0 12.7 + - - +
138P LEU* 1.3 74.7 - - - +
140P ASP* 1.3 65.8 + - - +
142P PHE* 3.5 1.4 + - - +
143P ALA* 2.9 25.9 + - - +
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Residues in contact with ASP 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P SER* 2.9 21.5 + - - +
137P HIS* 3.1 37.8 + - + +
139P GLU* 1.3 79.1 - - - +
141P PHE* 1.3 63.6 + - - +
143P ALA* 3.2 7.1 + - - +
144P ARG* 2.9 36.8 + - - +
223P GLU* 5.8 2.0 - - - +
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Residues in contact with PHE 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P HIS 2.8 12.8 + - - +
138P LEU* 3.0 8.3 + - + +
140P ASP* 1.3 77.2 - - - +
142P PHE* 1.3 69.7 + + - +
144P ARG* 2.9 15.3 + - - +
145P THR* 3.1 21.0 + - + +
147P VAL* 3.5 20.9 - - + -
215P ALA* 5.0 7.9 - - + -
216P GLN 3.3 17.9 - - - -
217P GLY* 3.4 26.7 - - - -
221P CYS* 4.4 4.9 - - - -
223P GLU* 3.0 32.5 - - + +
226P PHE* 3.4 23.3 - + + -
263P PHE* 3.2 33.7 - + - -
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Residues in contact with PHE 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P GLN* 5.1 6.6 + - - -
69P CYS* 4.4 6.3 - - + -
70P CYS* 3.9 37.7 - - + +
73P THR* 3.5 35.0 - - + -
74P CYS* 5.7 0.4 - - - -
138P LEU* 2.8 52.6 + - + +
139P GLU 4.0 1.3 - - - +
141P PHE* 1.3 79.7 - + + +
143P ALA* 1.3 61.8 + - - +
145P THR 2.9 21.0 + - - +
146P LEU* 5.7 0.7 - - - +
147P VAL* 3.6 29.6 - - + -
150P VAL* 4.1 9.2 - - + -
169P LEU* 3.7 21.8 - - + -
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Residues in contact with ALA 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P GLN* 5.8 1.4 + - - -
67P GLU* 5.8 8.3 - - - +
139P GLU 2.9 19.8 + - - +
140P ASP* 3.4 7.2 - - - +
142P PHE* 1.3 77.4 - - - +
144P ARG* 1.3 65.3 + - + +
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Residues in contact with ARG 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140P ASP* 2.9 25.6 + - - +
141P PHE* 2.9 9.5 + - + +
142P PHE 4.1 0.2 - - - -
143P ALA* 1.3 81.5 - - + +
145P THR* 1.3 64.8 + - + +
221P CYS* 4.4 24.4 + - + +
222P GLY 5.2 6.7 + - - -
223P GLU* 3.5 27.5 + - - +
224P ASP* 5.5 5.8 - - - +
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Residues in contact with THR 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P GLN* 5.5 1.8 - - - -
141P PHE* 3.1 26.2 + - + +
142P PHE* 2.9 23.9 - - - +
144P ARG* 1.3 80.9 - - + +
146P LEU* 1.3 82.8 + - - +
147P VAL* 4.7 0.7 - - - +
218P HIS* 3.6 41.5 + - + +
221P CYS* 4.4 10.5 - - + -
260P TYR* 3.9 11.3 + - - -
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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) + - + + + + + -
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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