Contacts of the helix formed by residues 135 - 151 (chain D) in PDB entry 6CKX
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 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D PHE 3.8 2.6 + - - +
134D ASP* 1.3 79.3 - - + +
136D PRO* 1.3 70.1 - - - +
137D LYS* 3.2 10.6 + - - +
138D GLU* 3.3 33.0 + - + +
139D GLU* 3.1 25.0 + - - +
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Residues in contact with PRO 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ILE* 3.7 29.0 - - + +
129D PHE* 4.1 20.2 - - + -
132D PHE* 3.5 24.6 - - + +
133D GLY 3.8 9.2 - - - +
134D ASP 3.4 11.4 - - - +
135D ASP* 1.3 85.8 - - - +
137D LYS* 1.3 61.5 + - - +
139D GLU* 3.5 2.8 + - - +
140D VAL* 3.3 25.8 + - - +
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764C LYS* 2.8 41.4 + - - +
765C GLU* 4.9 3.8 + - - -
113D CYS* 4.1 25.4 - - + -
114D LYS* 5.1 13.6 - - + +
117D ILE* 4.4 12.9 - - + +
135D ASP* 3.2 8.8 + - - +
136D PRO* 1.3 82.2 - - - +
138D GLU* 1.3 64.1 + - - +
140D VAL* 3.1 6.4 + - - +
141D MET* 3.1 41.5 + - + +
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Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ASP* 3.2 30.9 + - + +
137D LYS* 1.3 77.6 - - - +
139D GLU* 1.3 63.9 + - - +
141D MET* 3.2 12.9 + - - +
142D VAL* 3.0 45.9 + - + +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D VAL* 4.3 17.3 - - + +
131D GLN 4.8 5.2 - - - +
132D PHE* 3.7 30.5 - - - +
133D GLY* 4.7 5.8 - - - -
134D ASP 5.1 0.7 + - - -
135D ASP* 3.1 11.2 + - - +
136D PRO 3.7 5.8 - - - +
137D LYS 3.3 0.2 - - - -
138D GLU* 1.3 76.9 - - - +
140D VAL* 1.3 61.2 + - - +
142D VAL* 3.9 12.6 - - - +
143D LEU* 3.3 22.9 + - - +
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D VAL* 4.2 16.4 - - + +
97D ALA* 4.3 7.4 - - + +
98D CYS* 3.5 28.3 - - - +
101D PHE* 4.6 11.2 - - + -
113D CYS* 3.9 21.1 - - - -
116D ILE* 6.2 0.7 - - + -
117D ILE* 4.1 8.7 - - + -
132D PHE* 4.1 23.6 - - + -
136D PRO 3.3 12.5 + - - +
137D LYS 3.1 8.7 + - - +
139D GLU* 1.3 77.6 - - - +
141D MET* 1.3 65.2 + - - +
143D LEU* 3.2 4.4 + - - -
144D GLU* 3.1 18.0 + - - +
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Residues in contact with MET 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760C LEU* 5.6 3.6 - - - +
763C GLU 4.9 4.9 - - - +
764C LYS 3.6 18.8 - - - +
765C GLU* 3.6 3.8 - - - -
766C GLY* 2.9 40.4 - - - +
101D PHE* 4.1 21.3 - - + -
113D CYS* 4.1 15.0 - - + -
137D LYS* 3.1 29.4 + - + +
138D GLU* 3.2 15.5 + - - +
140D VAL* 1.3 76.7 - - - +
142D VAL* 1.3 63.0 + - + +
144D GLU* 3.1 23.0 + - - +
145D ARG* 3.6 5.7 + - - +
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLU* 3.0 39.2 + - + +
139D GLU* 3.9 13.2 - - - +
141D MET* 1.3 77.9 - - + +
143D LEU* 1.3 64.2 + - + +
144D GLU 3.3 0.5 + - - -
145D ARG* 3.4 20.1 + - - +
146D ILE* 3.8 16.5 + - + +
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PHE* 4.1 16.4 - - + -
90D PHE* 3.6 36.1 - - + -
94D VAL* 3.8 17.5 - - + -
95D THR* 3.6 38.8 - - + +
98D CYS* 3.7 13.2 - - + -
139D GLU 3.3 13.9 + - - +
140D VAL 3.2 6.3 + - - +
142D VAL* 1.3 81.0 - - + +
144D GLU* 1.3 54.7 + - - +
145D ARG 3.2 0.2 - - - -
146D ILE* 3.1 11.5 + - + +
147D LEU* 2.8 32.7 + - + +
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Residues in contact with GLU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760C LEU* 5.1 3.3 - - - +
766C GLY* 3.5 8.1 - - - -
767C PHE* 2.9 34.3 + - - +
98D CYS* 3.4 15.5 - - - -
101D PHE* 3.4 16.1 - - + -
102D LEU* 4.1 16.3 - - + +
105D LYS* 2.9 32.1 + - - -
140D VAL 3.1 10.0 + - - +
141D MET* 3.1 15.3 + - - +
143D LEU* 1.3 73.7 - - - +
145D ARG* 1.3 68.3 + - - +
147D LEU* 3.7 2.4 - - - +
148D LEU* 3.0 40.0 + - + +
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Residues in contact with ARG 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760C LEU* 4.3 18.3 - - + +
794C THR* 5.0 7.7 + - - +
795C ASP* 5.6 4.8 + - - +
807C GLY* 3.2 49.8 + - - +
808C ALA 6.0 0.2 - - - -
809C PHE* 3.5 34.7 - - + -
141D MET 3.6 3.6 + - - +
142D VAL* 3.4 14.2 + - - +
143D LEU 3.2 0.2 - - - -
144D GLU* 1.3 81.3 - - - +
146D ILE* 1.3 63.7 + - + +
148D LEU* 3.6 1.7 + - - +
149D GLN* 3.3 31.0 + - - +
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Residues in contact with ILE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PHE* 4.0 13.0 - - + -
85D HIS* 3.9 17.9 - - + +
90D PHE* 4.3 15.9 - - + -
142D VAL* 3.9 23.6 - - + +
143D LEU* 3.1 20.7 + - + +
145D ARG* 1.3 78.1 - - + +
147D LEU* 1.3 56.6 + - - +
149D GLN* 3.3 13.7 + - + +
150D THR* 2.6 47.6 + - - +
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D TYR* 4.3 5.4 - - + +
81D PHE* 3.6 33.6 - - + -
95D THR* 5.6 0.9 - - + -
98D CYS* 4.1 16.2 - - + +
99D CYS* 3.8 38.4 - - - -
102D LEU* 3.6 26.9 - - + -
143D LEU* 2.8 17.4 + - + +
144D GLU* 3.3 6.9 + - - +
146D ILE* 1.3 76.7 - - - +
148D LEU* 1.3 58.2 + - - +
150D THR* 3.0 7.2 + - - -
151D ILE* 2.9 44.9 + - + +
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Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760C LEU* 6.1 0.4 - - + -
767C PHE* 3.7 40.4 - - + -
772C ILE* 5.4 3.1 - - + -
809C PHE* 4.6 6.5 - - + -
102D LEU* 3.9 23.1 - - + -
144D GLU* 3.0 26.8 + - + +
145D ARG* 3.8 3.6 - - - +
147D LEU* 1.3 77.1 - - - +
149D GLN* 1.3 64.7 + - - +
151D ILE* 3.6 5.1 + - - -
152D LYS 3.1 2.6 + - - -
153D PHE* 3.1 56.6 + - + -
155D LEU* 3.8 28.5 - - + -
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722C ARG 5.2 4.2 + - - +
794C THR* 3.4 33.2 + - - +
809C PHE* 3.8 19.5 - - + -
145D ARG* 3.3 19.7 + - - +
146D ILE* 3.3 18.6 + - + +
148D LEU* 1.3 77.0 - - - +
150D THR* 1.3 64.3 + - - +
152D LYS* 3.0 19.3 + - - +
153D PHE* 4.7 6.1 - - + -
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Residues in contact with THR 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TRP* 3.9 9.9 - - - -
80D ARG 5.3 0.2 - - - -
81D PHE* 4.1 18.5 - - - +
84D PHE* 3.6 35.6 - - + -
85D HIS* 2.9 37.8 + - + +
146D ILE* 2.6 25.2 + - - +
147D LEU* 3.0 5.7 + - - -
149D GLN* 1.3 80.1 - - - +
151D ILE* 1.3 58.6 + - + +
152D LYS* 3.4 10.2 + - - +
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Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TRP* 3.5 21.8 - - + -
77D TYR* 3.9 48.7 - - + +
80D ARG* 4.7 14.1 - - + +
81D PHE 5.0 2.5 - - - +
102D LEU* 4.3 11.4 - - + -
147D LEU* 2.9 37.3 + - + +
148D LEU* 3.7 9.6 - - - +
150D THR* 1.3 75.9 - - - +
152D LYS* 1.3 66.4 + - - +
153D PHE 4.1 4.0 - - - +
154D ASP* 2.9 20.2 + - - +
155D LEU* 4.0 21.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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