Contacts of the helix formed by residues 156 - 175 (chain D) in PDB entry 6EKK
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 ASN 156 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D PHE* 3.9 18.6 - - - +
148D GLU 3.0 32.1 + - - +
149D THR* 3.3 11.0 - - - +
154D ASN 4.1 1.4 + - - -
155D VAL* 1.3 82.7 - - + +
157D VAL* 1.3 58.2 + - - +
159D GLU* 3.2 39.4 + - - +
160D MET* 3.2 16.3 + - - +
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Residues in contact with VAL 157 (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 LEU* 3.9 26.2 - - + +
27D ARG* 3.8 20.4 - - + -
149D THR* 4.2 3.6 - - - -
150D SER 3.5 27.1 - - - +
151D ALA* 4.0 4.0 - - - -
154D ASN* 3.8 19.6 - - - +
155D VAL 3.1 5.8 - - - +
156D ASN* 1.3 75.1 - - - +
158D GLU* 1.3 67.7 + - - +
159D GLU 3.2 1.1 - - - -
160D MET* 3.2 6.0 + - + +
161D PHE* 3.0 49.1 + - + -
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Residues in contact with GLU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PHE* 6.3 0.7 - - - -
154D ASN* 4.9 4.0 + - - +
157D VAL* 1.3 78.3 - - - +
159D GLU* 1.3 69.1 + - - +
161D PHE* 3.4 5.7 + - - +
162D ASN* 2.9 53.0 + - - +
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Residues in contact with GLU 159 (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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147D PHE* 3.8 12.4 - - + -
156D ASN* 3.2 42.8 + - - +
157D VAL 3.2 0.2 - - - -
158D GLU* 1.3 87.0 + - - +
160D MET* 1.3 62.8 + - - +
162D ASN* 3.4 12.2 - - - +
163D CYS* 3.1 23.4 + - - +
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Residues in contact with MET 160 (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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13D ILE* 6.0 0.2 - - + -
24D LEU* 4.2 23.1 - - + -
85D ILE* 3.9 19.1 - - + -
116D ILE* 3.5 22.4 - - + +
118D VAL* 3.5 31.6 - - + -
147D PHE* 3.8 23.5 - - + -
149D THR* 4.0 2.2 - - + -
156D ASN 3.2 16.5 + - - +
157D VAL* 3.2 4.4 + - + +
159D GLU* 1.3 78.8 - - - +
161D PHE* 1.3 101.3 + - + +
163D CYS* 3.3 10.4 + - - +
164D ILE 3.3 10.2 + - - -
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Residues in contact with PHE 161 (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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11D LEU* 5.7 1.1 - - + -
13D ILE* 5.4 0.2 - - + -
24D LEU* 3.3 31.4 - - + -
25D LEU* 3.7 20.4 - - + -
27D ARG 5.4 0.4 - - - -
28D PHE* 3.5 60.3 - + + -
61D ILE* 5.6 1.1 - - + -
85D ILE* 3.6 29.6 - - + -
157D VAL* 3.0 36.2 + - + +
158D GLU* 4.0 5.6 - - - +
160D MET* 1.3 90.9 - - + +
162D ASN* 1.3 61.6 + - - +
164D ILE* 3.4 6.8 - - + +
165D THR* 2.8 34.5 + - - -
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Residues in contact with ASN 162 (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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28D PHE* 5.9 2.1 - - - -
158D GLU* 2.9 47.0 + - - +
159D GLU* 3.4 13.7 - - - +
160D MET 3.3 0.2 - - - -
161D PHE* 1.3 77.0 - - - +
163D CYS* 1.3 56.6 + - - +
165D THR* 3.4 4.8 + - - -
166D GLU* 2.9 30.1 + - - +
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Residues in contact with CYS 163 (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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116D ILE* 3.8 14.6 - - + -
145D GLN* 3.5 28.0 - - - -
147D PHE* 3.4 40.2 - - + -
159D GLU 3.1 3.9 + - - +
160D MET 3.6 5.6 - - - +
161D PHE 3.2 0.4 - - - -
162D ASN* 1.3 77.0 - - - +
164D ILE* 1.3 60.4 + - - +
166D GLU* 3.1 16.2 + - - +
167D LEU* 2.9 37.8 + - - +
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Residues in contact with ILE 164 (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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11D LEU* 3.9 26.5 - - + -
83D GLY* 4.3 1.6 - - - -
84D VAL 4.0 27.6 - - - +
85D ILE* 3.9 32.3 - - + -
114D CYS* 4.2 11.0 - - + -
115D ARG* 4.2 15.9 - - - +
116D ILE* 3.8 16.3 - - + +
160D MET 3.3 3.7 + - - +
161D PHE* 3.4 21.3 - - + +
163D CYS* 1.3 77.8 - - - +
165D THR* 1.3 67.2 + - - +
167D LEU* 3.3 10.7 + - + -
168D VAL* 3.2 22.1 + - - +
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Residues in contact with THR 165 (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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11D LEU* 5.1 0.6 - - - +
28D PHE* 4.1 16.6 - - - -
52D ILE* 3.4 32.5 - - + -
57D VAL* 4.8 2.0 - - + -
59D LEU* 4.1 26.9 - - + +
161D PHE 2.8 23.4 + - - -
162D ASN* 3.6 5.8 - - - -
164D ILE* 1.3 81.1 - - - +
166D GLU* 1.3 61.0 + - - +
168D VAL* 3.2 11.1 - - + +
169D LEU* 3.1 31.4 + - + +
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Residues in contact with GLU 166 (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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162D ASN 2.9 17.7 + - - +
163D CYS* 3.4 15.5 - - - +
165D THR* 1.3 78.0 - - - +
167D LEU* 1.3 63.6 + - - +
169D LEU* 3.5 9.9 + - - +
170D ARG* 2.6 64.0 + - - +
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Residues in contact with LEU 167 (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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114D CYS* 3.6 16.7 - - + -
115D ARG 4.2 3.1 - - - +
116D ILE* 3.6 31.4 - - + -
145D GLN* 4.3 15.9 - - + +
163D CYS* 2.9 21.6 + - - +
164D ILE* 3.7 12.8 - - + +
165D THR 3.3 0.2 - - - -
166D GLU* 1.3 85.1 - - + +
168D VAL* 1.3 57.9 + - - +
170D ARG* 3.3 12.9 + - - +
171D ALA* 2.8 29.3 + - - +
201D SO4 3.9 23.8 - - - +
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Residues in contact with VAL 168 (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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9D PHE* 3.4 47.1 - - + -
11D LEU* 3.9 9.4 - - + -
59D LEU* 4.6 2.2 - - + -
82D HIS* 3.6 37.5 - - + +
83D GLY* 3.8 10.8 - - - +
114D CYS* 4.0 10.1 - - + -
164D ILE* 3.2 12.7 + - + +
165D THR* 3.2 20.4 - - - +
167D LEU* 1.3 72.6 - - - +
169D LEU* 1.3 65.1 + - - +
171D ALA* 3.8 2.6 - - - +
172D LYS* 3.1 17.7 + - - +
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Residues in contact with LEU 169 (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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7D HIS* 4.1 20.9 - - + +
9D PHE* 3.6 29.4 - - + -
52D ILE* 4.1 26.7 - - + +
53D ASN* 5.9 1.8 - - - +
55D GLU* 4.4 8.5 - - - +
57D VAL* 4.2 7.9 - - + -
165D THR* 3.1 40.1 + - + +
166D GLU* 3.7 8.1 - - - +
168D VAL* 1.3 76.5 - - - +
170D ARG* 1.3 56.9 + - - +
172D LYS* 3.3 3.3 + - + +
173D LYS* 3.0 29.9 + - - +
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Residues in contact with ARG 170 (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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166D GLU* 2.6 55.6 + - - +
167D LEU* 3.6 12.1 - - - +
169D LEU* 1.3 76.5 - - - +
171D ALA* 1.3 58.5 + - - +
173D LYS* 3.7 17.2 - - + +
174D ASP* 2.8 54.7 + - - +
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Residues in contact with ALA 171 (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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112D ASP 5.8 2.2 - - - +
114D CYS* 3.7 20.4 - - - -
167D LEU 2.8 17.0 + - - +
168D VAL* 3.8 5.2 - - - +
170D ARG* 1.3 78.7 - - - +
172D LYS* 1.3 57.2 + - - +
174D ASP* 3.8 4.4 - - - +
175D ASN* 3.0 42.3 + - - +
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Residues in contact with LYS 172 (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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6D ASP 4.3 2.6 + - - -
7D HIS* 2.9 49.2 + - + +
8D LEU 4.7 5.3 + - - +
9D PHE* 4.0 20.0 - - + -
82D HIS* 6.2 1.6 - - + -
168D VAL 3.1 17.1 + - - +
169D LEU* 3.7 3.1 - - + +
171D ALA* 1.3 76.3 - - - +
173D LYS* 1.3 66.3 + - - +
175D ASN* 3.6 8.1 - - - +
176D LEU* 3.3 30.7 - - + +
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Residues in contact with LYS 173 (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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169D LEU 3.0 17.7 + - - +
170D ARG* 3.7 16.8 - - + +
172D LYS* 1.3 79.8 - - - +
174D ASP* 1.3 71.6 + - - +
176D LEU* 3.3 20.7 - - - +
177D ALA* 4.2 3.5 + - - +
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Residues in contact with ASP 174 (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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170D ARG* 2.8 45.0 + - - +
171D ALA* 3.8 5.6 - - - +
173D LYS* 1.3 80.6 + - - +
175D ASN* 1.3 58.0 + - - +
176D LEU 2.7 17.4 + - - -
177D ALA* 3.2 21.7 + - - +
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Residues in contact with ASN 175 (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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112D ASP* 6.3 1.8 - - - +
171D ALA* 3.0 26.6 + - - +
172D LYS* 3.6 5.8 - - - +
173D LYS 3.5 0.2 - - - -
174D ASP* 1.3 77.2 - - - +
176D LEU* 1.3 66.2 + - - +
177D ALA 3.7 2.0 - - - +
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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