Contacts of the helix formed by residues 155 - 175 (chain D) in PDB entry 5EJK
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 MSE 155 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D PRO 6.1 1.1 - - - +
53D ARG* 5.8 8.5 - - + +
62D GLN* 3.7 26.7 - - - +
81D VAL* 4.7 13.7 - - + +
82D ASP 5.2 0.9 - - - +
83D THR* 3.8 44.4 - - + +
151D GLN* 3.8 14.1 - - + +
152D GLY* 2.9 17.9 + - - +
153D GLN 3.3 0.6 - - - -
154D ALA* 1.3 83.8 - - - +
156D VAL* 1.3 59.9 + - - +
157D GLU 3.4 0.7 - - - -
158D ARG* 3.2 11.1 - - - +
159D ALA* 2.9 26.0 + - - +
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLN* 3.2 31.2 - - + +
64D ASP* 4.1 23.6 - - + +
79D VAL* 4.0 22.0 - - + -
81D VAL* 4.3 9.0 - - + -
148D GLY* 6.1 5.6 - - - -
152D GLY 2.9 23.4 + - - +
153D GLN* 5.0 0.7 - - - -
155D MSE 1.3 72.2 - - - +
157D GLU* 1.3 72.7 + - + +
159D ALA* 3.2 4.5 + - - +
160D ASN* 2.9 34.0 + - - +
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Residues in contact with GLU 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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64D ASP* 6.2 0.2 - - - +
153D GLN* 3.1 46.4 + - - +
155D MSE 3.4 0.2 - - - -
156D VAL* 1.3 81.8 - - + +
158D ARG* 1.3 61.3 + - - +
160D ASN* 3.3 18.0 - - + +
161D ARG* 2.9 59.6 + - - +
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Residues in contact with ARG 158 (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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86D SER* 5.2 1.6 + - - -
153D GLN 4.4 0.2 + - - -
154D ALA* 3.2 27.4 + - - +
155D MSE 3.2 15.0 - - - +
156D VAL 3.2 0.4 - - - -
157D GLU* 1.3 78.1 - - - +
159D ALA* 1.3 56.8 + - - +
161D ARG* 4.0 8.7 - - - +
162D MSE 2.8 59.8 + - + +
201D ARG* 3.9 34.2 + - - +
202D GLY* 5.9 2.0 - - - -
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D VAL* 4.7 14.1 - - + -
81D VAL* 4.6 7.6 - - + -
88D ILE* 3.7 32.3 - - + -
155D MSE 2.9 13.1 + - - +
156D VAL* 3.2 12.1 + - - +
158D ARG* 1.3 74.1 - - - +
160D ASN* 1.3 66.9 + - - +
162D MSE 4.3 4.5 - - - -
163D MSE 2.9 30.4 + - - +
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Residues in contact with ASN 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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64D ASP* 4.6 5.1 + - - -
66D THR* 2.9 40.9 + - + +
79D VAL* 3.2 32.2 - - - +
156D VAL* 2.9 27.3 + - - +
157D GLU* 3.1 23.9 + - + +
159D ALA* 1.3 77.5 - - - +
161D ARG* 1.3 63.1 + - + +
163D MSE 3.2 2.7 + - - +
164D LYS* 2.9 34.7 + - - +
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Residues in contact with ARG 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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153D GLN* 5.0 7.1 + - - +
154D ALA* 6.0 1.0 - - - +
157D GLU* 2.9 55.4 + - - +
158D ARG* 4.5 5.9 - - - +
160D ASN* 1.3 76.7 - - + +
162D MSE 1.3 58.3 + - - +
164D LYS* 3.8 17.0 - - + +
165D ASP* 2.9 41.2 + - - +
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Residues in contact with MSE 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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88D ILE* 5.6 1.1 - - + -
158D ARG* 2.8 60.9 + - + +
159D ALA* 3.9 4.5 - - - +
161D ARG* 1.3 74.7 - - - +
163D MSE 1.3 61.6 + - - +
165D ASP* 4.4 3.0 - - - +
166D LYS* 2.9 34.6 + - - +
196D LEU* 3.8 27.5 - - + +
201D ARG* 3.7 43.1 - - + -
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Residues in contact with MSE 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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77D LEU* 4.1 11.0 - - + -
79D VAL* 5.1 3.4 - - + -
88D ILE* 3.8 24.9 - - + -
90D VAL* 3.7 45.3 - - + -
159D ALA 2.9 18.9 + - - +
160D ASN* 3.6 4.3 - - - +
162D MSE 1.3 76.0 - - - +
164D LYS* 1.3 60.9 + - + +
166D LYS* 4.5 2.0 - - - -
167D ILE* 2.9 61.0 + - + +
189D MSE 3.9 11.7 - - + -
192D ALA* 3.9 24.7 - - + -
193D MSE 4.9 9.2 - - + -
196D LEU* 4.5 2.9 - - - -
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Residues in contact with LYS 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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66D THR* 3.3 30.4 - - - +
67D LEU 3.2 30.2 + - - -
68D GLU* 3.2 39.8 + - + +
77D LEU* 6.2 1.1 - - + -
160D ASN* 2.9 25.7 + - - +
161D ARG* 3.9 14.7 - - + +
163D MSE 1.3 78.4 - - + +
165D ASP* 1.3 59.4 + - - +
167D ILE* 3.9 1.9 - - - +
168D ARG* 2.9 30.1 + - - +
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Residues in contact with ASP 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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39D HIS 6.0 2.0 - - - +
161D ARG* 2.9 29.0 + - - +
162D MSE 4.4 2.5 - - - +
164D LYS* 1.3 77.7 - - - +
166D LYS* 1.3 61.6 + - - +
168D ARG* 3.4 27.5 + - - +
169D VAL* 2.9 38.8 + - + +
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Residues in contact with LYS 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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12D LEU 4.1 13.2 + - - +
13D HIS* 3.4 32.1 + - + +
40D CYS* 5.9 2.8 - - - -
162D MSE 2.9 26.3 + - - +
163D MSE 4.0 2.7 - - - +
164D LYS 3.3 0.2 - - - -
165D ASP* 1.3 75.5 - - - +
167D ILE* 1.3 60.4 + - - +
169D VAL* 3.4 5.2 + - + +
170D LEU* 2.9 42.5 + - + +
192D ALA* 4.0 26.2 - - + +
195D ALA* 4.3 7.8 - - + +
196D LEU* 3.6 33.1 - - + +
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Residues in contact with ILE 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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68D GLU* 5.7 4.9 - - + -
70D ARG* 5.0 9.0 - - + -
71D MSE 3.7 40.4 - - + -
77D LEU* 4.5 10.3 - - + -
163D MSE 2.9 46.6 + - + +
164D LYS* 4.1 3.4 - - - +
166D LYS* 1.3 75.9 - - - +
168D ARG* 1.3 57.8 + - - +
170D LEU* 4.5 1.6 - - - -
171D ALA* 2.9 29.3 + - - +
180D ILE* 3.9 13.7 - - + -
188D MSE 3.7 12.5 - - + +
189D MSE 4.2 6.5 - - - -
192D ALA* 4.0 18.4 - - + -
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Residues in contact with ARG 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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39D HIS* 3.2 44.2 + - - +
68D GLU* 4.7 1.1 - - - +
70D ARG* 3.4 46.8 - - - +
164D LYS 2.9 21.4 + - - +
165D ASP* 3.6 26.1 + - - +
166D LYS 3.2 0.2 - - - -
167D ILE* 1.3 77.7 - - - +
169D VAL* 1.3 60.4 + - + +
171D ALA* 4.1 1.2 - - - +
172D GLU* 2.9 47.2 + - - +
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Residues in contact with VAL 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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13D HIS* 3.3 49.4 + - + +
37D CYS* 5.0 0.7 - - - -
39D HIS* 3.7 37.5 - - + +
40D CYS* 5.6 4.0 - - - -
165D ASP* 2.9 23.7 + - + +
166D LYS* 4.0 8.1 - - + +
168D ARG* 1.3 80.0 - - + +
170D LEU* 1.3 61.5 + - + +
172D GLU* 4.1 5.1 - - - +
173D GLY* 2.9 25.6 + - - -
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Residues in contact with LEU 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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11D ALA 3.2 27.4 - - - +
12D LEU* 4.4 14.1 - - + +
13D HIS* 5.0 3.6 - - + -
166D LYS* 2.9 30.4 + - + +
167D ILE* 4.7 0.4 - - - -
169D VAL* 1.3 77.7 - - + +
171D ALA* 1.3 57.1 + - - +
173D GLY* 3.3 2.2 + - - -
174D ASP* 2.8 35.4 + - - +
188D MSE 3.6 21.8 - - + +
191D LYS* 3.7 31.4 - - + +
192D ALA* 3.7 36.3 - - + +
195D ALA* 5.9 0.2 - - + -
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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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70D ARG* 5.5 5.4 - - - +
167D ILE* 2.9 19.0 + - + +
168D ARG* 4.1 2.9 - - - +
170D LEU* 1.3 76.9 - - - +
172D GLU* 1.3 57.5 + - + +
174D ASP* 3.0 4.8 + - - +
175D GLY 2.9 22.7 + - - -
176D PHE* 2.9 24.6 + - + +
180D ILE* 3.6 31.9 - - + -
188D MSE 3.5 11.8 - - + +
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Residues in contact with GLU 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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39D HIS* 2.8 43.0 + - + +
70D ARG* 3.9 20.7 + - - +
168D ARG* 2.9 36.7 + - - +
169D VAL* 4.1 4.0 - - - +
171D ALA* 1.3 76.5 - - - +
173D GLY* 1.3 62.6 + - - +
175D GLY* 3.1 13.7 + - - +
176D PHE 4.0 12.8 - - - +
177D MSE 4.0 22.1 - - - +
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Residues in contact with GLY 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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10D THR 5.7 3.1 - - - -
13D HIS* 5.4 5.8 - - - -
169D VAL 2.9 20.1 + - - -
170D LEU* 3.6 1.6 - - - -
172D GLU* 1.3 76.2 - - - +
174D ASP* 1.3 63.5 + - - +
175D GLY 3.7 0.2 + - - -
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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 LEU* 2.8 20.6 + - - +
171D ALA* 3.0 8.2 + - - +
173D GLY* 1.3 79.2 - - - +
175D GLY* 1.3 58.5 + - - +
176D PHE* 3.6 23.4 - - + -
188D MSE 3.8 20.2 - - - +
191D LYS* 4.8 12.6 - - - +
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Residues in contact with GLY 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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171D ALA 2.9 2.0 + - - -
172D GLU 3.1 12.0 + - - -
173D GLY 3.3 0.8 - - - -
174D ASP* 1.3 78.5 - - - +
176D PHE* 1.3 70.0 + - - +
177D MSE 3.9 3.3 + - - +
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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
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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