Contacts of the helix formed by residues 154 - 166 (chain D) in PDB entry 5SWW
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 THR 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D ILE 3.5 13.9 - - - +
153D MET* 1.3 72.6 - - - +
155D TYR* 1.3 68.7 + - - +
156D ASP* 3.7 11.8 + - - +
157D GLU* 2.4 43.2 + - - +
158D PHE* 3.1 20.3 + - - -
179D LEU* 4.4 0.2 - - - -
183D SER* 3.3 19.7 - - - +
187D SER* 4.5 8.5 - - - +
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Residues in contact with TYR 155 (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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154D THR* 1.3 75.3 - - - +
156D ASP* 1.3 71.3 + - - +
158D PHE* 3.4 2.2 + - - +
159D LYS* 2.9 63.2 + - + +
173D PHE* 3.7 35.4 + + - -
175D PRO* 4.1 24.2 - - + +
179D LEU* 3.8 21.6 - - + +
180D ASP* 4.1 15.6 + - - +
183D SER* 5.4 0.4 - - - -
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Residues in contact with ASP 156 (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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154D THR* 3.2 11.4 + - - +
155D TYR* 1.3 91.9 - - - +
157D GLU* 1.3 65.8 + - - +
159D LYS* 3.5 6.4 + - - +
160D HIS* 2.9 28.2 + - - +
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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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95D PHE* 4.2 12.8 - - + -
125D PHE* 3.9 36.9 - - + -
152D ILE 4.7 2.0 - - - -
153D MET* 3.7 20.2 - - + -
154D THR* 2.4 53.4 + - - +
156D ASP* 1.3 82.2 - - - +
158D PHE* 1.3 59.0 + - - +
160D HIS* 3.2 6.9 + - - +
161D CYS* 2.9 34.1 + - - -
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Residues in contact with PHE 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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18D PHE* 3.7 11.5 - + + -
22D PHE* 3.2 32.5 - - + -
24D ASN* 3.7 26.2 - - + -
127D ALA* 4.1 7.9 - - + -
153D MET* 3.6 52.7 - - + -
154D THR 3.1 21.2 + - - -
155D TYR 3.9 2.2 - - - +
157D GLU* 1.3 74.6 - - - +
159D LYS* 1.3 59.0 + - - +
161D CYS 3.4 0.5 + - - -
162D TRP* 2.9 29.3 + - - +
173D PHE* 3.5 23.3 - - + -
176D TRP* 3.5 15.7 - + - -
179D LEU* 3.6 24.9 - - + -
183D SER* 5.1 0.2 - - - -
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Residues in contact with LYS 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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155D TYR* 2.9 48.6 + - + +
156D ASP* 3.8 7.0 - - - +
158D PHE* 1.3 76.7 - - - +
160D HIS* 1.3 56.8 + - - +
162D TRP* 3.3 0.9 + - - +
163D ASP* 2.9 51.0 + - - +
172D PRO* 6.5 0.9 - - - -
173D PHE* 3.9 29.3 - - + +
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Residues in contact with HIS 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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36D GLU* 2.8 24.6 + - - -
52D ARG* 4.5 10.1 - - - -
95D PHE* 3.5 29.8 - + - -
156D ASP 2.9 18.7 + - - +
157D GLU* 3.5 6.7 - - - +
159D LYS* 1.3 77.4 - - - +
161D CYS* 1.3 54.7 + - - +
163D ASP* 3.2 4.7 + - - +
164D THR* 2.7 66.4 + - + +
165D PHE* 4.8 0.2 - + - -
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Residues in contact with CYS 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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18D PHE* 3.6 22.7 - - + -
22D PHE* 5.2 1.1 - - - -
34D CYS* 4.8 4.7 - - - -
95D PHE* 3.3 48.9 - - - -
153D MET* 3.8 8.5 - - - -
157D GLU 2.9 20.6 + - - +
158D PHE 3.9 1.3 - - - +
160D HIS* 1.3 75.8 - - - +
162D TRP* 1.3 57.7 + - - +
165D PHE* 2.9 41.1 + - + +
166D VAL* 3.3 10.3 + - - +
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Residues in contact with TRP 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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15D PRO* 4.1 18.2 - - + -
18D PHE* 3.6 24.2 - + + -
19D THR* 4.0 21.1 - - + -
158D PHE 2.9 18.7 + - - +
159D LYS 3.6 3.8 - - - +
161D CYS* 1.3 77.9 - - - +
163D ASP* 1.3 75.3 + - - +
166D VAL* 3.3 42.1 - - + +
168D HIS* 3.3 35.0 + - + +
171D CYS* 2.7 33.0 + - + -
172D PRO 3.5 11.0 - - - -
173D PHE* 3.5 34.5 - + + -
174D GLN* 5.6 1.3 - - + -
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Residues in contact with ASP 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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159D LYS* 2.9 44.9 + - - +
160D HIS* 3.2 4.9 + - - +
162D TRP* 1.3 94.3 - - - +
164D THR* 1.3 65.6 + - + +
166D VAL 4.6 0.6 - - - +
168D HIS* 3.1 29.4 + - + -
171D CYS 5.2 0.2 - - - +
172D PRO* 5.1 3.1 - - - +
173D PHE 4.7 3.3 + - - -
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Residues in contact with THR 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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10D ARG* 6.1 0.3 - - - -
12D LEU* 3.9 14.6 - - - +
52D ARG* 4.1 28.4 - - - +
160D HIS* 2.7 48.6 + - + +
163D ASP* 1.3 86.0 - - + +
165D PHE* 1.3 82.4 + - - +
166D VAL 3.7 0.9 - - - -
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Residues in contact with PHE 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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12D LEU* 3.8 9.4 - - - +
13D MET* 2.9 33.4 + - + +
34D CYS* 3.7 38.4 - - + -
35D TYR 3.6 9.0 - - - -
36D GLU* 3.5 31.9 - - + -
52D ARG* 3.6 20.0 - - + -
53D GLY* 3.3 30.7 - - - -
54D PHE* 4.9 6.1 - + + -
95D PHE* 3.9 15.5 - + - -
161D CYS* 2.9 24.0 + - + +
164D THR* 1.3 99.9 - - - +
166D VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 4.1 5.9 - - - +
13D MET* 3.7 15.7 - - + +
15D PRO* 3.9 13.9 - - + -
18D PHE* 3.5 35.9 - - + -
161D CYS 3.3 14.9 + - - +
162D TRP* 3.3 45.4 + - + +
163D ASP 4.6 1.0 - - - +
164D THR 5.0 0.3 - - - -
165D PHE* 1.3 81.2 + - - +
167D ASP* 1.3 65.1 + - - +
168D HIS* 2.8 32.3 + - - +
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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