Contacts of the helix formed by residues 159 - 176 (chain C) in PDB entry 1DE4
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 SER 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C PRO 4.3 2.0 + - - -
155C ARG* 3.7 2.8 - - - -
156C GLU* 2.7 43.5 + - - -
157C ALA 3.3 1.2 + - - -
158C GLY* 1.3 80.8 - - - +
160C GLN* 1.3 64.0 + - - +
161C LYS* 3.7 4.9 + - - +
162C ASP* 3.0 16.5 + - - +
163C GLU* 3.0 20.4 + - - +
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Residues in contact with GLN 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C SER* 1.3 74.0 - - - +
161C LYS* 1.3 54.7 + - + +
163C GLU* 2.9 27.3 + - - +
164C ASN* 2.6 65.9 + - - +
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Residues in contact with LYS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASN 2.5 24.5 + - - -
151C SER* 3.6 14.4 + - - +
152C TYR* 4.0 9.2 - - - +
153C VAL* 3.3 24.4 - - + +
154C PRO* 3.1 43.1 - - + +
155C ARG* 4.2 6.2 - - - +
159C SER* 3.3 4.1 + - - +
160C GLN* 1.3 80.1 - - + +
162C ASP* 1.3 62.4 + - - +
164C ASN* 3.5 12.1 - - - +
165C LEU* 3.0 23.4 + - - +
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Residues in contact with ASP 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ARG* 4.1 11.6 - - - +
156C GLU 3.5 10.8 - - - +
157C ALA* 3.6 1.7 - - - -
158C GLY* 3.0 17.4 + - - -
159C SER* 3.0 24.7 + - - +
160C GLN 3.0 0.6 - - - -
161C LYS* 1.3 75.8 - - - +
163C GLU* 1.3 64.9 + - - +
165C LEU* 3.1 7.2 + - - +
166C ALA* 2.9 18.7 + - - +
385C LYS 5.2 0.7 - - - +
386C ILE* 5.4 0.2 - - - -
387C LEU* 5.2 3.0 + - - -
409C ARG* 2.7 36.8 + - - +
410C ASP* 4.8 5.0 + - - -
454C SER* 2.8 26.3 + - - -
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C GLY 5.9 0.2 - - - +
159C SER 3.0 8.4 + - - +
160C GLN* 2.9 32.2 + - - +
162C ASP* 1.3 81.6 - - - +
164C ASN* 1.3 62.7 - - - +
166C ALA* 3.2 6.3 + - - +
167C LEU* 3.0 40.8 + - + +
183C ARG* 5.3 2.2 + - - -
385C LYS* 2.9 39.7 + - - -
387C LEU* 3.6 21.9 - - + +
409C ARG* 5.3 0.2 - - - +
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Residues in contact with ASN 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C SER* 4.0 11.8 + - - +
152C TYR* 4.0 15.6 - - + -
160C GLN* 2.6 45.2 + - - +
161C LYS* 3.5 17.1 - - - +
162C ASP 3.1 0.2 - - - -
163C GLU* 1.3 72.9 - - - +
165C LEU* 1.3 58.0 + - - +
167C LEU* 3.1 12.1 + - - +
168C TYR* 2.9 26.7 + - - +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LEU* 3.2 35.2 - - + -
152C TYR* 3.6 28.2 - - + -
155C ARG* 3.3 39.0 - - - +
161C LYS 3.0 11.0 + - - +
162C ASP 3.1 7.4 + - - +
164C ASN* 1.3 75.5 - - - +
166C ALA* 1.3 57.5 + - - +
168C TYR* 4.0 13.0 - - + -
169C VAL* 3.0 39.6 + - + +
409C ARG* 3.6 22.2 - - + +
423C THR* 4.9 5.6 - - + +
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ASP 2.9 7.4 + - - +
163C GLU* 3.3 13.5 - - - +
164C ASN 3.1 0.2 - - - -
165C LEU* 1.3 75.3 - - - +
167C LEU* 1.3 64.2 + - + +
169C VAL* 3.3 2.7 + - - +
170C GLU* 2.8 29.1 + - - +
387C LEU* 4.4 6.1 - - + -
389C ILE* 3.4 30.5 - - + +
409C ARG* 3.5 28.7 - - - +
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLU* 3.0 38.8 + - + +
164C ASN* 3.6 12.3 - - - +
166C ALA* 1.3 77.6 - - + +
168C TYR* 1.3 66.7 + - - +
170C GLU* 3.8 8.2 - - - +
171C ASN* 3.0 26.0 + - - +
183C ARG* 3.3 35.2 - - - +
387C LEU* 4.5 0.2 - - + -
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Residues in contact with TYR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C THR* 5.3 3.3 - - - +
146C LEU* 3.5 31.5 - - + +
147C LEU* 4.8 0.7 - - + -
152C TYR* 3.7 23.6 - - - +
164C ASN 2.9 13.3 + - - +
165C LEU* 3.4 24.2 - - + +
167C LEU* 1.3 76.5 - - - +
169C VAL* 1.3 63.2 + - + +
171C ASN* 3.2 6.8 + - + +
172C GLN* 3.0 67.1 + - + +
427C LEU* 3.8 19.2 - - + +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 3.0 22.0 + - + +
166C ALA* 3.7 5.6 - - - +
168C TYR* 1.3 79.8 - - + +
170C GLU* 1.3 65.4 + - - +
171C ASN 3.0 1.8 - - - -
172C GLN* 3.1 2.6 + - - +
173C PHE* 3.0 48.3 + - + -
389C ILE* 3.9 11.4 - - + -
409C ARG* 5.3 0.2 - - - -
423C THR* 4.2 21.1 - - + -
426C LEU* 4.9 2.5 - - + -
427C LEU* 3.9 25.1 - - + -
452C SER* 4.2 17.7 - - - +
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Residues in contact with GLU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ALA 2.8 17.6 + - - +
167C LEU* 3.3 9.3 + - - +
169C VAL* 1.3 77.5 - - - +
171C ASN* 1.3 60.3 + - - +
173C PHE* 3.6 6.4 + - - +
174C ARG* 3.4 51.3 + - - +
181C VAL* 3.7 8.2 - - + +
182C TRP* 4.4 2.5 - - - +
183C ARG* 2.7 60.2 + - - +
389C ILE* 3.7 19.5 - - + +
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Residues in contact with ASN 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C LEU 3.0 17.7 + - - +
168C TYR* 3.5 6.7 - - + +
169C VAL 3.0 0.2 - - - -
170C GLU* 1.3 76.0 - - - +
172C GLN* 1.3 63.3 + - - +
173C PHE 3.1 2.0 - - - -
174C ARG* 3.0 19.2 + - - +
175C GLU* 2.8 41.6 + - - +
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Residues in contact with GLN 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TYR* 3.0 61.6 + - + +
169C VAL 3.1 6.9 + - - +
171C ASN* 1.3 78.6 - - - +
173C PHE* 1.3 57.1 + - - +
175C GLU* 3.5 25.0 + - - +
176C PHE* 2.9 58.2 + - + -
427C LEU* 3.7 21.4 - - + +
428C LYS* 5.6 2.6 + - - -
431C GLN* 5.4 0.2 + - - -
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Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C VAL* 3.0 28.7 + - + -
170C GLU 3.6 9.4 - - - +
172C GLN* 1.3 79.8 - - - +
174C ARG* 1.3 60.6 + - - +
176C PHE* 3.2 23.5 + + - +
177C LYS 3.2 8.1 + - - -
178C LEU* 3.5 23.5 + - + +
181C VAL* 3.7 14.1 - - + -
389C ILE* 3.8 22.9 - - + -
390C PHE 3.4 22.0 - - - -
391C GLY* 3.6 20.6 - - - -
426C LEU* 4.0 15.9 - - + -
427C LEU* 4.3 10.1 - - + -
430C ALA* 3.9 18.2 - - + -
450C PHE* 3.6 22.9 - - + -
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Residues in contact with ARG 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLU* 3.4 45.5 + - - +
171C ASN* 3.0 23.0 + - - +
173C PHE* 1.3 74.4 - - - +
175C GLU* 1.3 57.5 + - - +
177C LYS* 2.7 31.0 + - - +
178C LEU 5.2 0.2 - - - +
181C VAL* 3.3 41.1 + - + +
182C TRP* 5.4 0.4 - - - +
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Residues in contact with GLU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ASN* 2.8 26.2 + - - +
172C GLN* 3.5 32.5 + - - +
174C ARG* 1.3 72.3 - - - +
176C PHE* 1.3 65.3 + - + +
177C LYS* 2.8 23.0 + - - +
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Residues in contact with PHE 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLN* 2.9 63.2 + - + +
173C PHE* 3.2 12.8 + + - +
175C GLU* 1.3 83.6 - - + +
177C LYS* 1.3 60.9 + - - +
178C LEU* 3.9 11.2 - - + -
427C LEU* 3.1 35.0 - - + -
428C LYS* 4.9 3.1 - - - -
430C ALA* 3.8 12.1 - - + -
431C GLN* 3.3 51.1 - - + -
434C SER* 2.4 34.1 + - - +
438C LEU* 4.1 2.9 - - - +
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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
------------------------------------------------------------
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