Contacts of the helix formed by residues 178 - 194 (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 GLY 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D ASN* 3.6 2.5 - - - +
176D TRP* 3.3 1.2 + - - -
177D ASP* 1.3 73.0 - - - +
179D LEU* 1.3 64.0 + - - +
181D GLU* 3.2 29.7 + - - -
182D HIS* 2.5 44.0 + - - +
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Residues in contact with LEU 179 (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 ASN* 3.0 10.1 + - - -
154D THR 4.4 0.2 - - - -
155D TYR* 3.8 26.9 - - + +
158D PHE* 3.6 28.3 - - + -
173D PHE* 3.6 32.1 - - + -
175D PRO* 3.9 9.2 - - + -
176D TRP* 3.4 52.9 + - + +
177D ASP 3.4 0.6 + - - -
178D GLY* 1.3 76.5 - - - +
180D ASP* 1.3 74.5 + - - +
181D GLU* 3.5 0.6 + - - -
183D SER* 2.9 28.3 + - - -
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Residues in contact with ASP 180 (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* 4.1 18.8 + - - +
175D PRO* 5.1 6.2 - - - +
176D TRP 5.4 0.3 - - - +
179D LEU* 1.3 89.1 + - - +
181D GLU* 1.3 64.7 + - - +
183D SER* 3.7 6.1 - - - -
184D GLN* 2.9 45.5 + - + +
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Residues in contact with GLU 181 (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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178D GLY* 3.2 34.0 + - - +
179D LEU 3.3 0.7 + - - -
180D ASP* 1.3 79.6 + - - +
182D HIS* 1.3 66.8 + - + +
184D GLN* 3.1 13.2 + - - +
185D ALA* 2.9 23.2 + - - +
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Residues in contact with HIS 182 (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 ASN* 3.4 34.3 - - + +
25D GLY* 3.7 22.9 + - - -
177D ASP 5.0 2.7 - - - -
178D GLY* 2.5 38.4 + - - +
181D GLU* 1.3 79.2 - - + +
183D SER* 1.3 57.2 + - - +
185D ALA* 4.4 7.2 - - + -
186D LEU* 2.9 39.8 + - + +
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Residues in contact with SER 183 (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 ASN* 3.6 6.9 - - - +
152D ILE* 3.9 5.4 - - - +
153D MET 2.8 26.5 + - - -
154D THR* 3.3 25.2 - - - +
179D LEU* 2.9 23.2 + - - -
180D ASP* 3.7 8.1 - - - -
182D HIS* 1.3 78.7 - - - +
184D GLN* 1.3 53.5 + - - +
186D LEU* 4.8 0.7 - - - -
187D SER* 2.6 38.2 + - - -
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Residues in contact with GLN 184 (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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180D ASP* 2.9 33.3 + - - +
181D GLU* 3.5 10.4 - - - +
183D SER* 1.3 74.7 - - - +
185D ALA* 1.3 60.6 + - - +
187D SER* 3.3 6.3 + - - -
188D GLY* 2.9 25.8 + - - -
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Residues in contact with ALA 185 (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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181D GLU 2.9 15.8 + - - +
182D HIS* 3.8 8.5 - - + +
184D GLN* 1.3 76.4 - - - +
186D LEU* 1.3 61.0 + - + +
188D GLY* 3.1 3.5 + - - -
189D ARG* 2.9 34.9 + - + +
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Residues in contact with LEU 186 (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 ASN* 4.5 13.2 - - + +
127D ALA 3.3 27.4 - - - +
128D ARG* 3.8 15.0 - - + -
129D ILE* 3.7 28.3 - - + +
152D ILE* 3.5 22.7 - - + +
182D HIS* 2.9 24.3 + - + +
183D SER* 5.3 0.2 - - - -
185D ALA* 1.3 77.3 - - + +
187D SER* 1.3 57.2 + - - +
189D ARG* 3.3 21.6 + - - +
190D LEU* 2.9 31.4 + - - +
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Residues in contact with SER 187 (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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152D ILE* 3.6 21.9 + - - +
154D THR* 4.5 8.8 - - - +
183D SER* 2.6 29.7 + - - -
184D GLN* 3.6 7.4 - - - -
186D LEU* 1.3 77.6 - - - +
188D GLY* 1.3 57.6 + - - +
190D LEU* 3.9 1.8 - - - +
191D ARG* 2.9 29.8 + - - +
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Residues in contact with GLY 188 (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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184D GLN 2.9 14.4 + - - -
185D ALA 3.1 4.0 + - - -
187D SER* 1.3 75.3 - - - +
189D ARG* 1.3 58.2 + - - +
191D ARG* 3.2 10.1 + - - +
192D ALA* 2.9 28.6 + - - +
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Residues in contact with ARG 189 (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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129D ILE* 4.0 16.3 + - + +
131D ASP* 3.5 29.9 + - - +
136D TYR* 3.2 41.6 + - - -
185D ALA* 2.9 20.4 + - + +
186D LEU* 3.7 29.9 - - - +
188D GLY* 1.3 76.1 - - - +
190D LEU* 1.3 57.7 + - - +
192D ALA* 3.1 8.8 + - - +
193D ILE* 2.9 35.6 + - + +
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Residues in contact with LEU 190 (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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129D ILE* 4.5 2.8 - - + +
140D LEU* 3.6 30.5 - - + -
150D VAL* 3.5 33.0 - - + +
151D SER* 3.7 18.6 - - - +
152D ILE* 3.7 21.8 - - + +
186D LEU 2.9 17.2 + - - +
187D SER* 4.0 2.7 - - - +
189D ARG* 1.3 75.8 - - - +
191D ARG* 1.3 58.0 + - - +
193D ILE* 4.2 6.3 - - + -
194D LEU* 2.9 55.0 + - + +
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Residues in contact with ARG 191 (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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187D SER 2.9 20.2 + - - +
188D GLY* 3.4 11.0 - - - +
190D LEU* 1.3 75.0 - - - +
192D ALA* 1.3 60.0 + - - +
194D LEU* 4.0 7.1 + - - +
195D GLN* 3.3 25.4 + - - +
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Residues in contact with ALA 192 (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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188D GLY 2.9 12.6 + - - +
189D ARG* 3.1 10.5 + - - +
191D ARG* 1.3 75.7 - - - +
193D ILE* 1.3 65.9 + - + +
195D GLN* 3.6 27.8 - - - +
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Residues in contact with ILE 193 (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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129D ILE* 5.1 2.2 - - + -
136D TYR* 3.7 13.7 - - + -
137D LYS* 3.6 58.6 - - + +
140D LEU* 3.7 25.1 - - + -
141D GLN* 3.3 30.9 + - + +
144D ARG* 4.5 0.7 + - - -
189D ARG* 2.9 29.5 + - + +
190D LEU* 3.0 7.3 + - + +
192D ALA* 1.3 82.0 - - + +
194D LEU* 1.3 63.7 + - + +
195D GLN* 3.1 7.1 + - - +
196D ASN* 4.7 1.7 - - - +
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Residues in contact with LEU 194 (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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140D LEU* 3.8 30.3 - - + +
141D GLN* 4.0 4.7 - - + +
144D ARG* 3.3 46.6 + - + +
150D VAL* 4.0 26.9 - - + +
190D LEU* 2.9 37.4 + - + +
191D ARG* 4.2 4.5 - - - +
192D ALA 3.5 0.2 - - - -
193D ILE* 1.3 80.0 - - + +
195D GLN* 1.3 61.0 + - - +
196D ASN 3.8 0.9 + - - +
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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
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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