Contacts of the helix formed by residues 168 - 180 (chain E) in PDB entry 1SSP
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 PRO 168 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A T 3.7 22.7 - - - +
5A ORP 3.5 11.7 - - - +
152E GLN* 5.5 1.6 - - - +
166E PRO 4.7 0.2 - - - +
167E PRO* 1.3 85.6 - - + +
169E SER* 1.3 62.5 + - - +
171E GLU* 3.2 9.3 + - + +
172E ASN* 3.0 26.5 + - - +
271E PRO* 3.4 31.4 - - + -
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Residues in contact with SER 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ORP 2.7 37.5 + - - -
147E TYR* 3.9 11.9 - - - -
158E PHE* 4.0 17.3 - - - -
167E PRO 3.3 0.2 - - - -
168E PRO* 1.3 72.8 - - - +
170E LEU* 1.3 58.3 + - - +
172E ASN* 3.1 6.1 + - - +
173E ILE* 2.9 30.5 + - - +
268E HIS* 3.8 2.8 - - - -
269E PRO* 3.7 13.4 - - - +
270E SER* 3.2 25.9 + - - +
271E PRO* 4.2 0.2 - - - +
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Residues in contact with LEU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E TYR* 3.5 14.6 + - - +
158E PHE 3.3 19.7 - - - +
160E VAL* 4.3 2.2 - - + -
166E PRO* 3.8 11.4 - - + -
167E PRO* 3.0 10.8 + - + +
169E SER* 1.3 76.5 - - - +
171E GLU* 1.3 62.3 + - - +
173E ILE* 3.1 23.1 + - + -
174E TYR* 2.8 56.0 + - + +
190E GLY* 3.3 40.2 - - - +
192E LEU* 4.1 12.3 - - + -
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Residues in contact with GLU 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E PRO* 3.3 28.8 - - + +
167E PRO 3.0 16.9 + - - +
168E PRO* 3.2 10.7 + - + +
170E LEU* 1.3 75.8 - - - +
172E ASN* 1.3 58.7 + - - +
174E TYR* 3.4 5.8 + - - +
175E LYS* 2.9 46.1 + - - +
186E HIS* 2.9 37.8 + - - -
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Residues in contact with ASN 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E PRO 3.0 14.7 + - - +
169E SER 3.3 2.9 - - - +
171E GLU* 1.3 75.2 - - - +
173E ILE* 1.3 64.9 + - - +
175E LYS* 3.1 23.0 + - - -
176E GLU* 2.9 21.5 + - - +
269E PRO* 2.8 31.3 + - + +
271E PRO* 3.7 17.4 - - - +
274E VAL* 3.6 22.4 - - + +
278E PHE* 3.7 2.9 - - - -
279E PHE* 3.4 31.4 - - + -
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Residues in contact with ILE 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E PHE* 3.4 45.3 - - + -
169E SER 2.9 18.2 + - - +
170E LEU* 3.1 18.6 + - + +
172E ASN* 1.3 74.1 - - - +
174E TYR* 1.3 57.5 + - + +
176E GLU* 3.3 3.6 + - - +
177E LEU* 2.9 30.1 + - + +
192E LEU* 5.5 1.1 - - + -
195E TRP* 3.8 29.8 - - + -
245E TRP* 3.6 19.1 - - + -
269E PRO* 3.8 13.9 - - + -
278E PHE* 3.8 8.7 - - + -
284E PHE* 3.9 14.2 - - + -
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Residues in contact with TYR 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E PRO* 3.9 4.7 - - + -
170E LEU* 2.8 42.0 + - + +
171E GLU* 3.5 10.1 - - - +
173E ILE* 1.3 75.8 - - + +
175E LYS* 1.3 59.4 + - - +
177E LEU* 3.3 7.0 + - + +
178E SER* 2.9 30.0 + - - -
184E PHE* 3.6 35.7 - + + -
186E HIS* 3.5 39.5 - + + -
187E PRO* 3.3 15.2 - - + +
189E HIS* 2.8 28.7 + - - -
190E GLY* 3.5 10.6 - - - -
191E ASP 4.4 0.3 + - - -
192E LEU* 3.8 13.9 - - + +
195E TRP* 4.6 3.6 - + - -
304E LEU* 3.9 9.5 - - + +
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Residues in contact with LYS 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B A 5.0 19.3 - - - -
171E GLU* 2.9 35.4 + - - +
172E ASN* 3.1 27.1 + - - +
174E TYR* 1.3 76.5 - - - +
176E GLU* 1.3 63.1 + - - +
178E SER* 3.4 8.7 + - - -
179E THR* 3.3 25.1 + - - +
279E PHE* 3.9 24.0 - - + -
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Residues in contact with GLU 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ASN 2.9 7.1 + - - +
173E ILE 3.6 2.9 - - - +
175E LYS* 1.3 74.5 - - - +
177E LEU* 1.3 59.9 + - - +
179E THR* 3.1 12.8 + - - -
180E ASP* 2.8 35.0 + - - +
278E PHE* 3.5 38.1 - - + +
279E PHE* 3.3 13.3 - - + -
280E GLY* 2.8 30.2 + - - -
281E CYS* 4.4 3.4 - - - -
282E ARG* 3.0 30.1 + - - +
284E PHE* 3.8 18.8 - - + -
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Residues in contact with LEU 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ILE* 2.9 23.7 + - + +
174E TYR* 3.3 4.0 + - + +
176E GLU* 1.3 75.2 - - - +
178E SER* 1.3 56.3 + - - +
180E ASP* 4.2 1.1 - - - -
181E ILE* 2.6 45.5 + - + +
184E PHE* 3.5 32.7 - - + +
195E TRP* 3.3 37.0 - - + -
284E PHE* 3.5 37.9 - - + -
301E TRP* 3.5 26.9 - - + -
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Residues in contact with SER 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E TYR 2.9 17.1 + - - -
175E LYS* 3.4 11.2 - - - -
176E GLU 3.1 0.2 - - - -
177E LEU* 1.3 78.5 - - - +
179E THR* 1.3 62.6 + - - +
181E ILE 3.4 11.8 - - - +
182E GLU* 4.7 4.9 + - - +
184E PHE* 3.9 22.5 + - - +
185E VAL* 5.3 2.3 - - - +
186E HIS 6.1 0.9 - - - -
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Residues in contact with THR 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E LYS 3.3 12.6 + - - +
176E GLU* 3.1 22.6 + - - -
178E SER* 1.3 80.0 - - - +
180E ASP* 1.3 61.2 + - - +
181E ILE 4.9 0.7 - - - -
182E GLU* 5.1 1.0 + - - -
280E GLY* 6.0 0.2 - - - -
282E ARG* 4.2 7.4 + - - -
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Residues in contact with ASP 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E GLU* 2.8 28.7 + - - +
177E LEU* 4.0 3.6 - - - +
179E THR* 1.3 80.4 + - - +
181E ILE* 1.3 61.8 + - + +
182E GLU 4.0 1.6 + - - -
282E ARG* 3.0 43.8 + - - +
284E PHE* 3.1 22.5 + - + +
285E SER* 2.6 49.6 + - - -
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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