Contacts of the helix formed by residues 173 - 185 (chain B) in PDB entry 1SA4
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 ASN 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLN* 2.9 26.0 + - + +
135B SER 5.9 1.1 - - - +
136B PRO* 5.4 1.6 + - - +
138B GLY* 5.3 1.0 - - - -
171B ILE 3.3 2.5 + - - +
172B ILE* 1.3 69.8 - - - +
174B ARG* 1.3 57.7 + - - +
175B GLU* 3.3 16.0 - - - +
176B LYS* 3.0 41.5 + - + +
177B LEU* 3.0 27.2 + - - +
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 3.2 23.8 + - + +
173B ASN* 1.3 69.6 + - - +
175B GLU* 1.3 78.4 + - - +
177B LEU* 3.7 7.3 - - - +
178B LEU* 3.1 18.9 + - - +
214B THR* 2.8 24.4 + - - -
215B ASN* 2.9 32.1 + - - +
216B ILE* 3.8 12.7 - - + +
415B PHE* 3.6 25.5 - - + -
418B LYS* 3.7 32.7 - - - +
419B PRO* 3.0 27.9 + - - +
421B PRO* 3.6 16.3 - - + +
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN* 3.3 13.4 - - - +
174B ARG* 1.3 88.2 + - - +
176B LYS* 1.3 64.9 + - + +
178B LEU* 3.5 3.1 + - - +
179B GLN* 3.3 35.9 + - - +
421B PRO* 3.7 28.4 - - + +
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B SER 5.3 0.2 - - - +
136B PRO 3.3 24.0 + - - +
137B GLU* 3.5 17.4 - - - +
138B GLY* 3.5 17.5 - - - -
173B ASN* 3.0 34.0 + - + +
175B GLU* 1.3 76.4 - - + +
177B LEU* 1.3 61.0 + - - +
179B GLN* 3.3 31.7 + - - +
180B TYR* 2.8 30.1 + - - +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLN* 5.9 0.4 - - - +
138B GLY* 4.1 0.4 - - - -
139B GLY* 4.0 20.9 - - - +
140B PHE* 5.7 2.2 - - + -
153B THR* 3.9 24.9 - - + -
157B VAL* 4.8 4.7 - - + -
172B ILE* 4.1 20.9 - - + -
173B ASN 3.0 18.5 + - - +
174B ARG* 3.7 6.5 - - - +
176B LYS* 1.3 76.7 - - - +
178B LEU* 1.3 57.5 + - - +
180B TYR* 3.2 7.8 + - + +
181B LEU* 2.9 38.3 + - + +
210B VAL* 4.4 19.5 - - + -
214B THR* 4.0 13.7 - - + +
216B ILE* 3.6 21.5 - - + -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG 3.1 13.3 + - - +
175B GLU 3.9 4.0 - - - +
177B LEU* 1.3 75.4 - - - +
179B GLN* 1.3 67.0 + - + +
181B LEU* 3.2 4.6 + - + +
182B TYR* 3.0 52.6 + - + -
216B ILE* 3.1 40.6 - - + +
218B THR* 3.9 18.4 - - + -
221B LEU* 4.0 15.0 - - + -
420B VAL* 4.2 4.3 - - + -
421B PRO* 4.0 29.8 - - + +
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Residues in contact with GLN 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLU 5.1 1.3 - - - +
175B GLU* 3.3 21.9 + - - +
176B LYS* 3.3 42.7 + - - +
178B LEU* 1.3 78.5 - - + +
180B TYR* 1.3 62.9 + - - +
182B TYR* 3.2 10.8 + - - +
183B SER* 3.0 22.1 + - - -
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLU* 3.7 23.2 + - - +
138B GLY 3.6 18.6 - - - -
139B GLY* 4.0 11.0 - - - -
148B PRO* 2.9 50.7 + - + -
149B HIS* 3.4 7.3 + - - -
150B LEU* 4.4 7.2 - - + -
153B THR* 4.4 9.6 - - - -
176B LYS 2.8 17.1 + - - +
177B LEU* 3.3 8.5 - - + +
179B GLN* 1.3 77.3 - - - +
181B LEU* 1.3 70.9 + - + +
183B SER* 2.5 34.0 + - - -
184B LEU* 3.3 37.6 + - + +
194B HIS* 3.8 8.1 - - - -
195B VAL* 4.5 5.6 - - + -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LEU* 3.7 30.1 - - + -
177B LEU* 2.9 20.5 + - + +
178B LEU* 3.2 7.8 + - - +
180B TYR* 1.3 80.2 - - + +
182B TYR* 1.3 64.9 + - - +
184B LEU* 3.0 17.6 + - + +
185B LYS 3.2 9.7 + - - -
191B PHE* 3.7 11.3 - - + -
207B ALA* 4.0 21.5 - - + +
210B VAL* 4.3 9.6 - - + -
211B ALA* 4.0 27.6 - - + -
216B ILE* 4.0 17.3 - - + -
221B LEU* 4.1 22.2 - - + -
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LEU* 3.0 45.7 + - + +
179B GLN* 3.3 12.8 - - - +
180B TYR 3.2 0.2 - - - -
181B LEU* 1.3 75.5 - - - +
183B SER* 1.3 58.4 + - - +
184B LEU 3.0 5.2 + - - -
185B LYS* 3.2 23.1 + - - +
218B THR* 2.7 32.2 + - + +
220B ASP* 3.0 28.9 + - - -
221B LEU* 3.8 19.1 - - + -
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 5.1 1.5 + - - -
179B GLN 3.0 11.6 + - - -
180B TYR* 2.5 36.7 + - - -
182B TYR* 1.3 75.3 - - - +
184B LEU* 1.3 64.9 + - - +
185B LYS 5.2 0.7 - - - -
186B GLN* 5.3 1.0 + - - -
192B LEU* 4.9 5.2 - - - +
195B VAL* 4.6 10.3 - - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LEU* 3.6 24.0 - - + -
180B TYR* 3.5 42.4 - - + +
181B LEU* 3.0 10.3 + - + +
183B SER* 1.3 88.1 - - - +
185B LYS* 1.3 64.3 - - - +
186B GLN* 3.3 9.9 + - - -
191B PHE* 3.4 7.8 - - + -
192B LEU* 3.0 51.1 + - + +
193B MET 4.3 1.1 - - - +
194B HIS* 3.5 32.3 - - - +
195B VAL* 3.6 9.0 - - + +
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B LEU 3.2 5.0 + - - +
182B TYR* 3.2 18.9 + - + +
183B SER 5.2 0.7 - - - +
184B LEU* 1.3 77.4 - - - +
186B GLN* 1.3 83.0 + - - +
187B PRO* 4.6 1.6 - - - +
189B GLY* 3.7 16.2 - - - -
190B SER 3.8 1.6 - - - +
191B PHE* 3.5 27.8 - - + -
220B ASP 3.5 7.0 + - - +
221B LEU* 2.8 30.8 + - + +
223B GLU* 2.9 35.7 + - - +
225B THR* 3.9 2.5 - - - -
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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