Contacts of the helix formed by residues 174 - 185 (chain T) in PDB entry 3P71
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 ASP 174 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171T ASP* 3.2 24.6 + - + +
172T LEU 4.5 0.7 - - - -
173T ARG* 1.3 78.2 - - - +
175T LEU* 1.3 61.9 + - - +
176T SER* 3.0 22.4 + - - -
177T GLU* 3.3 27.7 + - - +
178T LEU* 3.3 13.0 + - - +
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Residues in contact with LEU 175 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172T LEU 3.9 12.8 - - - +
173T ARG 3.8 3.7 + - - +
174T ASP* 1.3 71.3 + - - +
176T SER* 1.3 58.9 + - - +
178T LEU* 3.7 13.9 - - + +
179T GLU* 3.0 31.9 + - - +
208T GLN 5.9 0.2 - - - +
211T ASN* 3.5 39.7 - - + +
212T LEU* 3.9 34.8 - - + -
215T TRP* 4.0 25.2 + - + -
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Residues in contact with SER 176 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174T ASP* 3.0 15.4 + - - -
175T LEU* 1.3 75.0 - - - +
177T GLU* 1.3 67.6 + - - +
179T GLU* 4.3 3.2 - - - +
180T GLU* 3.3 27.6 + - - +
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Residues in contact with GLU 177 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124T PRO* 5.5 3.5 - - - +
169T GLY 4.0 0.7 - - - +
170T ALA* 3.8 8.4 - - + -
171T ASP* 3.4 33.1 + - - +
174T ASP* 3.3 26.9 + - - +
175T LEU 3.4 0.2 - - - -
176T SER* 1.3 81.5 + - - +
178T LEU* 1.3 63.6 + - - +
180T GLU* 3.9 6.9 - - - +
181T LYS* 2.8 60.8 + - + +
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Residues in contact with LEU 178 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97T LEU* 4.8 3.4 - - + -
121T VAL* 3.7 34.5 - - + -
168T ILE* 5.7 1.3 - - + +
170T ALA* 4.5 11.6 - - + +
171T ASP 4.7 5.2 - - - +
172T LEU* 4.1 14.4 - - + +
174T ASP 3.3 11.3 + - - +
175T LEU* 3.7 17.7 - - + +
176T SER 3.4 0.2 - - - -
177T GLU* 1.3 78.7 - - - +
179T GLU* 1.3 64.9 + - - +
181T LYS* 3.9 2.4 - - - +
182T LEU* 3.1 40.7 + - + +
212T LEU* 3.9 19.7 - - + -
215T TRP* 3.7 28.5 - - + -
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Residues in contact with GLU 179 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175T LEU 3.0 17.4 + - - +
176T SER* 4.4 3.6 - - - +
178T LEU* 1.3 77.0 - - - +
180T GLU* 1.3 63.9 + - - +
181T LYS 3.4 0.2 + - - -
182T LEU* 3.4 3.4 + - - +
183T LYS* 3.1 55.1 + - + +
187T MET* 5.6 2.2 - - + -
215T TRP* 2.7 46.6 + - + +
219T SER* 4.5 3.0 + - - +
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Residues in contact with GLU 180 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176T SER 3.3 18.7 + - - +
177T GLU* 3.9 7.5 - - - +
179T GLU* 1.3 79.8 - - - +
181T LYS* 1.3 55.2 + - + +
183T LYS* 3.3 5.2 + - - +
184T LYS* 2.8 54.9 + - + +
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Residues in contact with LYS 181 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124T PRO* 6.1 0.2 - - - +
158T HIS* 5.9 2.6 - - - +
159T ILE* 3.8 22.6 - - + +
168T ILE* 3.7 32.1 - - + -
169T GLY 3.1 15.2 + - - +
170T ALA* 4.5 1.6 - - + -
177T GLU* 2.8 52.0 + - + +
178T LEU* 4.0 2.2 - - - +
179T GLU 3.3 0.4 - - - -
180T GLU* 1.3 80.6 - - + +
182T LEU* 1.3 60.5 + - - +
184T LYS* 3.3 20.8 - - + +
185T CYS* 3.0 33.3 + - - -
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Residues in contact with LEU 182 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95T VAL* 4.0 24.2 - - + -
97T LEU* 5.8 0.2 - - + -
119T PHE* 3.8 20.1 - - + -
121T VAL* 4.4 4.5 - - + -
168T ILE* 3.7 23.1 - - + +
178T LEU* 3.1 36.3 + - + +
179T GLU 3.8 3.6 - - - +
181T LYS* 1.3 75.6 - - - +
183T LYS* 1.3 58.3 + - - +
185T CYS* 3.1 13.9 + - - +
186T ASN 3.2 0.3 + - - -
187T MET* 2.9 47.5 + - + +
215T TRP* 3.6 33.0 - - + -
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Residues in contact with LYS 183 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179T GLU* 3.1 49.7 + - + +
180T GLU* 3.7 5.6 - - - +
182T LEU* 1.3 73.2 - - - +
184T LYS* 1.3 58.4 + - - +
186T ASN* 2.8 27.2 + - - +
187T MET* 4.1 26.5 - - + +
189T THR* 4.6 17.4 + - - -
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Residues in contact with LYS 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159T ILE* 5.1 10.9 - - + +
161T ASP* 4.3 4.2 - - - +
180T GLU* 2.8 39.4 + - + +
181T LYS* 3.3 29.2 - - + +
183T LYS* 1.3 72.5 - - - +
185T CYS* 1.3 61.0 + - - +
186T ASN* 3.3 14.7 + - - +
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Residues in contact with CYS 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117T LYS* 2.9 25.6 + - - -
119T PHE* 3.6 14.6 - - + -
159T ILE* 3.9 28.3 - - - -
161T ASP* 3.5 26.7 - - - +
166T ALA* 4.2 5.8 - - + -
168T ILE* 3.9 16.4 - - + -
181T LYS 3.0 20.6 + - - +
182T LEU 3.1 7.5 + - - +
184T LYS* 1.3 76.2 - - - +
186T ASN* 1.3 67.4 + - - +
187T MET 3.4 0.7 + - - -
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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