Contacts of the helix formed by residues 190 - 196 (chain D) in PDB entry 3SPD
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 LEU 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D ALA* 3.8 17.9 - - + -
172D PRO* 3.7 14.4 - - + +
173D PHE* 3.5 46.4 - - + +
185D PRO* 3.9 18.2 - - + -
186D THR 5.1 1.1 - - - +
188D GLY 3.5 1.4 - - - -
189D THR* 1.3 93.3 - - - +
191D THR* 1.3 66.8 + - - +
192D SER* 2.9 5.6 + - - -
193D LEU* 3.0 40.6 + - + +
194D PHE* 4.0 7.1 - - - -
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Residues in contact with THR 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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188D GLY* 4.1 19.2 + - - +
189D THR 3.4 2.6 + - - -
190D LEU* 1.3 77.0 - - - +
192D SER* 1.3 65.0 + - - +
193D LEU 3.3 1.4 + - - -
194D PHE* 3.4 25.9 + - - +
195D GLN* 4.8 5.0 + - - +
1H G 4.9 7.5 - - + +
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Residues in contact with SER 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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189D THR 4.9 3.5 + - - -
190D LEU* 2.9 3.3 + - - -
191D THR* 1.3 79.1 + - - +
193D LEU* 1.3 69.7 + - - +
194D PHE 3.1 3.4 + - - -
195D GLN* 3.3 20.5 + - - +
196D GLU* 3.9 14.8 + - - +
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Residues in contact with LEU 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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167D ILE* 3.8 22.3 - - + +
171D SER* 3.5 23.1 - - - +
172D PRO* 3.9 21.3 - - + -
173D PHE* 3.9 12.3 - - + +
190D LEU* 3.0 40.2 + - + +
192D SER* 1.3 81.8 + - - +
194D PHE* 1.3 64.2 + - + +
195D GLN 3.1 2.0 + - - -
196D GLU* 3.1 43.5 + - - +
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Residues in contact with PHE 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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163D SER* 5.2 0.3 - - - -
164D ALA* 3.5 40.9 + - + -
167D ILE* 3.6 15.4 - - + +
168D SER* 4.0 9.0 - - - -
173D PHE* 3.8 38.1 - + + -
190D LEU 4.0 10.1 - - - -
191D THR* 3.5 18.2 - - - +
192D SER 3.1 2.2 - - - -
193D LEU* 1.3 79.2 - - + +
195D GLN* 1.3 71.0 + - - +
196D GLU 3.4 0.4 - - - -
209D ARG* 3.0 25.1 + - - -
1H G 3.1 62.4 - + + +
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Residues in contact with GLN 195 (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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191D THR 4.8 4.6 + - - +
192D SER* 3.3 13.9 + - - +
193D LEU 3.1 1.0 - - - -
194D PHE* 1.3 94.5 + - - +
196D GLU* 1.3 67.0 + - - +
197D ASP* 5.1 0.7 - - - +
209D ARG* 3.4 21.7 + - - +
10G A 4.5 12.4 + - - -
1H G 4.2 12.1 + - - -
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Residues in contact with GLU 196 (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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167D ILE* 4.1 6.8 - - + +
192D SER* 3.9 12.5 + - - +
193D LEU* 3.1 44.3 + - - +
194D PHE 3.4 0.2 - - - -
195D GLN* 1.3 79.8 - - - +
197D ASP* 1.3 71.1 + - - +
198D LEU 3.7 0.3 + - - -
209D ARG* 2.7 25.6 + - - -
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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