Contacts of the helix formed by residues 175 - 183 (chain D) in PDB entry 2R92
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 PHE 175 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ALA* 5.2 14.4 - - + -
27D LEU* 4.1 16.4 - - + -
29D LEU* 4.6 17.9 - - + -
47D LEU* 6.0 0.4 - - - +
49D ALA* 4.2 2.4 - - + +
173D HIS* 3.1 25.1 + - + +
174D PRO* 1.3 74.6 - - - +
176D GLU* 1.3 63.8 + - + +
178D ALA* 3.7 1.6 + - - +
179D GLN* 3.0 38.4 + - + +
195D ILE* 6.3 1.1 - - + -
197D SER* 5.5 2.2 - - - -
1G MET* 3.3 41.7 - - + -
3G PHE* 4.5 16.6 - + + -
82G PHE* 5.0 8.3 - + + -
85G GLU* 3.4 37.0 - - + -
86G VAL 6.0 0.2 - - - -
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Residues in contact with GLU 176 (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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27D LEU* 3.9 16.2 - - + +
172D LEU* 3.7 13.3 - - + +
173D HIS* 2.8 34.6 + - - +
175D PHE* 1.3 72.8 - - + +
177D VAL* 1.3 56.2 + - - +
178D ALA 2.5 16.6 + - - -
179D GLN* 2.7 18.7 + - - -
180D LEU* 2.8 18.0 + - - +
195D ILE* 4.2 5.4 - - + -
197D SER* 2.8 52.3 + - - +
198D LEU* 3.5 26.8 - - + +
201D LYS* 3.7 8.8 + - - +
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Residues in contact with VAL 177 (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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49D ALA 5.9 0.2 - - - -
51D ASN* 4.4 6.6 + - - -
164D ILE* 6.4 1.1 - - + -
167D LEU* 3.8 48.8 - - + +
168D LYS* 4.7 15.9 - - + +
172D LEU* 3.4 33.7 - - + +
173D HIS 2.8 24.4 + - - +
174D PRO* 3.7 10.5 - - + +
176D GLU* 1.3 74.7 - - - +
178D ALA* 1.3 57.9 + - - +
180D LEU* 4.4 10.1 - - - -
181D GLY 4.2 0.5 + - - -
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Residues in contact with ALA 178 (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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49D ALA* 3.8 12.3 - - + -
50D LEU 4.2 11.0 - - - +
51D ASN* 3.1 12.8 - - - +
174D PRO 3.1 15.9 + - - +
175D PHE 3.7 2.7 - - - +
176D GLU 2.5 5.5 + - - -
177D VAL* 1.3 74.0 - - - +
179D GLN* 1.3 60.4 + - - +
180D LEU 3.1 1.6 - - - -
181D GLY 2.8 17.7 + - - -
182D SER* 3.0 15.2 + - - -
1G MET 3.3 27.6 - - - +
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Residues in contact with GLN 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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175D PHE* 3.0 36.3 + - + +
176D GLU* 2.7 12.2 + - - +
178D ALA* 1.3 75.7 - - - +
180D LEU* 1.3 58.0 + - - +
182D SER* 4.0 11.8 + - - -
183D LEU* 3.1 43.3 + - + +
194D LEU 5.5 0.9 - - - +
195D ILE* 3.7 27.4 - - + +
1G MET* 3.7 28.0 - - - +
85G GLU* 4.4 2.2 + - - +
86G VAL* 3.0 33.0 + - - +
87G VAL* 5.4 2.4 - - - +
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Residues in contact with LEU 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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153D ARG* 3.5 15.2 + - - -
167D LEU* 4.4 27.4 - - + -
170D THR* 6.2 0.2 - - + -
172D LEU* 3.8 29.2 - - + -
176D GLU* 2.8 18.5 + - - +
177D VAL* 4.7 2.2 - - - +
179D GLN* 1.3 76.3 - - - +
181D GLY* 1.3 60.7 + - - +
183D LEU 3.6 8.3 - - - +
185D CYS* 5.6 2.9 - - - -
191D ALA* 4.9 5.8 - - + -
195D ILE* 3.3 24.9 - - + -
198D LEU* 4.4 12.8 - - + -
207D LEU* 4.5 22.7 - - + -
210D ILE* 5.7 3.8 - - + -
211D LEU* 5.5 8.2 - - + +
214D LEU* 3.8 13.6 - - + +
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Residues in contact with GLY 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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51D ASN* 4.1 20.0 - - - +
52D LEU 5.1 1.0 - - - +
153D ARG* 3.4 26.7 + - - +
154D PHE* 3.7 10.8 - - - -
163D VAL* 5.0 7.2 - - - -
167D LEU* 4.3 11.1 - - - +
177D VAL 4.2 2.6 + - - -
178D ALA 2.8 9.3 + - - -
180D LEU* 1.3 81.8 - - - +
182D SER* 1.3 56.9 + - - +
183D LEU 3.6 0.2 - - - -
214D LEU* 5.2 1.3 - - - -
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Residues in contact with SER 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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51D ASN* 3.7 4.5 - - - +
52D LEU* 3.4 53.3 + - - +
151D PHE 5.2 4.8 - - - +
153D ARG* 5.0 7.5 - - - +
178D ALA 3.0 17.4 + - - -
179D GLN* 4.0 12.6 + - - -
181D GLY* 1.3 75.6 - - - +
183D LEU* 1.3 70.1 + - - +
184D ALA 4.2 1.1 + - - -
88G ASP* 4.6 3.3 - - - +
144G ARG* 4.7 1.2 + - - -
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Residues in contact with LEU 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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52D LEU* 6.2 0.7 - - + -
153D ARG* 3.8 5.7 + - - -
179D GLN* 3.1 46.6 + - + +
180D LEU* 3.6 13.7 - - - +
181D GLY 3.6 0.6 - - - -
182D SER* 1.3 84.7 - - - +
184D ALA* 1.3 64.3 + - - +
185D CYS* 3.3 16.7 + - - +
194D LEU* 4.9 7.4 - - + -
195D ILE* 4.7 11.9 - - + -
211D LEU* 5.4 0.7 - - - +
86G VAL* 3.8 29.2 - - + +
87G VAL* 4.8 1.1 - - + -
88G ASP* 3.5 21.3 - - - +
144G ARG* 3.5 26.7 - - - +
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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