Contacts of the helix formed by residues 173 - 185 (chain D) in PDB entry 2RHM
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 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D GLN 3.8 1.9 + - - +
172D ILE* 1.3 70.1 - - - +
174D MSE 1.3 63.7 + - - +
175D ASN* 2.9 24.3 + - - +
176D ALA* 3.1 33.1 + - + +
177D ILE* 3.5 9.9 + - - +
196D GOL 3.0 16.9 + - - +
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Residues in contact with MSE 174 (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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19D THR* 4.3 10.5 - - + +
20D LEU* 3.8 45.5 - - + +
23D ALA* 3.4 31.9 - - + -
24D LEU* 5.5 1.1 - - - -
172D ILE* 3.5 14.8 + - + +
173D ASP* 1.3 73.3 + - - +
175D ASN* 1.3 62.2 + - - +
177D ILE* 3.0 27.9 + - - +
178D VAL* 3.1 18.9 + - + +
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Residues in contact with ASN 175 (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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173D ASP* 2.9 11.2 + - - +
174D MSE 1.3 78.2 - - - +
176D ALA* 1.3 59.4 + - - +
178D VAL* 3.1 10.0 + - - +
179D GLN* 2.8 60.0 + - - +
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Residues in contact with ALA 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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173D ASP* 3.1 34.8 + - + +
175D ASN* 1.3 77.7 - - - +
177D ILE* 1.3 57.1 + - - +
179D GLN* 3.5 7.6 + - - +
180D TRP* 3.0 27.4 + - - +
196D GOL 4.4 11.4 - - - -
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Residues in contact with ILE 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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20D LEU* 4.1 18.4 - - + -
24D LEU* 4.2 8.7 - - + -
108D ILE* 4.0 25.1 - - + -
162D LEU* 4.5 14.1 - - + -
164D VAL* 3.9 26.9 - - + -
172D ILE* 3.7 30.1 - - + -
173D ASP 3.8 8.3 - - - +
174D MSE 3.0 13.8 + - - +
176D ALA* 1.3 75.4 - - - +
178D VAL* 1.3 65.3 + - - +
180D TRP* 3.3 8.2 + - - +
181D VAL* 3.1 21.5 + - - +
196D GOL 4.5 11.4 - - - -
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Residues in contact with VAL 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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23D ALA 4.1 18.6 - - - +
24D LEU* 3.9 21.5 - - + -
27D GLY* 4.1 21.3 - - - +
28D LEU* 3.7 19.7 - - + +
174D MSE 3.1 19.7 + - + +
175D ASN* 3.5 12.1 - - - +
177D ILE* 1.3 75.9 - - - +
179D GLN* 1.3 76.9 + - - +
181D VAL* 3.2 5.9 + - - +
182D ARG* 3.1 23.3 + - - +
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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 ASN* 2.8 50.7 + - - +
176D ALA* 3.8 7.4 - - - +
178D VAL* 1.3 87.1 - - - +
180D TRP* 1.3 58.3 + - - +
182D ARG* 3.2 27.5 + - - +
183D GLN* 2.9 27.3 + - - +
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Residues in contact with TRP 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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106D ILE* 3.6 21.3 - - + -
107D GLN 3.8 4.7 - - - -
108D ILE* 3.9 13.9 - - + -
160D PRO* 3.7 31.6 - - + -
161D LEU 3.9 8.5 - - - -
162D LEU* 3.7 58.1 - - + +
176D ALA 3.0 15.5 + - - +
177D ILE* 3.4 10.5 - - - +
178D VAL 3.2 0.2 - - - -
179D GLN* 1.3 73.0 - - - +
181D VAL* 1.3 86.8 + - + +
183D GLN* 3.1 16.2 + - + +
184D HIS* 3.2 41.2 + + - -
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Residues in contact with VAL 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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7D ILE* 3.8 23.6 - - + -
24D LEU* 3.8 11.7 - - + -
28D LEU* 3.7 24.7 - - + -
106D ILE* 4.1 15.4 - - + +
108D ILE* 3.8 20.9 - - + -
177D ILE 3.1 14.9 + - - +
178D VAL 3.2 6.7 + - - +
180D TRP* 1.3 92.9 - - + +
182D ARG* 1.3 58.8 + - - +
184D HIS* 3.0 18.8 + - - +
185D LEU* 3.1 17.3 + - + +
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Residues in contact with ARG 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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27D GLY 3.1 26.5 + - - -
28D LEU* 3.8 29.9 + - + +
29D ARG* 6.1 0.4 - - - +
178D VAL* 3.1 14.0 + - - +
179D GLN* 3.4 36.3 + - - +
181D VAL* 1.3 71.6 - - - +
183D GLN* 1.3 63.2 + - - +
184D HIS 2.9 6.4 + - - -
185D LEU* 3.2 33.1 + - + +
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Residues in contact with GLN 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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179D GLN 2.9 15.4 + - - +
180D TRP* 3.1 16.5 + - + +
182D ARG* 1.3 72.2 - - - +
184D HIS* 1.3 75.0 + - + +
185D LEU 4.7 2.7 - - - +
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Residues in contact with HIS 184 (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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104D THR* 5.7 4.7 - - - +
106D ILE* 3.8 17.5 - - + +
160D PRO* 3.5 34.9 - - + +
180D TRP* 3.2 56.0 + + - +
181D VAL 3.0 8.1 + - - +
182D ARG 2.9 0.8 - - - -
183D GLN* 1.3 93.7 + - + +
185D LEU* 1.3 63.7 + - - +
186D GLN* 3.5 4.5 + - - +
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Residues in contact with LEU 185 (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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5D ALA* 3.4 33.0 - - + -
7D ILE* 4.8 4.7 - - + -
28D LEU* 4.7 9.2 - - + -
30D LEU* 5.6 4.0 - - + -
78D SER* 4.9 5.8 - - - +
106D ILE* 3.8 10.3 - - + -
181D VAL* 3.1 22.7 + - + +
182D ARG* 3.2 39.5 + - + +
183D GLN 4.7 2.3 - - - +
184D HIS* 1.3 78.9 - - - +
186D GLN* 1.3 62.6 + - - +
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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