Contacts of the helix formed by residues 173 - 189 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A GLY 4.7 2.2 - - - +
182B ARG* 5.6 1.9 + - - -
171C GLN 4.0 1.9 + - - +
172C ILE* 1.3 74.5 - - - +
174C MSE 1.3 62.8 + - - +
175C ASN* 3.3 18.4 + - - +
176C ALA* 3.4 21.7 + - + +
177C ILE* 3.4 23.2 + - - +
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Residues in contact with MSE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A GLY 5.0 8.3 - - - +
1A MSE 3.7 35.2 - - + -
29B ARG* 3.9 28.7 - - - +
19C THR* 5.0 3.8 - - + +
20C LEU* 4.2 33.2 - - + +
23C ALA* 3.7 34.1 - - + -
24C LEU* 5.4 0.7 - - - -
172C ILE* 3.7 7.8 + - + -
173C ASP* 1.3 71.5 + - - +
175C ASN* 1.3 60.8 + - - +
177C ILE* 3.0 15.5 + - - +
178C VAL* 2.8 41.8 + - + +
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Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY 3.6 15.1 - - - +
28B LEU* 3.0 30.1 + - - +
29B ARG* 3.3 28.9 - - - +
182B ARG* 4.3 20.3 + - - +
185B LEU* 6.4 0.4 - - - +
173C ASP* 3.3 9.8 + - - +
174C MSE 1.3 78.8 - - - +
176C ALA* 1.3 56.7 + - - +
178C VAL* 3.8 7.9 - - - +
179C GLN* 2.9 32.2 + - - +
182C ARG* 4.3 2.8 + - - +
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Residues in contact with ALA 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ARG* 4.4 8.0 - - - +
173C ASP* 3.4 29.7 + - + +
174C MSE 3.2 0.4 - - - -
175C ASN* 1.3 77.2 - - - +
177C ILE* 1.3 59.6 + - + +
179C GLN* 3.3 7.0 + - - +
180C TRP* 2.8 29.6 + - - +
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Residues in contact with ILE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU* 4.3 20.6 - - + -
24C LEU* 4.6 4.9 - - + -
108C ILE* 4.2 21.5 - - + -
162C LEU* 4.2 18.8 - - + -
164C VAL* 3.8 30.7 - - + -
172C ILE* 3.9 16.2 - - + -
173C ASP 3.4 15.9 + - - +
174C MSE 3.0 16.6 + - - +
176C ALA* 1.3 76.0 - - + +
178C VAL* 1.3 64.0 + - - +
180C TRP* 3.5 7.1 + - - +
181C VAL* 3.3 22.7 + - - +
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ARG* 5.7 2.0 - - - +
23C ALA 4.5 11.4 - - - +
24C LEU* 4.0 20.2 - - + -
27C GLY* 4.4 8.5 - - - -
28C LEU* 3.9 21.3 - - + -
174C MSE 2.8 35.6 + - + +
175C ASN* 3.8 9.4 - - - +
177C ILE* 1.3 76.1 - - - +
179C GLN* 1.3 57.5 + - - +
181C VAL* 3.3 4.0 + - - +
182C ARG* 2.9 62.6 + - - +
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Residues in contact with GLN 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ASN* 4.0 2.1 + - - +
179B GLN* 2.6 37.6 + - - +
182B ARG* 3.4 29.7 - - - +
175C ASN 2.9 15.4 + - - +
176C ALA* 3.5 8.7 - - - +
178C VAL* 1.3 74.7 - - - +
180C TRP* 1.3 64.7 + - - +
182C ARG* 3.2 30.2 + - - +
183C GLN* 3.0 29.4 + - - +
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Residues in contact with TRP 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ILE* 3.6 23.1 - - + -
107C GLN 4.0 4.9 - - - -
108C ILE* 4.2 5.4 - - + -
160C PRO* 3.8 21.1 - - + -
161C LEU 3.7 11.4 - - - -
162C LEU* 3.5 62.6 - - + +
176C ALA 2.8 16.9 + - - +
177C ILE* 3.5 8.5 - - - +
179C GLN* 1.3 76.6 - - - +
181C VAL* 1.3 74.5 + - + +
183C GLN* 3.5 5.0 + - - +
184C HIS* 3.1 52.6 + + - -
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.7 24.7 - - + -
24C LEU* 3.8 9.0 - - + -
28C LEU* 3.7 25.4 - - + -
106C ILE* 4.5 8.5 - - + -
108C ILE* 3.5 30.1 - - + -
177C ILE 3.3 14.6 + - - +
178C VAL 3.3 7.1 + - - +
179C GLN 3.2 0.6 - - - -
180C TRP* 1.3 87.1 - - + +
182C ARG* 1.3 65.9 + - - +
184C HIS* 3.1 7.5 + - - +
185C LEU* 3.0 23.9 + - + +
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Residues in contact with ARG 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR 5.1 0.2 + - - -
27B GLY* 3.9 31.1 + - - -
175B ASN* 3.6 29.3 + - - +
178B VAL* 5.2 2.3 - - - +
179B GLN* 4.2 3.8 - - - +
182B ARG* 5.1 2.4 - - - +
27C GLY* 3.5 22.6 + - - -
28C LEU* 3.4 17.5 - - + +
175C ASN* 4.3 3.4 + - - +
178C VAL* 2.9 44.5 + - - +
179C GLN* 3.2 46.9 + - - +
181C VAL* 1.3 76.2 - - - +
183C GLN* 1.3 57.8 - - - +
185C LEU* 3.2 14.3 + - - +
186C GLN* 3.0 27.7 + - - +
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Residues in contact with GLN 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C GLN* 3.0 22.8 + - - +
180C TRP* 3.8 7.2 - - - +
181C VAL 3.2 0.4 + - - -
182C ARG* 1.3 76.4 - - - +
184C HIS* 1.3 60.2 + - + +
186C GLN* 3.4 7.7 + - - +
187C SER* 3.0 28.1 + - - -
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Residues in contact with HIS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C THR* 6.0 0.9 - - - +
106C ILE* 3.7 27.0 - - + +
160C PRO* 3.5 25.6 - - + +
180C TRP* 3.1 65.1 + + - -
181C VAL 3.1 4.6 + - - +
183C GLN* 1.3 77.7 - - + +
185C LEU* 1.3 59.7 + - - +
187C SER* 3.5 9.1 + - - -
188C GLY* 2.9 25.5 + - - -
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ALA* 3.2 34.5 - - + -
7C ILE* 4.3 12.3 - - + -
28C LEU* 4.1 26.0 - - + -
30C LEU* 4.6 7.4 - - + -
78C SER* 4.6 6.5 - - - +
106C ILE* 3.7 11.4 - - + -
181C VAL* 3.0 24.2 + - + +
182C ARG* 3.2 10.3 + - + +
184C HIS* 1.3 77.2 - - - +
186C GLN* 1.3 60.7 + - - +
188C GLY* 3.3 9.7 + - - -
189C THR* 3.4 13.9 + - - -
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Residues in contact with GLN 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C ARG 3.0 12.7 + - - +
183C GLN* 3.7 10.3 - - - +
185C LEU* 1.3 72.8 - - - +
187C SER* 1.3 66.6 + - - +
189C THR* 3.5 17.4 + - - -
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C GLN 3.0 16.7 + - - -
184C HIS* 3.8 11.2 - - - -
186C GLN* 1.3 76.9 - - - +
188C GLY* 1.3 61.0 + - - +
189C THR 3.4 6.6 + - - +
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Residues in contact with GLY 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLN* 4.7 2.3 - - - +
3C THR* 4.6 12.9 + - - +
104C THR* 5.0 19.9 + - - -
184C HIS 2.9 17.1 + - - -
185C LEU* 3.3 4.5 + - - -
186C GLN 3.2 0.4 - - - -
187C SER* 1.3 74.2 - - - +
189C THR* 1.3 65.0 + - - +
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Residues in contact with THR 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLN* 3.9 32.3 - - - -
185C LEU 3.4 10.6 + - - -
186C GLN* 3.5 13.2 + - - -
187C SER 3.3 9.2 - - - +
188C GLY* 1.3 82.2 - - - +
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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