Contacts of the helix formed by residues 173 - 188 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLN 3.6 4.7 + - - +
172A ILE* 1.3 71.5 - - - +
174A MSE 1.3 64.1 + - - +
175A ASN* 3.1 21.0 + - - +
176A ALA* 3.3 35.8 + - + +
177A ILE* 3.6 11.4 + - - +
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Residues in contact with MSE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 4.6 11.9 - - + +
20A LEU* 4.0 43.5 - - + +
23A ALA* 3.6 29.4 - - + -
24A LEU* 5.5 1.3 - - - -
172A ILE* 3.6 15.2 + - + +
173A ASP* 1.3 72.9 + - - +
175A ASN* 1.3 64.2 + - - +
177A ILE* 3.2 18.7 + - - +
178A VAL* 3.1 24.8 + - + +
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 3.1 10.5 + - - +
174A MSE 1.3 77.4 - - - +
176A ALA* 1.3 58.8 + - - +
178A VAL* 3.0 10.9 + - - +
179A GLN* 2.8 55.8 + - - +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 3.3 32.8 + - + +
174A MSE 3.3 0.4 - - - -
175A ASN* 1.3 79.4 - - - +
177A ILE* 1.3 58.2 + - + +
179A GLN* 3.4 6.8 + - - +
180A TRP* 2.9 29.0 + - - +
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.0 23.3 - - + -
24A LEU* 4.3 4.7 - - + -
108A ILE* 3.8 26.2 - - + -
162A LEU* 4.1 13.5 - - + -
164A VAL* 4.0 24.2 - - + -
172A ILE* 3.7 30.7 - - + -
173A ASP 3.6 8.3 - - - +
174A MSE 3.5 14.4 - - - +
175A ASN 3.1 0.4 - - - -
176A ALA* 1.3 75.8 - - + +
178A VAL* 1.3 65.7 + - - +
180A TRP* 3.2 7.8 + - - +
181A VAL* 3.1 22.3 + - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 4.2 17.7 - - + +
24A LEU* 4.0 21.5 - - + -
27A GLY* 4.4 17.5 - - - +
28A LEU* 3.8 24.0 - - + +
174A MSE 3.1 19.6 + - + +
175A ASN* 3.0 14.5 + - - +
177A ILE* 1.3 76.5 - - - +
179A GLN* 1.3 73.7 + - - +
181A VAL* 3.2 4.9 + - - +
182A ARG* 2.8 28.3 + - + +
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASN* 2.8 45.0 + - - +
176A ALA* 3.9 6.1 - - - +
178A VAL* 1.3 88.9 - - - +
180A TRP* 1.3 61.8 + - - +
182A ARG* 3.9 24.2 + - - +
183A GLN* 2.8 32.7 + - - +
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Residues in contact with TRP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 3.6 23.6 - - + -
107A GLN 3.9 8.7 - - - -
108A ILE* 4.1 2.7 - - + -
160A PRO* 3.7 26.0 - - + -
161A LEU 4.0 7.6 - - - -
162A LEU* 3.6 57.1 - - + +
176A ALA 2.9 15.1 + - - +
177A ILE* 3.2 11.4 + - - +
179A GLN* 1.3 79.0 - - - +
181A VAL* 1.3 86.1 + - + +
183A GLN* 3.4 4.5 + - - +
184A HIS* 3.1 51.5 + + - -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.9 23.1 - - + -
24A LEU* 4.0 8.7 - - + -
28A LEU* 3.8 24.0 - - + -
106A ILE* 4.2 9.9 - - + -
108A ILE* 3.5 33.0 - - + -
177A ILE 3.1 11.9 + - - +
178A VAL 3.6 5.6 - - - +
180A TRP* 1.3 90.3 - - + +
182A ARG* 1.3 59.3 + - - +
184A HIS* 3.0 7.6 + - - +
185A LEU* 2.9 31.6 + - + +
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Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY 4.6 4.8 + - - -
28A LEU* 3.7 44.1 + - + +
178A VAL* 2.8 21.8 + - - +
179A GLN* 3.9 28.2 + - - +
181A VAL* 1.3 74.7 - - - +
183A GLN* 1.3 56.1 + - - +
185A LEU* 3.3 18.6 + - + +
186A GLN* 3.0 27.8 + - + +
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLN 2.8 21.4 + - - +
180A TRP* 3.7 6.5 - - - +
182A ARG* 1.3 73.1 - - - +
184A HIS* 1.3 60.6 + - + +
186A GLN* 3.3 8.5 + - - +
187A SER* 2.9 27.3 + - - -
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Residues in contact with HIS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 4.1 19.9 - - + +
160A PRO* 3.5 31.0 - - + +
180A TRP* 3.1 56.1 + + - -
181A VAL* 3.0 9.0 + - - +
183A GLN* 1.3 79.3 - - + +
185A LEU* 1.3 62.4 + - - +
187A SER* 3.4 11.5 + - - -
188A GLY* 3.2 17.3 + - - -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 3.3 34.8 - - + -
7A ILE* 4.7 4.9 - - + -
28A LEU* 4.3 26.5 - - + -
30A LEU* 4.7 10.3 - - + -
78A SER* 4.9 4.9 - - - +
106A ILE* 3.5 12.3 - - + -
181A VAL* 2.9 19.6 + - + +
182A ARG* 3.5 24.0 - - + +
183A GLN 3.3 0.2 - - - -
184A HIS* 1.3 74.8 - - - +
186A GLN* 1.3 64.9 + - - +
188A GLY* 3.2 3.7 + - - -
189A THR* 3.1 22.2 + - - -
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Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 3.0 15.3 + - + +
183A GLN* 3.5 11.2 - - - +
185A LEU* 1.3 75.8 - - - +
187A SER* 1.3 62.4 + - - +
188A GLY 3.4 0.5 + - - -
189A THR* 3.4 19.0 + - - +
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLN 2.9 16.8 + - - -
184A HIS* 3.5 16.2 - - - -
185A LEU 3.2 0.2 - - - -
186A GLN* 1.3 77.6 - - - +
188A GLY* 1.3 58.6 + - - +
189A THR 3.8 2.3 + - - +
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLN* 4.6 6.6 - - - +
3A THR* 4.7 9.1 + - - +
104A THR* 5.6 11.0 - - - +
184A HIS 3.2 10.2 + - - -
185A LEU* 3.2 8.6 + - - -
187A SER* 1.3 74.8 - - - +
189A THR* 1.3 66.6 + - - +
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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