Contacts of the helix formed by residues 139 - 149 (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 SER 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C ARG* 1.3 81.0 - - - +
140C PRO* 1.3 76.3 - - - +
141C ALA* 3.6 9.0 + - - +
142C ASP* 2.5 35.9 + - - -
143C LEU* 2.9 21.2 + - - +
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Residues in contact with PRO 140 (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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138C ARG 4.5 0.9 - - - +
139C SER* 1.3 87.2 - - - +
141C ALA* 1.3 56.1 + - - +
143C LEU* 3.2 8.2 + - + +
144C GLU* 2.8 29.7 + - - +
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Residues in contact with ALA 141 (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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139C SER* 3.2 8.0 + - - +
140C PRO* 1.3 76.7 - - - +
142C ASP* 1.3 61.4 + - - +
144C GLU* 3.4 7.5 + - - +
145C LEU* 3.0 28.1 + - - +
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Residues in contact with ASP 142 (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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137C ASP* 3.3 39.5 - - + +
138C ARG 3.7 0.9 + - - -
139C SER* 2.5 47.5 + - - +
141C ALA* 1.3 78.1 - - - +
143C LEU* 1.3 56.5 + - - +
145C LEU* 3.2 13.8 + - - +
146C VAL* 3.0 31.8 + - + +
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Residues in contact with LEU 143 (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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118C VAL* 3.5 28.2 - - + +
121C ILE* 6.4 1.6 - - + -
122C LEU* 6.0 4.9 - - + -
138C ARG* 5.1 4.0 - - - +
139C SER 2.9 12.1 + - - +
140C PRO* 3.7 9.9 - - + +
142C ASP* 1.3 74.6 - - - +
144C GLU* 1.3 60.6 + - - +
146C VAL* 3.2 8.0 + - - -
147C ARG* 2.9 33.4 + - - +
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Residues in contact with GLU 144 (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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140C PRO 2.8 17.4 + - - +
141C ALA* 3.8 8.3 - - - +
142C ASP 3.3 0.2 - - - -
143C LEU* 1.3 75.3 - - - +
145C LEU* 1.3 55.7 + - - +
147C ARG* 3.4 12.1 + - - +
148C SER* 2.7 35.1 + - - -
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Residues in contact with LEU 145 (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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141C ALA 3.0 14.9 + - - +
142C ASP* 3.4 16.6 - - - +
144C GLU* 1.3 75.0 - - - +
146C VAL* 1.3 64.8 + - + +
148C SER* 4.0 5.6 - - - +
149C ARG* 3.0 57.7 + - + +
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Residues in contact with VAL 146 (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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13C PRO 5.6 0.7 - - - +
114C GLY* 4.0 6.9 - - - -
117C LEU* 3.7 34.4 - - + +
118C VAL* 4.1 10.5 - - + -
121C ILE* 3.8 26.7 - - + -
137C ASP 5.9 2.7 - - - +
142C ASP 3.0 20.2 + - - +
143C LEU* 3.2 11.6 + - - +
145C LEU* 1.3 76.9 - - + +
147C ARG* 1.3 62.6 + - - +
149C ARG* 3.5 36.6 + - - +
150C GLY 5.2 1.0 + - - -
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Residues in contact with ARG 147 (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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114C GLY* 3.5 25.1 + - - -
115C ASP* 3.7 40.8 + - - +
118C VAL* 3.9 28.2 - - + +
143C LEU* 2.9 19.9 + - - +
144C GLU* 3.7 11.0 - - - +
145C LEU 3.2 0.4 - - - -
146C VAL* 1.3 78.8 - - - +
148C SER* 1.3 58.8 + - - +
150C GLY 5.2 1.4 + - - -
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Residues in contact with SER 148 (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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144C GLU 2.7 23.3 + - - -
145C LEU* 3.8 7.1 + - - +
147C ARG* 1.3 76.5 - - - +
149C ARG* 1.3 64.2 + - - +
150C GLY* 3.3 4.4 + - - -
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Residues in contact with ARG 149 (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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12C HIS* 3.7 40.3 + - + +
13C PRO* 4.5 16.9 + - - +
117C LEU* 6.0 0.8 - - - +
145C LEU* 3.0 41.5 + - + +
146C VAL* 3.5 43.0 + - - +
147C ARG 3.6 1.2 - - - -
148C SER* 1.3 77.3 - - - +
150C GLY* 1.3 67.4 + - - +
151C ASP 5.2 0.5 - - - +
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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