Contacts of the helix formed by residues 155 - 162 (chain H) in PDB entry 1RBO
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 ILE 155 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H GLY* 1.3 71.1 - - - +
156H GLN* 1.3 66.5 + - - +
158H GLU* 3.3 4.5 + - - +
159H ARG* 3.0 32.3 + - + +
324H ASP 5.4 0.6 + - - -
350H ARG* 3.9 29.6 - - + +
373H GLY* 3.2 24.8 + - - +
374H VAL 3.8 16.8 - - - +
375H LEU* 3.6 31.4 - - + +
397H ASP* 3.9 20.0 - - + +
108I ARG* 3.7 23.8 - - - +
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Residues in contact with GLN 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H GLY 3.5 0.6 - - - -
155H ILE* 1.3 78.8 - - - +
157H VAL* 1.3 82.8 + - + +
159H ARG* 3.3 4.5 + - - +
160H ASP* 3.1 37.4 + - - +
108I ARG* 3.3 12.5 - - - +
109I GLU* 3.1 31.6 - - - +
110I VAL* 3.6 21.9 - - + +
181L SER* 3.7 26.1 - - - +
182L ALA 5.0 2.0 - - - +
211L PHE 4.4 10.2 + - - +
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Residues in contact with VAL 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H HIS* 3.7 35.0 - - + +
154H GLY 3.3 2.0 + - - +
156H GLN* 1.3 94.0 - - + +
158H GLU* 1.3 57.7 + - - +
160H ASP* 3.2 7.6 + - - +
161H LYS* 2.9 41.2 + - + +
182L ALA* 5.8 4.7 - - + -
216L ASP* 3.5 39.9 - - + +
220L PHE* 5.2 3.6 - - + -
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Residues in contact with GLU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H HIS* 4.7 0.6 - - - +
154H GLY 3.0 18.3 + - - +
155H ILE* 3.7 4.7 - - - +
156H GLN 3.3 0.2 - - - -
157H VAL* 1.3 76.8 - - - +
159H ARG* 1.3 64.0 + - + +
161H LYS* 3.3 2.8 + - - +
162H LEU* 3.1 41.6 + - + +
169H LEU* 4.1 3.3 - - + +
199H PHE* 4.0 5.5 - - - -
290H LEU* 3.8 36.5 - - + +
324H ASP* 3.8 13.3 - - - +
325H HIS* 2.7 42.1 + - - -
375H LEU* 3.5 18.0 - - + +
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Residues in contact with ARG 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ILE* 3.0 27.2 + - + +
156H GLN* 3.8 3.8 - - - +
158H GLU* 1.3 77.5 - - + +
160H ASP* 1.3 52.4 + - - +
162H LEU* 5.0 2.2 - - - -
163H ASN* 2.7 32.1 + - - -
164H LYS* 2.9 45.2 + - + +
165H TYR* 3.6 26.8 - - + +
166H GLY 4.7 2.5 - - - -
167H ARG 3.0 20.0 + - - +
168H PRO* 4.6 0.4 - - - +
169H LEU* 4.2 22.3 - - + +
375H LEU* 5.4 6.1 - - + +
396H ASP* 2.7 34.3 + - - +
397H ASP* 3.0 26.5 + - - +
398H SER 4.7 0.8 - - - +
108I ARG* 5.7 0.4 - - - +
110I VAL* 5.5 11.2 - - + -
111I GLN 5.1 3.4 - - - -
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Residues in contact with ASP 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H GLN* 3.1 36.3 + - - +
157H VAL* 3.5 10.3 - - - +
158H GLU 3.2 0.2 - - - -
159H ARG* 1.3 75.1 - - - +
161H LYS* 1.3 64.0 + - - +
163H ASN* 3.5 8.5 + - - -
165H TYR* 2.8 28.1 + - - -
65I ARG* 4.2 5.2 - - - -
109I GLU 4.8 1.7 - - - +
110I VAL* 5.4 2.8 - - - +
111I GLN* 5.3 3.6 + - - +
181L SER* 4.6 3.1 + - - -
183L LYS* 3.4 34.5 + - + +
220L PHE* 3.7 28.0 - - + -
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Residues in contact with LYS 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H HIS* 3.6 21.8 + - - -
157H VAL* 2.9 31.5 + - + +
158H GLU* 3.3 6.7 + - - +
160H ASP* 1.3 74.0 - - - +
162H LEU* 1.3 66.0 + - + +
235H ILE* 4.0 0.2 - - - +
288H GLY* 4.6 11.3 + - - -
290H LEU* 5.5 8.7 - - + +
60I GLY* 3.8 25.7 - - - +
62I TYR* 3.9 8.8 - - - -
65I ARG* 2.8 31.8 + - - +
215L ARG* 5.6 0.8 - - - +
216L ASP* 2.9 33.0 + - - +
219L LEU* 4.0 20.5 - - + +
220L PHE* 4.0 18.6 - - + -
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Residues in contact with LEU 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H GLU* 3.1 32.0 + - + +
159H ARG* 4.3 1.1 - - - +
161H LYS* 1.3 80.4 - - + +
163H ASN* 1.3 71.3 + - - +
164H LYS* 3.4 29.2 + - + +
169H LEU* 4.8 3.4 - - + -
199H PHE* 3.7 36.1 - - + -
235H ILE* 3.4 39.1 - - + +
236H LYS 5.7 0.4 - - - +
263H PRO* 4.3 18.6 - - + -
290H LEU* 4.1 17.5 - - + -
13I GLU* 4.9 1.2 - - - +
60I GLY* 6.2 0.4 - - - -
62I TYR* 5.0 2.7 - - + -
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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