Contacts of the helix formed by residues 155 - 159 (chain H) in PDB entry 1RQF
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 155 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H ILE 4.3 1.6 - - - +
128H PRO* 3.6 5.3 - - - +
129H GLY* 2.6 35.5 + - - -
131H ALA 3.5 8.6 - - - +
132H MET* 3.8 15.6 - - + +
153H HIS 3.6 5.9 + - - -
154H THR* 1.3 72.7 - - - +
156H GLY* 1.3 64.0 + - - +
157H ALA* 2.8 36.1 + - - +
158H TYR* 3.3 46.7 + - + +
159H PHE* 3.8 6.4 - - - -
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Residues in contact with GLY 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H GLY* 3.5 22.2 - - - -
124H LEU 5.2 0.7 - - - -
125H SER 4.1 1.6 - - - -
131H ALA 3.0 16.5 + - - -
132H MET 3.9 0.7 - - - -
133H VAL* 3.3 28.7 - - - +
155H ASP* 1.3 68.4 - - - +
157H ALA* 1.3 57.0 + - - +
158H TYR 3.0 5.6 - - - -
159H PHE* 2.9 19.5 + - - +
160H GLY 3.0 9.2 + - - -
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Residues in contact with ALA 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H LEU* 5.1 4.3 - - + +
85H ALA* 3.5 14.6 - - - +
125H SER 3.5 12.7 + - - +
126H ASP* 3.7 28.4 - - - +
127H ILE 3.9 1.6 - - - +
128H PRO* 3.8 23.1 - - + -
131H ALA 4.5 0.6 + - - -
155H ASP* 2.8 17.1 + - - +
156H GLY* 1.3 77.2 - - - +
158H TYR* 1.3 62.4 + - + +
159H PHE 3.0 4.0 + - - -
160H GLY* 3.6 7.0 + - - +
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Residues in contact with TYR 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H PHE* 6.3 0.4 - + - -
22H PHE* 3.8 33.0 - + + -
77H GLU* 4.5 10.3 - - + -
78H MET* 3.4 49.3 - - + +
81H GLY* 3.4 28.7 - - - +
82H LEU* 3.7 15.0 - - + -
84H HIS* 2.9 27.9 + - - -
85H ALA* 3.5 11.7 + - - -
128H PRO* 4.9 4.2 - - + +
154H THR* 4.9 0.4 - - + -
155H ASP* 3.5 42.5 + - + +
156H GLY 3.0 1.4 - - - -
157H ALA* 1.3 84.2 - - + +
159H PHE* 1.3 61.1 + - + +
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Residues in contact with PHE 159 (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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21H PHE* 3.4 48.9 - - + -
22H PHE* 4.1 16.8 - + - -
84H HIS* 3.7 17.0 - + - -
85H ALA* 4.8 4.9 - - - +
88H ILE* 3.6 12.2 - - + +
89H LEU* 5.9 0.5 - - - +
97H MET* 4.4 3.1 - - + -
121H PRO* 3.5 22.7 - - + +
122H ILE* 4.5 15.3 - - - +
133H VAL* 3.7 17.5 - - + -
154H THR* 3.5 26.7 - - + -
155H ASP 3.8 9.9 - - - -
156H GLY 2.9 6.1 + - - +
158H TYR* 1.3 88.2 - - + +
160H GLY* 1.3 65.5 + - - +
163H PHE* 3.2 22.9 - - + +
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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