Contacts of the helix formed by residues 119 - 123 (chain A) in PDB entry 1RRM
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 VAL 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.7 25.8 - - + -
77A VAL* 3.9 22.2 - - + -
78A LYS* 4.2 6.5 - - + -
106A ALA* 5.1 1.6 - - + -
110A ILE* 3.8 19.1 - - + -
116A PHE 2.9 13.8 + - - -
117A ALA 3.6 10.5 - - - +
118A ASP* 1.3 81.5 - - - +
120A ARG* 1.3 63.4 - - - +
121A SER 3.1 2.0 - - - -
122A LEU* 3.0 30.5 + - + +
152A TYR* 6.1 0.4 - - + -
154A ILE* 4.3 12.8 - - + -
163A PHE* 3.5 20.5 - - + -
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Residues in contact with ARG 120 (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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74A ILE* 4.0 14.1 - - + +
78A LYS* 5.8 3.4 - - - +
118A ASP* 2.7 38.9 + - - +
119A VAL* 1.3 73.9 - - - +
121A SER* 1.3 56.1 + - - +
122A LEU 3.0 5.0 + - - -
123A GLU* 3.3 21.1 + - - +
156A ASP* 2.8 48.7 + - - +
158A GLU* 3.3 29.9 + - - +
159A LYS* 3.8 16.8 - - - +
163A PHE* 3.6 16.8 - - + -
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU 4.4 1.0 + - - -
116A PHE* 3.3 35.6 + - - +
118A ASP* 2.8 34.4 + - - -
120A ARG* 1.3 76.3 - - - +
122A LEU* 1.3 59.9 + - - +
123A GLU 3.3 4.0 + - - +
127A PRO* 4.9 5.7 - - - +
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Residues in contact with LEU 122 (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 ALA* 5.0 1.3 - - - +
109A ILE* 4.1 4.0 - - + -
110A ILE* 3.9 31.4 - - + -
116A PHE* 3.4 41.1 - - + +
119A VAL* 3.0 20.7 + - + +
121A SER* 1.3 77.2 - - - +
123A GLU* 1.3 67.6 + - - +
124A GLY 3.5 0.5 + - - -
126A SER* 2.6 42.9 + - - +
128A THR* 4.1 7.9 - - + -
152A TYR* 3.4 26.2 - - + +
165A CYS* 3.4 18.4 - - - +
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Residues in contact with GLU 123 (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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120A ARG 3.3 15.6 + - - +
121A SER 3.3 5.4 - - - +
122A LEU* 1.3 82.0 - - - +
124A GLY* 1.3 64.3 + - - +
125A LEU 3.9 1.6 + - - -
126A SER* 4.6 1.9 + - - -
127A PRO* 5.7 1.2 - - - +
161A ARG* 2.9 43.8 + - - -
163A PHE* 3.4 20.1 - - + +
164A VAL 3.5 13.5 - - - +
165A CYS* 3.8 6.3 - - - -
359A ASP 5.2 2.3 - - - +
360A ASP* 6.0 0.2 - - - -
361A VAL* 4.3 13.1 - - + +
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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