Contacts of the helix formed by residues 105 - 115 (chain A) in PDB entry 1RYF
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 5.7 0.4 - - - -
102A SER* 2.9 20.1 + - - +
103A LEU 3.5 0.6 - - - -
104A VAL* 1.3 80.0 - - - +
106A PRO* 1.3 66.5 - - - +
107A ALA* 3.8 8.1 + - - +
108A SER* 2.9 42.2 + - - -
109A PHE* 3.1 6.0 + - - +
156A ILE* 5.0 1.6 - - - -
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Residues in contact with PRO 106 (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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104A VAL* 3.7 7.4 - - - +
105A SER* 1.3 86.7 - - - +
107A ALA* 1.3 57.1 + - - +
109A PHE* 3.1 4.6 + - + +
110A GLU* 3.0 28.5 + - - +
148A LEU* 4.5 2.9 - - + -
153A LEU* 4.1 38.8 - - + -
154A THR 3.5 24.9 - - - +
156A ILE* 4.1 21.3 - - + -
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Residues in contact with ALA 107 (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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11A ASP* 4.3 2.7 - - - +
105A SER* 3.1 7.7 + - - +
106A PRO* 1.3 78.9 - - - +
108A SER* 1.3 62.1 + - - +
109A PHE 3.4 0.2 + - - -
110A GLU* 3.4 7.8 + - - +
111A ASN* 3.2 28.0 + - - +
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Residues in contact with SER 108 (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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11A ASP* 3.3 21.4 + - - +
14A VAL* 3.6 25.4 - - - -
100A CYS 5.0 1.0 - - - +
101A PHE* 3.4 10.5 - - - +
102A SER 2.9 24.2 + - - -
105A SER* 2.9 30.9 + - - -
107A ALA* 1.3 79.1 - - - +
109A PHE* 1.3 61.7 + - - +
111A ASN* 3.4 10.4 + - - +
112A VAL* 3.5 8.3 + - - +
116A TRP* 5.2 1.2 - - - -
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Residues in contact with PHE 109 (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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101A PHE* 3.4 48.7 - + + -
105A SER 3.1 5.6 + - - +
106A PRO* 3.1 9.5 + - + +
108A SER* 1.3 78.7 + - - +
110A GLU* 1.3 68.5 + - - +
112A VAL* 3.0 21.0 + - + +
156A ILE* 3.6 32.8 - - + -
160A GLN* 3.4 33.2 - - + -
161A GLY* 4.0 3.6 - - - -
164A MET* 3.5 46.1 - - + +
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Residues in contact with GLU 110 (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 PRO 3.0 12.2 + - - +
107A ALA* 3.4 10.5 + - - +
109A PHE* 1.3 80.1 - - + +
111A ASN* 1.3 64.2 + - - +
113A ARG* 2.9 50.8 + - - +
114A ALA* 3.1 32.7 + - + +
164A MET* 4.6 4.5 - - - +
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Residues in contact with ASN 111 (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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11A ASP* 2.9 40.4 + - - +
107A ALA* 3.2 12.7 + - - +
108A SER 3.7 5.4 - - - +
109A PHE 3.2 1.2 - - - -
110A GLU* 1.3 77.8 - - - +
112A VAL* 1.3 65.5 + - - +
113A ARG 3.2 0.2 - - - -
114A ALA* 3.8 15.1 - - - +
115A LYS* 2.9 30.0 + - + +
116A TRP* 3.0 16.1 + - + +
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Residues in contact with VAL 112 (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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99A ILE* 4.1 12.1 - - + -
100A CYS 4.8 1.3 - - - +
101A PHE* 3.7 30.5 - - + -
108A SER 3.5 11.6 + - - +
109A PHE* 3.0 18.2 + - + +
111A ASN* 1.3 78.0 - - - +
113A ARG* 1.3 58.7 + - - +
116A TRP* 4.3 8.5 - - + -
117A TYR* 2.9 33.4 + - - +
131A LEU* 3.7 13.5 - - + -
164A MET* 3.9 14.8 - - + -
168A ILE* 3.6 30.5 - - + -
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Residues in contact with ARG 113 (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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110A GLU* 2.9 42.5 + - - +
112A VAL* 1.3 79.4 - - - +
114A ALA* 1.3 64.0 + - - +
115A LYS 3.4 0.2 - - - -
117A TYR* 4.0 6.6 - - + -
118A PRO* 3.2 22.7 - - - +
164A MET* 3.9 30.6 - - + +
167A GLU* 4.6 23.8 + - + +
168A ILE* 4.2 14.1 - - + -
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Residues in contact with ALA 114 (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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110A GLU* 3.1 31.8 + - + +
111A ASN* 4.2 11.9 - - - +
113A ARG* 1.3 80.2 - - - +
115A LYS* 1.3 57.8 + - - +
118A PRO* 4.0 9.4 - - - +
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Residues in contact with LYS 115 (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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11A ASP* 4.7 5.3 + - - +
111A ASN* 2.9 26.0 + - - +
113A ARG 3.4 0.2 - - - -
114A ALA* 1.3 79.5 - - - +
116A TRP* 1.3 106.0 + - + +
117A TYR 3.5 1.3 - - - -
118A PRO* 3.5 6.1 - - - +
119A GLU* 3.0 48.3 + - - +
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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