Contacts of the helix formed by residues 115 - 129 (chain A) in PDB entry 1RIF
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 HIS 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ILE* 5.9 3.6 - - + -
113A GLU 4.2 8.0 + - - -
114A PRO* 1.3 77.5 - - - +
116A TRP* 1.3 70.8 + + + +
117A TYR* 3.2 43.9 + + + -
118A GLN* 2.7 29.7 + - + +
119A LYS* 3.0 21.8 + - - +
143A LEU* 6.3 0.2 - - + -
57B ASN* 5.9 6.5 + - - -
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Residues in contact with TRP 116 (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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93A ARG* 6.1 0.2 - - - +
114A PRO 4.0 0.4 + - - -
115A HIS* 1.3 75.4 - + + +
117A TYR* 1.3 95.3 + + + +
119A LYS* 3.2 13.3 + - - +
120A ASP* 2.9 57.4 + - - +
282A PRO* 4.0 13.5 - - + -
220B LYS* 3.1 54.1 - - + +
221B GLU* 2.8 36.6 - - - -
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Residues in contact with TYR 117 (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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115A HIS* 3.4 40.4 + + + -
116A TRP* 1.3 125.2 - + + +
118A GLN* 1.3 88.4 + - + +
120A ASP* 3.7 5.3 - - - +
121A ALA* 3.0 28.9 + - - +
135A LEU* 4.7 5.4 - - + +
138A SER 4.5 3.8 + - - -
139A ALA* 3.8 36.6 - - + -
282A PRO* 4.5 18.0 - - + +
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Residues in contact with GLN 118 (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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114A PRO* 3.2 15.1 - - + +
115A HIS* 2.7 48.8 + - - +
117A TYR* 1.3 95.2 + - + +
119A LYS* 1.3 61.4 + - - +
121A ALA* 3.4 1.6 + - - +
122A VAL* 3.0 36.6 + - + +
139A ALA 3.1 10.6 + - - +
140A GLY* 3.0 31.7 + - - -
143A LEU* 3.5 20.1 - - + +
144A ILE* 3.9 17.0 - - + +
147A LEU* 5.6 1.8 - - + -
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Residues in contact with LYS 119 (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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93A ARG* 3.8 17.5 - - - +
96A PHE* 3.4 10.9 - - - -
97A ASP* 5.0 3.3 + - - +
100A LEU* 3.7 28.7 - - + +
113A GLU* 5.5 6.8 + - - +
114A PRO* 3.5 39.5 + - + +
115A HIS 3.0 15.9 + - - +
116A TRP* 3.4 13.2 - - - +
118A GLN* 1.3 76.7 - - - +
120A ASP* 1.3 56.8 + - - +
122A VAL* 4.7 1.6 - - - -
123A PHE* 3.0 30.0 + - - +
147A LEU* 5.8 1.8 - - + -
220B LYS* 6.3 0.4 - - - +
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Residues in contact with ASP 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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93A ARG* 3.0 34.9 + - - +
116A TRP* 2.9 44.1 + - - +
117A TYR* 3.7 6.7 - - - +
119A LYS* 1.3 77.4 - - - +
121A ALA* 1.3 57.2 + - - +
123A PHE* 3.2 2.6 + - - +
124A GLU* 2.8 33.6 + - + +
280A PHE* 4.6 11.4 - - + -
282A PRO* 5.4 3.1 - - + -
220B LYS* 4.8 8.4 + - - +
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Residues in contact with ALA 121 (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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117A TYR 3.0 17.9 + - - +
118A GLN 3.7 4.5 - - - +
120A ASP* 1.3 76.9 - - - +
122A VAL* 1.3 56.8 + - - +
124A GLU* 3.4 2.3 + - - +
125A GLY* 3.0 26.0 + - - -
133A LEU* 4.0 15.8 - - + +
135A LEU* 3.6 26.9 - - + -
144A ILE* 3.9 11.7 - - + -
280A PHE* 3.8 18.8 - - + -
282A PRO* 5.3 0.2 - - + -
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Residues in contact with VAL 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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96A PHE* 3.5 25.1 - - + -
99A TRP* 5.0 0.4 - - + -
118A GLN 3.0 21.2 + - - +
119A LYS* 3.8 3.8 - - - +
121A ALA* 1.3 75.0 - - - +
123A PHE* 1.3 64.0 + - - +
125A GLY* 3.3 1.0 + - - -
126A LEU* 3.0 35.8 + - + +
144A ILE* 3.7 35.0 - - + +
147A LEU* 3.9 28.7 - - + -
148A LEU* 3.9 15.1 - - + +
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Residues in contact with PHE 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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91A LEU* 3.4 39.7 - - + -
93A ARG* 3.5 58.6 - - + +
96A PHE* 3.7 23.1 - + + -
119A LYS 3.0 18.4 + - - +
120A ASP 3.6 4.0 - - - +
122A VAL* 1.3 77.9 - - - +
124A GLU* 1.3 67.8 + - + +
126A LEU* 4.0 2.5 - - - +
127A VAL* 3.1 49.1 + - + +
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Residues in contact with GLU 124 (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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120A ASP* 2.8 19.2 + - + +
121A ALA 3.6 4.5 - - - +
123A PHE* 1.3 78.5 - - + +
125A GLY* 1.3 63.0 + - - +
127A VAL* 5.1 0.2 - - - -
128A ASN* 2.8 47.8 + - - +
131A ARG* 3.3 28.6 + - - +
133A LEU* 5.2 0.9 - - + -
280A PHE* 3.3 53.2 - - + -
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Residues in contact with GLY 125 (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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121A ALA 3.0 14.7 + - - -
122A VAL 3.8 2.2 - - - -
123A PHE 3.2 0.2 - - - -
124A GLU* 1.3 75.9 - - - +
126A LEU* 1.3 58.6 + - - +
128A ASN 3.6 0.3 - - - -
129A ARG* 2.8 26.9 + - - -
131A ARG* 4.3 8.1 - - - -
133A LEU* 4.7 3.6 - - - +
148A LEU* 4.8 2.2 - - - -
256A PHE* 3.3 36.2 - - - -
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Residues in contact with LEU 126 (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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89A GLU* 2.9 25.6 - - + +
91A LEU* 5.4 5.8 - - + -
96A PHE* 4.1 13.5 - - + -
122A VAL* 3.0 35.6 + - + +
123A PHE* 4.0 3.4 - - - +
125A GLY* 1.3 75.3 - - - +
127A VAL* 1.3 62.0 + - + +
129A ARG 3.2 8.0 + - - -
148A LEU* 3.5 22.2 - - + +
151A TYR* 3.4 60.1 - - + -
228A MET* 4.3 9.2 - - + -
254A PHE* 3.5 17.0 - - + -
256A PHE* 4.1 0.2 - - - -
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Residues in contact with VAL 127 (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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88A LYS* 3.2 24.0 - - + +
89A GLU* 2.8 37.0 + - - +
91A LEU* 3.9 15.5 - - + +
123A PHE* 3.1 53.0 + - + +
124A GLU* 5.1 0.2 - - - -
126A LEU* 1.3 76.6 - - - +
128A ASN* 1.3 74.4 + - - +
129A ARG* 3.5 0.5 + - - -
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Residues in contact with ASN 128 (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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87A GLU 5.2 1.1 - - - +
88A LYS* 2.7 38.7 + - - +
124A GLU* 2.8 52.5 + - - +
127A VAL* 1.3 84.9 - - - +
129A ARG* 1.3 58.7 + - - +
130A ARG* 2.8 27.5 + - - +
131A ARG* 3.5 33.7 + - + +
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Residues in contact with ARG 129 (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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10A PHE* 5.5 3.4 - - - -
87A GLU* 3.2 53.5 + - - +
88A LYS 4.0 10.8 + - - -
89A GLU* 2.7 45.8 + - - +
125A GLY 2.8 16.2 + - - -
126A LEU 3.2 4.6 + - - -
127A VAL 3.3 8.5 - - - -
128A ASN* 1.3 76.5 - - - +
130A ARG* 1.3 78.4 + - - +
156A TYR* 4.1 1.6 + - - -
253A MET* 3.6 38.2 - - + +
254A PHE* 3.2 38.8 - - + -
255A LYS 3.2 2.6 + - - -
256A PHE* 3.4 7.6 - - - -
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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