Contacts of the helix formed by residues 115 - 133 (chain l) in PDB entry 5OOM
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 ARG 115 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2193A U 3.4 33.0 + - - -
2194A U 3.4 24.7 + - - -
2195A A 3.4 34.0 + - - +
78I LEU* 5.8 0.7 - - - -
81I LEU* 4.6 19.1 - - + +
85I GLU* 3.1 33.9 + - - -
114l SER* 1.3 89.1 + - - +
116l GLU* 1.3 56.9 + - - +
117l TYR 3.3 0.5 + - - -
118l TRP* 3.4 5.1 + - - +
119l ARG* 2.9 40.2 + - - +
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Residues in contact with GLU 116 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2191A A 3.8 6.8 + - - +
2192A A 4.7 11.3 + - - +
142J ARG* 3.1 39.3 + - - -
114l SER* 4.3 8.5 + - - +
115l ARG* 1.3 77.0 - - + +
117l TYR* 1.3 62.9 + - + +
119l ARG* 3.8 13.0 - - + +
120l ARG* 2.9 29.6 + - - +
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Residues in contact with TYR 117 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114l SER* 3.4 24.8 + - - +
115l ARG 3.2 0.4 - - - -
116l GLU* 1.3 82.3 - - + +
118l TRP* 1.3 96.1 + + - +
120l ARG* 3.2 7.4 + - + +
121l LEU* 2.9 39.2 + - + +
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Residues in contact with TRP 118 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2195A A 5.6 0.9 - - - +
77I GLY* 3.3 29.4 + - - -
78I LEU* 3.2 50.6 - - + +
81I LEU* 5.5 1.1 - - + -
114l SER 3.2 23.8 - - - +
115l ARG 3.4 5.8 + - - +
117l TYR* 1.3 97.4 - + - +
119l ARG* 1.3 59.3 + - - +
121l LEU* 3.6 46.0 - - + +
122l ARG* 2.9 38.0 + - - +
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Residues in contact with ARG 119 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2192A A 2.4 48.3 + - - -
2193A U 3.2 43.6 + - - -
2194A U 4.5 0.4 - - - -
2195A A 2.4 41.9 + - - +
2196A A 4.0 14.6 - - - +
115l ARG* 2.9 29.4 + - - +
116l GLU* 4.0 9.8 - - - +
117l TYR 3.3 0.2 - - - -
118l TRP* 1.3 78.3 - - - +
120l ARG* 1.3 55.9 + - - +
122l ARG* 3.3 13.3 + - - +
123l LYS* 2.9 62.8 + - - +
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Residues in contact with ARG 120 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2190A C 2.8 50.1 + - - -
2191A A 5.0 11.0 - - - +
116l GLU 2.9 20.4 + - - +
117l TYR* 3.4 8.3 - - + +
119l ARG* 1.3 73.9 - - - +
121l LEU* 1.3 59.4 + - - +
123l LYS* 3.3 11.4 + - - +
124l GLN* 3.0 56.5 + - - +
127l TRP* 3.9 14.2 - - - -
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Residues in contact with LEU 121 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117l TYR* 2.9 32.0 + - + +
118l TRP* 3.6 43.5 - - + +
119l ARG 3.3 0.2 - - - -
120l ARG* 1.3 76.1 - - - +
122l ARG* 1.3 57.7 + - - +
124l GLN* 3.4 9.0 + - - +
125l ASN* 3.0 57.0 + - - +
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Residues in contact with ARG 122 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2195A A 3.7 44.1 + - - -
2196A A 4.5 4.9 - - - +
2214A A 3.3 40.3 + - - -
2215A C 4.3 17.4 + - - -
78I LEU* 5.0 17.2 - - - +
118l TRP* 2.9 30.6 + - - +
119l ARG* 3.6 11.0 - - - +
121l LEU* 1.3 79.6 - - + +
123l LYS* 1.3 56.3 + - - +
125l ASN* 3.2 11.3 + - + +
126l ILE* 2.9 45.8 + - + +
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Residues in contact with LYS 123 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2190A C 4.9 9.4 - - - +
2191A A 3.2 50.0 + - - +
2192A A 5.2 3.8 + - - -
2196A A 3.4 28.1 + - - +
2197A G 3.8 28.2 - - - +
2198A A 5.1 1.6 - - - +
119l ARG* 2.9 42.7 + - + +
120l ARG* 3.3 13.4 + - - +
122l ARG* 1.3 75.9 - - - +
124l GLN* 1.3 58.5 + - + +
126l ILE* 3.4 7.5 + - + +
127l TRP* 3.0 43.5 + - + -
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Residues in contact with GLN 124 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120l ARG* 3.0 56.8 + - - +
121l LEU* 3.9 7.3 - - - +
123l LYS* 1.3 76.8 - - - +
125l ASN* 1.3 61.0 + - - +
127l TRP* 3.4 24.4 + - + +
128l ARG* 2.9 27.0 + - - +
131l ARG* 5.1 1.2 + - - -
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Residues in contact with ASN 125 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2213A A 5.2 0.9 - - - -
2214A A 6.3 2.2 - - - -
121l LEU* 3.0 44.3 + - - +
122l ARG* 3.5 10.7 - - + +
124l GLN* 1.3 76.5 - - - +
126l ILE* 1.3 59.8 + - + +
128l ARG* 3.2 19.8 + - - +
129l HIS* 3.0 28.6 + - - +
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Residues in contact with ILE 126 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2196A A 4.2 8.5 - - - +
2197A G 3.4 37.9 - - + +
2213A A 3.6 51.8 - - + +
2214A A 4.0 11.7 - - - +
122l ARG* 2.9 37.6 + - + +
123l LYS* 3.7 7.0 - - - +
125l ASN* 1.3 73.6 - - + +
127l TRP* 1.3 61.5 + - - +
129l HIS* 3.4 2.6 + - - +
130l ASN* 2.8 44.3 + - - +
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Residues in contact with TRP 127 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2189A C 3.9 19.7 - + + -
2190A C 3.1 27.4 - - - -
2197A G 3.4 38.7 + - - -
2198A A 3.4 20.5 + - - -
120l ARG* 3.9 15.5 - - - -
123l LYS* 3.0 25.4 + - + +
124l GLN* 3.6 22.4 - - + +
126l ILE* 1.3 77.1 - - - +
128l ARG* 1.3 57.3 + - - +
130l ASN* 3.3 8.4 + - - +
131l ARG* 2.9 43.0 + - + +
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Residues in contact with ARG 128 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N GLU* 4.3 26.0 + - - +
124l GLN 2.9 13.9 + - - +
125l ASN* 3.5 22.8 + - - +
126l ILE 3.2 0.4 - - - -
127l TRP* 1.3 77.4 - - - +
129l HIS* 1.3 56.7 + - - +
131l ARG* 3.1 25.8 + - - +
132l LEU* 2.9 50.3 + - + +
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Residues in contact with HIS 129 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2197A G 5.5 0.4 + - - -
2212A C 3.5 17.0 + - + -
2213A A 3.4 53.2 + - - +
125l ASN 3.0 16.0 + - - +
126l ILE 3.9 2.2 - - - +
128l ARG* 1.3 75.8 - - - +
130l ASN* 1.3 61.6 + - - +
132l LEU* 3.8 13.9 - - + +
133l SER* 2.9 44.2 + - - -
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Residues in contact with ASN 130 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2197A G 3.5 39.2 + - - -
2199A A 4.8 3.2 + - - -
2200A A 3.3 49.1 - - - +
2212A C 5.0 0.2 - - - +
126l ILE* 2.8 43.2 + - - +
127l TRP* 3.5 10.6 - - + +
129l HIS* 1.3 81.1 + - - +
131l ARG* 1.3 62.8 + - + +
133l SER* 3.2 18.0 + - - -
134l LYS* 3.5 2.6 - - - +
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Residues in contact with ARG 131 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N ASN* 6.0 3.4 - - - +
166N ARG 4.4 11.1 + - - -
168N GLU* 2.8 40.5 + - - +
171N GLU* 3.2 38.4 + - - +
124l GLN 5.1 1.2 + - - -
127l TRP* 2.9 24.7 + - - +
128l ARG* 3.7 26.2 - - - +
130l ASN* 1.3 78.4 - - + +
132l LEU* 1.3 60.9 + - - +
134l LYS* 3.7 36.6 + - - +
135l ASN* 5.7 0.5 - - - +
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Residues in contact with LEU 132 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N GLU* 4.3 15.7 - - + +
170N GLU* 3.6 46.1 - - + +
171N GLU* 3.8 25.9 - - + +
128l ARG* 2.9 40.4 + - + +
129l HIS* 3.9 12.6 - - + +
131l ARG* 1.3 76.6 - - - +
133l SER* 1.3 56.1 + - - +
134l LYS* 3.2 9.5 + - - +
135l ASN* 4.4 8.0 + - - +
136l LYS* 5.2 2.6 + - - +
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Residues in contact with SER 133 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2200A A 2.4 52.7 + - - -
129l HIS* 2.9 35.3 + - - -
130l ASN* 3.2 3.7 + - - -
132l LEU* 1.3 75.6 - - - +
134l LYS* 1.3 58.0 + - - +
135l ASN 3.5 0.9 - - - -
136l LYS* 3.8 22.0 + - - -
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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