Contacts of the helix formed by residues 112 - 128 (chain B) in PDB entry 3RFU
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 ASN 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B ILE 6.2 0.2 - - - -
110B SER 3.0 5.0 - - - +
111B GLY* 1.3 73.3 - - - +
113B GLY* 1.3 57.4 + - - +
116B TRP* 2.4 63.7 + - - +
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PHE* 4.5 12.6 - - - -
109B ILE* 4.5 1.9 - - - -
110B SER* 2.7 17.5 + - - +
112B ASN* 1.3 80.1 + - - +
114B SER* 1.3 63.0 + - - -
116B TRP* 3.7 0.7 - - - +
117B ILE* 3.0 30.3 + - - +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.0 29.5 + - - +
103B HIS* 5.1 6.5 + - - -
108B PHE 4.7 1.6 + - - -
109B ILE* 4.2 13.2 - - - +
110B SER* 2.6 31.0 + - - +
113B GLY* 1.3 69.7 - - - -
115B SER* 1.3 63.8 + - - -
116B TRP 3.1 0.3 + - - -
117B ILE* 3.2 7.7 + - - +
118B GLN* 3.0 32.2 + - - +
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B SER* 2.8 10.1 + - - -
111B GLY* 2.9 31.1 + - - -
114B SER* 1.3 75.5 + - - +
116B TRP* 1.3 55.9 + - - +
118B GLN* 4.0 8.7 - - - +
119B LEU* 3.0 26.2 + - - +
167B VAL* 3.7 21.7 - - - +
183B VAL* 4.7 4.0 - - - +
184B VAL* 4.7 11.5 + - - +
186B VAL* 4.8 12.8 - - - +
188B PHE* 3.9 4.9 - - - -
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Residues in contact with TRP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLY 3.1 19.2 + - - -
112B ASN* 2.4 56.4 + - - +
113B GLY 3.7 1.1 - - - +
115B SER* 1.3 77.6 - - - +
117B ILE* 1.3 59.8 + - + +
119B LEU* 3.4 19.9 - - + +
120B LEU* 3.0 53.1 + - + +
167B VAL* 3.3 23.4 + - + +
168B LEU* 3.5 39.0 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B PRO* 6.1 0.7 - - + -
98B LEU* 3.5 27.4 - - + -
108B PHE 6.0 1.8 - - - +
113B GLY* 3.0 21.6 + - - +
114B SER* 5.0 1.6 - - - -
116B TRP* 1.3 73.0 - - + +
118B GLN* 1.3 68.0 + - - +
119B LEU 3.0 1.3 + - - -
120B LEU* 3.1 7.3 + - + +
121B LEU* 3.1 41.5 + - + +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 4.2 21.1 - - + +
98B LEU* 3.5 24.8 - - + +
99B GLU* 3.0 43.0 + - - +
114B SER* 3.0 24.1 + - - +
115B SER* 4.0 4.7 - - - +
117B ILE* 1.3 77.3 - - - +
119B LEU* 1.3 61.9 + - - +
121B LEU* 4.3 0.3 - - - +
122B ALA* 3.0 30.1 + - - +
186B VAL* 3.4 35.4 - - - +
188B PHE* 3.8 13.9 - - + +
189B GLU 4.6 2.2 - - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B SER 3.0 19.0 + - - +
116B TRP* 3.4 27.8 - - + +
117B ILE 3.0 0.4 - - - -
118B GLN* 1.3 76.6 - - - +
120B LEU* 1.3 71.5 + - + +
121B LEU 3.0 0.7 + - - -
122B ALA* 4.2 0.2 - - - +
123B THR* 2.8 47.5 + - + +
164B MET* 3.5 29.2 - - + +
167B VAL* 3.4 34.5 - - + -
168B LEU* 5.1 4.9 - - + +
188B PHE* 3.3 14.7 - - + -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TRP* 3.0 36.6 + - + +
117B ILE* 3.1 7.1 + - + +
119B LEU* 1.3 90.8 - - + +
121B LEU* 1.3 66.4 + - + +
123B THR* 3.7 6.4 - - + +
124B PRO* 3.1 21.4 - - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.7 47.3 - - + +
94B PRO* 4.0 24.2 - - + -
95B VAL* 3.7 11.4 - - + +
98B LEU* 5.5 0.2 - - + -
117B ILE* 3.1 32.0 + - + +
118B GLN* 5.4 0.2 - - - -
120B LEU* 1.3 84.0 - - + +
122B ALA* 1.3 61.2 + - - +
123B THR 3.1 1.1 - - - -
124B PRO* 2.8 19.7 - - + +
125B VAL* 3.1 14.9 + - - +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 4.2 6.8 - - + +
118B GLN 3.0 19.8 + - - +
121B LEU* 1.3 77.5 - - - +
123B THR* 1.3 57.0 + - - +
125B VAL* 3.0 28.7 - - + +
126B VAL* 3.1 20.5 + - + +
160B TRP* 4.7 2.4 - - - -
188B PHE* 3.7 39.9 - - + +
192B ALA* 4.4 4.5 - - + +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU* 2.8 37.3 + - + +
120B LEU* 3.7 14.4 - - + +
122B ALA* 1.3 78.6 - - - +
124B PRO* 1.3 74.4 - - + +
127B LEU* 3.0 50.1 + - - +
160B TRP* 3.4 27.8 + - - +
164B MET* 5.0 0.8 - - - -
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Residues in contact with PRO 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 4.0 17.0 - - + -
120B LEU 3.1 16.6 - - - +
121B LEU* 2.8 20.2 - - + +
123B THR* 1.3 95.4 - - + +
125B VAL* 1.3 57.8 + - - +
126B VAL 3.1 5.2 - - - -
127B LEU* 5.0 0.7 - - + -
128B TRP* 2.8 44.7 + - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ALA* 3.2 37.9 - - + +
91B LEU* 4.5 10.0 - - + +
92B THR* 3.4 16.6 - - - +
121B LEU 3.1 10.6 + - - +
122B ALA* 3.0 33.4 - - - +
124B PRO* 1.3 75.8 - - - +
126B VAL* 1.3 58.5 + - + +
128B TRP* 5.6 2.9 - - - -
129B GLY* 3.0 17.4 - - - +
192B ALA* 3.5 24.0 - - + -
195B THR* 3.2 12.8 + - - +
196B THR* 3.7 7.2 - - + -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ALA 3.1 19.0 + - - +
123B THR 4.2 1.6 - - - +
125B VAL* 1.3 81.8 - - + +
127B LEU* 1.3 69.9 + - + +
129B GLY* 3.1 11.8 - - - -
130B GLY* 3.8 1.6 - - - -
134B PHE* 3.0 33.0 - - + -
156B ILE* 3.5 25.4 - - + -
160B TRP* 4.1 25.6 - - + -
191B ALA* 3.5 38.8 - - + -
195B THR* 4.0 4.9 - - + -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B THR* 3.0 33.9 + - - +
124B PRO* 5.0 0.7 - - + -
126B VAL* 1.3 82.9 - - + +
128B TRP* 1.3 66.1 + - - +
129B GLY 2.7 4.3 + - - -
131B TRP* 3.1 30.5 - - + +
134B PHE* 4.7 9.4 - - + -
160B TRP* 3.9 36.6 - - + -
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Residues in contact with TRP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ARG* 4.0 30.1 - - - -
84B ARG* 3.0 67.2 + - + +
87B ILE* 4.6 20.1 - - + +
88B ALA* 6.5 0.9 - - + -
91B LEU* 6.1 1.1 - - + -
124B PRO* 2.8 25.7 + - + +
125B VAL* 5.6 2.0 - - - -
127B LEU* 1.3 79.6 - - - +
129B GLY* 1.3 74.6 + - - +
131B TRP* 3.3 7.2 + - + +
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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