Contacts of the helix formed by residues 112 - 128 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A SER 3.0 5.0 - - - +
111A GLY* 1.3 72.7 - - - +
113A GLY* 1.3 56.5 + - - +
116A TRP* 2.4 63.7 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.5 13.0 - - - -
109A ILE* 4.5 1.7 - - - -
110A SER* 2.7 17.6 + - - +
112A ASN* 1.3 81.2 + - - +
114A SER* 1.3 62.3 + - - -
116A TRP* 3.7 0.5 - - - +
117A ILE* 3.0 30.5 + - - +
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Residues in contact with SER 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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98A LEU* 4.0 30.1 + - - +
103A HIS* 5.1 5.8 + - - -
108A PHE 4.7 1.8 + - - -
109A ILE* 4.2 14.1 - - - +
110A SER* 2.6 30.2 + - - +
113A GLY* 1.3 71.2 - - - -
115A SER* 1.3 63.3 + - - -
116A TRP 3.1 0.2 + - - -
117A ILE* 3.2 8.0 + - - +
118A GLN* 3.0 31.2 + - - +
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Residues in contact with SER 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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110A SER* 2.8 11.1 + - - -
111A GLY* 2.9 31.0 + - - -
114A SER* 1.3 75.2 + - - +
116A TRP* 1.3 55.2 + - - +
118A GLN* 4.0 8.6 - - - +
119A LEU* 3.0 26.7 + - - +
167A VAL* 3.7 21.7 - - - +
183A VAL* 4.7 4.9 - - - +
184A VAL* 4.7 11.4 + - - +
186A VAL* 4.8 12.9 - - - +
188A PHE* 3.9 4.9 - - - -
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Residues in contact with TRP 116 (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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111A GLY 3.1 19.2 + - - -
112A ASN* 2.4 56.0 + - - +
113A GLY* 3.7 1.1 - - - +
114A SER 3.1 0.8 - - - -
115A SER* 1.3 76.1 - - - +
117A ILE* 1.3 60.4 + - + +
119A LEU* 3.4 18.6 - - + +
120A LEU* 3.0 51.6 + - + +
167A VAL* 3.3 23.2 + - + +
168A LEU* 3.5 38.4 - - + -
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Residues in contact with ILE 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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94A PRO* 6.1 0.4 - - + -
98A LEU* 3.5 26.2 - - + -
108A PHE 6.0 2.0 - - - +
113A GLY* 3.0 21.7 + - - +
114A SER* 3.2 1.8 + - - -
116A TRP* 1.3 73.2 - - - +
118A GLN* 1.3 68.1 + - - +
119A LEU 3.0 1.1 + - - -
120A LEU* 3.1 7.9 + - + +
121A LEU* 3.1 40.2 + - + +
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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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95A VAL* 4.2 20.0 - - + +
98A LEU* 3.5 24.7 - - + +
99A GLU* 3.0 44.0 + - - +
114A SER* 3.0 23.9 + - - +
115A SER* 4.0 5.1 - - - +
117A ILE* 1.3 77.1 - - - +
119A LEU* 1.3 62.8 + - - +
121A LEU* 4.3 0.3 - - - +
122A ALA* 3.0 30.0 + - - +
186A VAL* 3.3 36.9 - - - +
188A PHE* 3.8 13.8 - - + +
189A GLU 4.6 2.2 - - - +
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Residues in contact with LEU 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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115A SER 3.0 18.3 + - - +
116A TRP* 3.4 29.4 - - + +
117A ILE 3.0 0.2 - - - -
118A GLN* 1.3 77.4 - - - +
120A LEU* 1.3 71.8 + - + +
121A LEU 3.0 1.3 + - - -
122A ALA 3.9 0.2 - - - -
123A THR* 2.8 50.8 + - + +
164A MET* 3.5 26.7 - - + +
167A VAL* 3.4 33.9 - - + -
168A LEU* 5.1 4.9 - - + +
188A PHE* 3.3 14.0 - - + -
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Residues in contact with LEU 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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116A TRP* 3.0 36.7 + - + +
117A ILE* 3.1 7.8 + - + +
119A LEU* 1.3 92.3 - - + +
121A LEU* 1.3 65.7 + - + +
123A THR* 3.7 6.8 - - + +
124A PRO* 3.1 21.6 - - - +
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Residues in contact with LEU 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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91A LEU* 3.7 46.6 - - + +
94A PRO* 4.0 24.5 - - + -
95A VAL* 3.7 11.0 - - + +
98A LEU* 5.5 0.2 - - + -
117A ILE* 3.1 31.6 + - + +
120A LEU* 1.3 86.0 - - + +
122A ALA* 1.3 61.8 + - - +
123A THR 3.1 1.8 - - - -
124A PRO* 2.8 19.8 - - + +
125A VAL* 3.1 14.8 + - - +
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Residues in contact with ALA 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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95A VAL* 4.2 7.1 - - + +
118A GLN 3.0 19.8 + - - +
121A LEU* 1.3 77.2 - - - +
123A THR* 1.3 57.9 + - - +
124A PRO 3.4 0.2 - - - -
125A VAL* 3.0 28.8 - - + +
126A VAL* 3.0 20.4 + - + +
160A TRP* 4.9 2.0 - - - -
188A PHE* 3.7 39.5 - - + +
191A ALA* 5.4 0.2 - - + -
192A ALA* 4.4 4.9 - - + +
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Residues in contact with THR 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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119A LEU* 2.8 39.1 + - + +
120A LEU* 3.7 14.1 - - + +
122A ALA* 1.3 78.3 - - - +
124A PRO* 1.3 75.6 - - + +
127A LEU* 3.0 50.6 + - - +
160A TRP* 3.4 28.2 + - - +
164A MET* 5.0 1.1 - - - -
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Residues in contact with PRO 124 (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* 4.0 17.5 - - + -
120A LEU 3.1 17.5 - - - +
121A LEU* 2.8 20.6 - - + +
123A THR* 1.3 93.2 - - + +
125A VAL* 1.3 58.3 + - - +
126A VAL 3.1 4.5 - - - -
127A LEU* 5.0 0.7 - - + -
128A TRP* 2.8 43.7 + - + +
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Residues in contact with VAL 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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88A ALA* 3.2 38.7 - - + +
91A LEU* 4.5 10.0 - - + +
92A THR* 3.4 16.6 - - - +
121A LEU 3.1 10.4 + - - +
122A ALA* 3.0 33.4 - - - +
124A PRO* 1.3 76.2 - - - +
126A VAL* 1.3 56.5 + - + +
128A TRP* 5.6 2.5 - - - -
129A GLY* 3.0 17.2 - - - +
192A ALA* 3.5 24.9 - - + -
195A THR* 3.2 12.4 + - - +
196A THR* 3.7 7.0 - - + -
199A LEU* 5.6 0.2 - - - +
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Residues in contact with VAL 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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122A ALA 3.0 19.1 + - - +
123A THR 4.2 1.3 - - - +
125A VAL* 1.3 82.5 - - + +
127A LEU* 1.3 68.3 - - + +
129A GLY* 3.1 12.6 - - - -
130A GLY* 3.8 1.2 - - - -
134A PHE* 3.1 32.3 - - + -
156A ILE* 3.5 27.1 - - + -
160A TRP* 4.1 24.7 - - + -
191A ALA* 3.5 38.6 - - + -
195A THR* 4.0 5.2 - - + -
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Residues in contact with LEU 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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123A THR* 3.0 33.2 + - - +
124A PRO* 5.0 0.7 - - + -
126A VAL* 1.3 78.8 - - + +
128A TRP* 1.3 64.5 + - - +
129A GLY 2.7 3.8 + - - -
131A TRP* 3.1 30.9 - - + +
134A PHE* 4.7 8.1 - - + -
160A TRP* 3.9 39.5 - - + -
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Residues in contact with TRP 128 (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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83A ARG* 3.9 29.8 - - - -
84A ARG* 3.0 66.6 + - + +
87A ILE* 4.6 20.2 - - + +
88A ALA* 6.1 1.1 - - + -
91A LEU* 6.1 1.3 - - + -
124A PRO* 2.8 26.1 + - + +
125A VAL* 5.6 2.0 - - - -
127A LEU* 1.3 79.1 - - - +
129A GLY* 1.3 74.5 + - - +
131A TRP* 3.3 7.9 + - + +
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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