Contacts of the helix formed by residues 119 - 134 (chain A) in PDB entry 3FUV
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 PRO 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLN* 4.0 23.1 - - - +
53A VAL* 4.9 6.7 - - + +
54A GLY* 5.7 4.7 - - - -
117A ASN* 3.6 10.1 - - - +
118A LEU* 1.4 85.6 - - + +
120A TYR* 1.3 65.4 + - - +
121A HIS* 3.1 36.1 - - + +
122A ILE* 3.2 20.6 - - + +
123A ALA* 3.0 21.7 + - - +
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Residues in contact with TYR 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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118A LEU 3.5 2.7 + - - -
119A PRO* 1.3 73.0 - - - +
121A HIS* 1.3 72.9 + + + +
122A ILE 3.3 1.0 + - - -
123A ALA* 3.5 12.5 + - - +
124A THR* 4.6 3.3 + - - -
125A PRO* 5.5 0.2 - - - +
143A VAL* 6.5 0.4 - - - -
144A GLN* 3.6 45.8 - - + +
146A GLU* 3.4 27.0 + - - -
147A VAL* 3.7 25.3 - - + +
150A ARG* 4.7 3.4 + - - -
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Residues in contact with HIS 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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27A GLN* 5.5 2.2 + - - -
76A LYS* 5.9 7.6 - - + -
101A LEU* 5.8 0.3 - - - +
119A PRO* 3.1 32.7 - - + +
120A TYR* 1.3 87.5 - + + +
122A ILE* 1.3 71.1 + - + +
125A PRO* 3.8 15.2 - - - +
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Residues in contact with ILE 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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53A VAL* 4.3 9.2 - - + -
99A ASP* 6.4 0.2 - - - -
100A ALA* 3.0 36.6 - - + +
101A LEU* 4.0 24.0 - - + -
118A LEU* 4.4 9.2 - - + -
119A PRO* 3.2 33.2 - - + +
121A HIS* 1.3 91.4 - - + +
123A ALA* 1.3 66.1 + - - +
124A THR 3.4 1.8 - - - -
125A PRO* 3.2 6.2 - - - +
126A LEU* 2.8 35.2 + - + +
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Residues in contact with ALA 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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118A LEU* 3.8 14.1 - - + -
119A PRO 3.0 17.6 + - - +
120A TYR* 3.5 9.4 + - - +
122A ILE* 1.3 79.4 - - - +
124A THR* 1.3 63.4 + - - +
126A LEU* 4.7 0.2 - - - -
127A VAL* 3.0 30.8 + - + +
143A VAL* 3.3 34.3 - - + -
147A VAL* 4.7 7.6 - - + -
151A MET* 4.9 1.3 - - + -
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Residues in contact with THR 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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120A TYR 4.6 3.8 + - - -
123A ALA* 1.3 74.4 - - - +
125A PRO* 1.3 75.9 - - + +
127A VAL* 3.8 0.3 - - - +
128A THR* 2.9 32.7 + - - +
147A VAL* 3.3 26.7 - - - +
150A ARG* 5.5 2.1 + - - -
151A MET* 4.1 6.0 - - - +
163A LEU* 3.8 34.9 - - + +
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Residues in contact with PRO 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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101A LEU* 4.1 23.6 - - + -
120A TYR 5.5 0.2 - - - +
121A HIS 3.8 15.5 - - - +
122A ILE* 3.2 13.9 - - - +
124A THR* 1.3 96.3 - - + +
126A LEU* 1.3 62.0 + - - +
128A THR* 3.9 5.5 - - - -
129A ARG* 3.1 24.3 + - - +
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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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53A VAL* 4.1 19.3 - - + -
100A ALA 4.1 6.3 - - - +
101A LEU* 3.8 16.1 - - + +
105A TRP* 3.4 39.7 - - + +
114A LEU* 4.7 4.0 - - + -
118A LEU* 3.7 32.5 - - + -
122A ILE* 2.8 29.6 + - + +
123A ALA 4.0 2.2 - - - +
125A PRO* 1.3 72.1 - - - +
127A VAL* 1.3 65.2 + - + +
129A ARG* 3.1 7.0 + - + +
130A LEU* 3.0 41.9 + - + +
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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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114A LEU* 5.0 5.8 - - + -
118A LEU* 3.8 19.1 - - + -
123A ALA 3.0 19.3 + - - +
124A THR 4.0 1.6 - - - +
126A LEU* 1.3 76.1 - - + +
128A THR* 1.3 63.0 + - - +
130A LEU* 3.3 6.4 + - - +
131A LEU* 2.8 37.2 + - + +
139A LEU* 4.1 6.3 - - + -
141A PHE* 3.8 26.7 - - + -
151A MET* 4.1 14.8 - - + -
163A LEU* 6.1 0.9 - - + -
167A VAL* 5.1 2.5 - - + -
197A LEU* 3.5 32.1 - - + -
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Residues in contact with THR 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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124A THR* 2.9 28.8 + - - +
125A PRO* 3.9 5.2 - - - -
127A VAL* 1.3 72.7 - - - +
129A ARG* 1.3 65.3 + - - +
131A LEU* 3.4 10.0 + - - +
132A LYS* 3.0 52.5 + - + +
163A LEU* 3.9 19.9 - - - +
166A ARG* 4.4 16.2 - - + +
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Residues in contact with ARG 129 (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 LEU* 2.6 38.9 + - + +
102A LEU 5.2 0.6 + - - -
103A TYR 3.2 19.6 + - - -
104A PRO* 4.5 0.2 - - - +
105A TRP* 3.7 17.3 - - + +
106A GLU* 2.9 30.9 + - - -
125A PRO 3.1 12.4 + - - +
126A LEU* 3.4 11.7 - - + +
128A THR* 1.3 81.8 - - - +
130A LEU* 1.3 68.5 + - + +
132A LYS* 3.2 10.8 + - - +
133A THR* 3.1 28.7 + - + +
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Residues in contact with LEU 130 (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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105A TRP* 3.6 46.7 - - + -
114A LEU* 3.8 39.5 - - + -
126A LEU* 3.0 34.0 + - + +
127A VAL* 3.9 4.0 - - - +
129A ARG* 1.3 77.3 - - + +
131A LEU* 1.3 64.2 + - - +
133A THR* 2.8 24.9 + - + -
134A GLY 3.7 1.6 + - - -
135A ARG 4.6 0.7 + - - -
136A PHE* 3.7 34.2 + - + +
139A LEU* 4.3 12.3 - - + -
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Residues in contact with LEU 131 (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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127A VAL* 2.8 34.8 + - + +
128A THR* 3.8 7.6 - - - +
130A LEU* 1.3 75.9 - - - +
132A LYS* 1.3 62.9 + - - +
134A GLY* 3.1 15.1 + - - -
139A LEU* 3.7 22.9 - - + -
166A ARG* 4.6 4.3 - - + +
167A VAL* 3.9 35.2 - - + +
170A HIS* 3.4 44.2 + - + +
171A ALA* 4.0 17.3 - - + -
197A LEU* 4.1 4.7 - - + -
199A PRO* 4.2 14.6 - - + +
202A ALA 4.5 0.3 - - - +
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Residues in contact with LYS 132 (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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128A THR* 3.0 38.8 + - + +
129A ARG* 3.2 8.0 + - - +
131A LEU* 1.3 73.1 - - - +
133A THR* 1.3 63.9 + - - +
134A GLY* 3.1 3.4 + - - -
166A ARG* 3.6 42.7 - - - +
170A HIS* 3.9 11.2 - - + +
203A LEU* 4.6 7.8 - - - +
204A ASP* 4.4 24.3 + - + +
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Residues in contact with THR 133 (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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105A TRP* 4.5 9.0 - - + -
106A GLU* 4.2 30.5 - - + +
129A ARG* 3.1 20.8 + - + +
130A LEU* 2.8 21.7 + - + +
132A LYS* 1.3 76.7 - - - +
134A GLY* 1.3 60.1 + - - +
135A ARG* 3.1 36.7 + - - +
136A PHE* 3.9 5.2 - - - -
203A LEU* 4.3 6.8 - - - +
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Residues in contact with GLY 134 (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 GLN* 4.8 8.7 + - - +
130A LEU 3.7 1.0 + - - -
131A LEU 3.1 12.2 + - - -
132A LYS 3.1 4.6 - - - -
133A THR* 1.3 77.3 + - - +
135A ARG* 1.3 58.2 + - - +
136A PHE 3.6 4.8 - - - +
199A PRO* 5.8 5.8 - - - +
201A GLY* 4.9 12.9 - - - -
202A ALA 4.8 6.3 - - - -
203A LEU* 3.9 20.7 - - - +
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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