Contacts of the helix formed by residues 115 - 131 (chain A) in PDB entry 1F7V
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLY 5.1 1.0 + - - -
98A ASP* 3.3 26.2 + - - +
99A PHE 2.7 24.7 + - - +
100A LEU 4.1 8.9 + - - -
101A GLU* 4.0 8.9 - - - +
113A PHE 3.7 0.4 + - - -
114A PHE* 1.3 71.0 - - - +
116A PRO* 1.3 69.8 - - - +
117A GLN* 2.7 30.3 + - - +
118A PHE* 3.0 7.1 + - + +
119A LEU* 3.0 21.7 + - - +
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Residues in contact with PRO 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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101A GLU* 3.4 17.3 - - - +
114A PHE 3.2 11.6 - - - +
115A ASN* 1.3 86.2 - - - +
117A GLN* 1.3 52.9 + - - +
119A LEU* 3.2 13.3 + - + +
120A ALA* 2.7 36.9 + - - +
519A LEU 5.8 0.7 - - - +
525A LYS* 3.8 50.0 - - + +
528A ILE* 3.7 12.0 - - + +
529A ARG* 4.7 13.2 - - + -
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Residues in contact with GLN 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 ASN* 2.7 22.2 + - - +
116A PRO* 1.3 71.8 - - + +
118A PHE* 1.3 62.2 + - - +
120A ALA* 3.3 4.6 + - - +
121A LYS* 3.0 51.6 + - - +
516A PHE* 2.7 26.4 + - - +
517A SER* 3.0 37.6 + - - +
519A LEU* 4.4 10.7 + - - +
520A LYS* 4.8 2.6 - - - +
528A ILE* 5.8 1.0 - - - +
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Residues in contact with PHE 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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4A THR* 4.7 8.7 - - + -
8A ILE* 4.2 14.4 - - + -
31A ILE* 4.4 2.7 - - + -
34A LEU* 3.8 13.2 - - + -
35A MET* 3.5 27.6 - - + -
98A ASP* 3.2 33.4 - - + +
99A PHE* 3.4 47.3 - + - -
115A ASN* 3.0 11.1 + - + +
117A GLN* 1.3 79.8 - - - +
119A LEU* 1.3 65.7 + - - +
121A LYS* 3.6 7.6 + - - +
122A LEU* 3.4 46.7 + - + +
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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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31A ILE* 3.4 34.3 - - + -
35A MET* 3.9 10.5 - - + -
114A PHE* 3.7 38.6 - - + -
115A ASN 3.0 13.6 + - - +
116A PRO* 3.4 14.4 - - + +
118A PHE* 1.3 77.4 - - - +
120A ALA* 1.3 55.7 + - - +
122A LEU* 3.0 2.6 + - - -
123A VAL* 2.7 44.2 + - + +
528A ILE* 3.8 9.4 - - + +
529A ARG* 3.8 36.6 - - + -
532A GLY* 6.0 2.0 - - - -
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Residues in contact with ALA 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 PRO 2.7 21.0 + - - +
117A GLN* 3.3 9.4 + - - +
119A LEU* 1.3 74.8 - - - +
121A LYS* 1.3 63.2 + - - +
122A LEU 3.1 1.4 + - - -
123A VAL* 5.1 0.2 - - - -
124A ILE* 3.2 29.0 + - + +
125A PRO* 3.3 5.0 - - - +
516A PHE* 4.0 28.5 - - + +
519A LEU* 4.9 0.4 - - + -
528A ILE* 3.8 26.6 - - + +
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Residues in contact with LYS 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 GLN* 3.0 39.1 + - - +
118A PHE* 4.0 7.4 - - - +
120A ALA* 1.3 74.8 - - - +
122A LEU* 1.3 66.1 + - + +
125A PRO* 3.2 21.1 - - - +
516A PHE* 4.0 26.6 - - + -
517A SER* 5.3 4.6 - - - +
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Residues in contact with LEU 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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8A ILE* 4.1 22.2 - - + -
12A LYS* 6.3 1.1 - - - +
31A ILE* 3.9 23.3 - - + -
34A LEU* 4.2 4.9 - - + -
118A PHE* 3.4 43.3 + - + +
119A LEU 3.0 6.0 + - - +
121A LYS* 1.3 86.4 - - + +
123A VAL* 1.3 64.4 + - - +
124A ILE 3.6 0.2 - - - -
125A PRO* 3.7 1.6 - - - +
126A ASP* 3.1 25.7 + - - +
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Residues in contact with VAL 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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31A ILE* 4.0 35.2 - - + -
119A LEU* 2.7 34.3 + - + +
120A ALA* 5.1 1.1 - - - -
122A LEU* 1.3 69.6 - - - +
124A ILE* 1.3 61.4 + - + +
126A ASP* 3.1 5.8 + - - +
127A ILE* 2.7 56.6 + - + +
134A TYR* 3.5 19.5 - - + +
528A ILE* 5.6 3.8 - - + +
531A LEU* 4.3 5.2 - - + -
532A GLY* 4.1 13.0 - - - +
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Residues in contact with ILE 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 ALA* 3.2 16.4 + - + +
123A VAL* 1.3 75.3 - - + +
125A PRO* 1.3 61.4 - - + +
127A ILE* 3.0 7.4 + - - +
128A LEU* 2.6 55.1 + - + +
516A PHE* 3.4 35.9 - - + -
519A LEU* 3.9 17.7 - - + -
528A ILE* 5.1 2.5 - - + -
531A LEU* 4.6 9.6 - - + -
583A ALA* 3.4 20.6 - - + +
584A LEU* 4.1 20.9 - - + +
587A ALA* 4.1 10.8 - - + -
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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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120A ALA 3.3 4.3 - - - +
121A LYS 3.2 28.0 - - - +
122A LEU 3.7 2.9 - - - +
123A VAL 3.6 2.0 - - - -
124A ILE* 1.3 94.8 - - + +
126A ASP* 1.3 55.5 + - - +
128A LEU* 3.6 3.3 - - + -
129A THR* 2.7 38.0 + - - +
512A ILE* 3.8 31.6 - - + +
516A PHE* 3.8 18.6 - - + -
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Residues in contact with ASP 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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28A ASP 5.1 4.6 - - - +
29A VAL* 4.9 4.3 - - - +
122A LEU 3.1 18.9 + - - +
123A VAL* 3.1 7.8 + - - +
125A PRO* 1.3 78.6 - - - +
127A ILE* 1.3 57.1 + - - +
129A THR* 3.8 3.1 - - - -
130A ARG* 2.7 82.6 + - - +
134A TYR* 3.5 16.5 - - - -
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Residues in contact with ILE 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 VAL* 2.7 43.7 + - + +
124A ILE* 3.4 3.1 - - - +
126A ASP* 1.3 73.2 - - - +
128A LEU* 1.3 57.7 + - - +
131A LYS* 2.9 31.2 + - - +
134A TYR* 3.4 44.0 - - + -
531A LEU* 4.1 9.9 - - + -
587A ALA* 3.8 41.5 - - + +
590A GLN* 3.8 16.1 - - + +
591A VAL* 3.9 14.8 - - + -
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Residues in contact with LEU 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 ILE* 2.6 37.1 + - + +
125A PRO 3.8 0.7 - - - +
127A ILE* 1.3 74.4 - - + +
129A THR* 1.3 58.5 + - - +
131A LYS* 3.5 27.6 - - - +
508A GLN* 4.5 10.1 - - + +
511A TRP* 3.7 42.8 - - + -
512A ILE* 3.7 31.8 - - + +
583A ALA* 4.3 2.9 - - + +
586A GLY 4.0 5.6 - - - +
587A ALA* 3.6 35.2 - - + +
590A GLN* 5.3 3.4 - - + -
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Residues in contact with THR 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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125A PRO* 2.7 25.8 + - - +
126A ASP* 3.9 3.6 - - - -
128A LEU* 1.3 74.7 - - - +
130A ARG* 1.3 69.8 + - + +
131A LYS* 3.3 6.9 - - - +
512A ILE* 3.4 19.7 - - - +
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Residues in contact with ARG 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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28A ASP 4.5 0.6 + - - -
29A VAL* 3.4 38.9 + - - +
126A ASP* 2.7 65.4 + - - +
129A THR* 1.3 76.9 - - + +
131A LYS* 1.3 70.1 + - - +
132A GLU* 3.0 10.5 + - - +
133A ASP* 2.9 34.7 + - + +
134A TYR* 2.8 39.9 + - - +
136A SER* 3.3 18.4 + - - -
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Residues in contact with LYS 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 ILE* 2.9 17.7 + - - +
128A LEU* 3.5 22.9 - - - +
129A THR 4.1 4.9 - - - +
130A ARG* 1.3 77.3 - - - +
132A GLU* 1.3 70.1 + - - +
133A ASP 2.6 12.3 + - - -
134A TYR* 2.8 17.2 + - - +
508A GLN* 3.2 34.9 + - - +
590A GLN* 3.2 30.0 - - - +
594A ASN* 2.9 10.6 + - - -
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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