Contacts of the helix formed by residues 98 - 113 (chain A) in PDB entry 1FUU
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 THR 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ALA* 3.3 1.9 + - - +
97A PRO* 1.3 94.0 - - + +
99A ARG* 1.3 65.0 + - - +
100A GLU* 3.7 9.7 + - - +
101A LEU* 3.1 30.3 + - + +
102A ALA* 2.9 22.5 + - - +
145A THR* 3.6 10.4 - - - +
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Residues in contact with ARG 99 (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 THR* 1.3 72.5 - - - +
100A GLU* 1.3 57.8 + - - +
102A ALA* 3.1 3.1 + - - +
103A LEU* 2.9 49.2 + - - +
124A ILE* 3.5 30.8 - - + +
125A GLY* 3.1 50.2 + - - +
126A GLY* 4.6 3.2 + - - -
145A THR* 3.8 8.2 - - + +
148A ARG* 5.6 5.4 - - - +
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Residues in contact with GLU 100 (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 THR* 3.7 7.5 + - - +
99A ARG* 1.3 81.5 - - - +
101A LEU* 1.3 90.5 + - - +
103A LEU* 3.2 10.1 + - - +
104A GLN* 2.9 29.6 + - - +
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Residues in contact with LEU 101 (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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96A ALA* 3.8 12.6 - - + -
97A PRO* 3.4 34.3 - - + -
98A THR* 3.1 26.1 + - + +
100A GLU* 1.3 99.5 - - - +
102A ALA* 1.3 63.0 + - - +
104A GLN* 3.3 7.7 + - + +
105A ILE* 3.1 27.1 + - + +
169A ASP* 5.8 0.9 - - - +
170A GLU* 3.9 22.0 - - - +
173A GLU* 6.1 0.4 - - + -
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Residues in contact with ALA 102 (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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96A ALA* 3.9 9.8 - - + +
98A THR 2.9 13.1 + - - +
99A ARG* 3.5 7.9 - - - +
101A LEU* 1.3 72.7 - - - +
103A LEU* 1.3 61.1 + - - +
105A ILE* 3.0 6.0 + - - +
106A GLN* 2.9 26.3 + - - +
122A ALA* 5.7 0.7 - - + -
124A ILE* 3.8 22.9 - - + -
143A VAL* 3.9 16.1 - - + +
144A GLY* 3.9 21.5 - - - -
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Residues in contact with LEU 103 (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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99A ARG* 2.9 35.4 + - - +
100A GLU* 3.6 7.6 - - - +
102A ALA* 1.3 72.2 - - - +
104A GLN* 1.3 66.2 + - - +
106A GLN* 3.2 25.2 + - - +
107A LYS* 3.0 23.0 + - - +
122A ALA* 4.3 5.4 - - + -
124A ILE* 3.4 29.2 - - + -
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Residues in contact with GLN 104 (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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39A TYR* 5.0 3.1 + - - -
69A THR* 5.7 0.9 + - - -
72A THR* 5.8 2.9 - - - +
100A GLU* 2.9 23.7 + - - +
101A LEU* 3.5 12.6 - - + +
102A ALA 3.2 0.2 - - - -
103A LEU* 1.3 77.4 - - - +
105A ILE* 1.3 65.5 + - + +
107A LYS* 3.0 33.5 + - - +
108A VAL* 2.9 36.4 + - + +
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Residues in contact with ILE 105 (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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72A THR* 4.3 17.5 - - + +
75A PHE* 4.0 16.4 - - + -
94A MSE 3.2 39.9 - - + -
95A LEU 5.2 1.1 - - - +
96A ALA* 4.0 17.9 - - + -
101A LEU* 3.1 15.1 + - + +
102A ALA 3.0 7.9 + - - +
104A GLN* 1.3 79.0 - - + +
106A GLN* 1.3 62.5 + - - +
108A VAL* 3.0 8.3 + - - +
109A VAL* 2.9 29.1 + - + +
143A VAL* 3.9 7.6 - - + -
169A ASP* 3.4 28.5 - - + +
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Residues in contact with GLN 106 (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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102A ALA 2.9 12.6 + - - +
103A LEU* 3.2 21.7 + - - +
105A ILE* 1.3 75.8 - - - +
107A LYS* 1.3 61.9 + - - +
109A VAL* 4.2 7.3 - - - +
110A MSE 2.8 47.5 + - + +
120A VAL* 2.7 37.4 + - + +
121A HIS* 4.1 0.2 - - - +
122A ALA* 3.4 29.0 - - - +
143A VAL* 3.9 16.1 - - + +
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Residues in contact with LYS 107 (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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39A TYR* 5.3 0.4 - - - -
103A LEU 3.0 12.7 + - - +
104A GLN* 3.0 34.0 + - - +
106A GLN* 1.3 79.4 - - - +
108A VAL* 1.3 58.7 + - + +
110A MSE 3.7 5.7 - - - +
111A ALA* 3.2 23.0 + - - +
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Residues in contact with VAL 108 (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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39A TYR* 3.9 30.3 - - + +
69A THR* 4.8 5.6 - - - +
72A THR* 3.6 34.8 - - + -
73A GLY* 4.6 5.2 - - - +
76A SER* 4.1 2.5 - - - +
104A GLN* 2.9 34.0 + - + +
105A ILE 3.0 5.6 + - - +
107A LYS* 1.3 77.9 - - + +
109A VAL* 1.3 57.0 + - - +
111A ALA* 3.3 6.7 + - - +
112A LEU* 3.0 44.5 + - + +
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Residues in contact with VAL 109 (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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76A SER* 4.1 20.2 - - - +
80A LEU* 3.8 10.6 - - + +
94A MSE 3.7 28.0 - - + -
105A ILE* 2.9 21.5 + - + +
106A GLN* 4.2 3.1 - - - -
108A VAL* 1.3 75.7 - - - +
110A MSE 1.3 54.5 + - - +
112A LEU* 3.3 7.7 + - - +
113A ALA* 2.8 33.9 + - + +
120A VAL* 3.4 31.6 - - + -
141A ILE* 4.1 17.3 - - + -
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Residues in contact with MSE 110 (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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106A GLN* 2.8 40.2 + - + +
107A LYS* 3.7 6.7 - - - +
109A VAL* 1.3 75.5 - - - +
111A ALA* 1.3 65.1 + - - +
113A ALA* 3.2 7.2 + - - +
114A PHE* 3.1 20.8 + - - -
118A ILE 4.6 7.9 - - - +
120A VAL* 3.9 33.7 - - + +
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Residues in contact with ALA 111 (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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35A GLY* 4.5 5.6 - - - +
39A TYR* 3.4 32.7 - - + +
107A LYS 3.2 15.1 + - - +
108A VAL 3.7 1.8 - - - +
110A MSE 1.3 78.3 - - - +
112A LEU* 1.3 60.7 + - - +
114A PHE* 2.8 33.1 + - - +
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Residues in contact with LEU 112 (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 ASN 4.8 0.5 - - - +
32A LEU* 3.9 15.7 - - + +
35A GLY* 3.5 27.5 - - - +
36A VAL* 4.3 4.7 - - - -
39A TYR* 3.6 33.4 - - + -
41A PHE* 3.9 15.5 - - + -
73A GLY* 4.3 5.6 - - - -
76A SER* 3.6 31.0 - - - -
77A ILE* 3.8 24.0 - - + +
80A LEU* 3.6 15.9 - - + -
108A VAL* 3.0 27.8 + - + +
109A VAL 3.6 0.9 - - - +
111A ALA* 1.3 76.5 - - - +
113A ALA* 1.3 56.7 + - - +
114A PHE 3.5 0.9 + - - -
116A MSE 4.5 1.7 - - - +
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Residues in contact with ALA 113 (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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80A LEU* 3.8 22.0 - - + -
109A VAL* 2.8 19.3 + - + +
110A MSE 3.4 9.4 - - - +
111A ALA 3.0 0.4 - - - -
112A LEU* 1.3 75.7 - - - +
114A PHE* 1.3 57.2 + - - +
115A HIS 3.2 2.7 - - - -
116A MSE 2.8 44.3 + - + +
118A ILE* 4.3 14.1 + - + +
120A VAL* 5.9 1.1 - - + -
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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