Contacts of the helix formed by residues 90 - 107 (chain A) in PDB entry 2FG5
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 GLN 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS* 1.3 68.7 - - - +
91A ASP* 1.3 66.6 + - - +
93A PHE* 2.8 29.3 + - + +
94A TYR* 3.4 34.4 + - + +
127A GLU* 3.1 42.0 + - - +
128A VAL* 3.8 13.5 - - + -
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Residues in contact with ASP 91 (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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13A ASP* 5.3 2.9 - - - +
89A LYS* 3.3 6.0 - - + +
90A GLN* 1.3 82.9 - - - +
92A SER* 1.3 60.5 + - - +
94A TYR* 3.0 29.5 + - - +
95A THR* 3.1 16.7 + - - +
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 4.7 10.0 + - - +
16A VAL* 3.8 17.7 - - - -
84A VAL 4.7 1.9 - - - +
85A TYR* 3.3 13.3 - - - +
86A ASP* 2.9 35.2 + - - +
89A LYS* 2.5 27.4 + - - +
91A ASP* 1.3 77.1 - - - +
93A PHE* 1.3 55.9 + - - +
94A TYR 3.5 0.2 - - - -
95A THR* 3.8 9.4 - - - -
96A LEU* 3.3 17.3 + - - +
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.9 23.6 - + + -
90A GLN* 2.8 15.3 + - + +
92A SER* 1.3 79.5 + - - +
94A TYR* 1.3 68.3 + + + -
96A LEU* 3.4 37.4 - - + +
97A LYS* 3.5 36.9 - - - +
115A ILE* 5.4 1.1 - - + -
128A VAL* 3.8 29.4 - - + -
132A ASP* 3.9 17.3 - - + -
133A ALA* 3.7 36.1 - - + -
136A TYR* 4.1 13.2 - + + -
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Residues in contact with TYR 94 (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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90A GLN* 3.6 47.9 + - + +
91A ASP* 3.0 20.3 + - - +
93A PHE* 1.3 83.2 - + + +
95A THR* 1.3 65.5 + - - +
96A LEU 3.1 1.1 - - - -
97A LYS* 3.1 38.8 + - + +
98A LYS* 3.2 12.3 + - - +
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 3.2 39.8 + - + +
68A HIS* 6.4 0.9 - - + -
91A ASP* 3.1 11.9 + - - +
92A SER 3.8 9.9 - - - -
93A PHE 3.4 0.2 - - - -
94A TYR* 1.3 72.9 - - - +
96A LEU* 1.3 64.8 + - - +
98A LYS* 3.2 9.3 + - + +
99A TRP* 3.0 45.5 + - + +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 3.4 51.5 - - + +
84A VAL 4.0 6.5 - - - +
85A TYR* 4.0 9.0 - - + -
92A SER 3.3 11.2 + - - +
93A PHE* 3.4 39.9 - - + +
94A TYR 3.1 0.2 - - - -
95A THR* 1.3 80.4 - - - +
97A LYS* 1.3 55.3 + - - +
99A TRP* 3.3 4.9 + - - +
100A VAL* 3.0 33.8 + - + +
115A ILE* 3.7 23.6 - - + -
136A TYR* 3.8 23.6 - - + -
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Residues in contact with LYS 97 (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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93A PHE* 3.5 47.1 - - - +
94A TYR* 3.1 26.9 + - + +
96A LEU* 1.3 77.5 - - - +
98A LYS* 1.3 57.0 + - - +
100A VAL* 3.4 2.8 + - - +
101A LYS* 3.1 45.0 + - - +
136A TYR* 3.3 47.6 + - + +
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Residues in contact with LYS 98 (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 TYR 3.2 11.2 + - - +
95A THR* 3.2 12.5 + - + +
97A LYS* 1.3 76.3 - - - +
99A TRP* 1.3 62.0 + - + +
101A LYS* 3.7 13.0 + - - +
102A GLU* 3.4 23.0 + - - +
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Residues in contact with TRP 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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11A LEU* 3.7 38.5 - - + +
12A GLY* 3.8 33.3 - - - +
13A ASP* 4.8 0.6 - - - +
61A THR* 6.0 0.2 - - - -
63A GLY* 5.4 1.8 - - - -
68A HIS* 3.6 38.2 - + + -
71A ALA* 3.7 27.8 - - + -
75A TYR* 4.5 3.4 - + - -
83A ILE* 3.9 14.8 - - + -
95A THR* 3.0 46.1 + - + +
96A LEU* 3.6 6.1 - - - +
98A LYS* 1.3 77.2 - - + +
100A VAL* 1.3 58.6 + - - +
102A GLU* 3.5 27.3 + - - +
103A LEU* 2.9 33.0 + - + +
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Residues in contact with VAL 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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83A ILE* 3.8 14.1 - - + +
96A LEU* 3.0 21.1 + - + +
97A LYS 3.5 3.6 - - - +
99A TRP* 1.3 74.9 - - - +
101A LYS* 1.3 60.7 + - + +
103A LEU* 3.2 7.3 + - - +
104A LYS* 2.9 43.3 + - + +
113A MET* 3.7 28.7 - - + +
115A ILE* 5.4 0.4 - - + -
136A TYR* 3.4 29.6 - - + +
140A ILE* 4.0 18.6 - - + -
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Residues in contact with LYS 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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97A LYS* 3.1 34.2 + - - +
98A LYS* 3.8 10.6 - - - +
99A TRP 3.2 0.2 - - - -
100A VAL* 1.3 78.4 - - + +
102A GLU* 1.3 63.9 + - - +
104A LYS* 3.0 17.3 + - - +
105A GLU* 3.1 14.8 + - - +
136A TYR* 6.0 0.4 - - - -
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Residues in contact with GLU 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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68A HIS* 4.8 5.0 - - - +
71A ALA* 4.6 1.6 - - - +
72A PRO* 4.5 8.1 - - - +
75A TYR* 3.0 35.0 + - + +
98A LYS 3.4 14.4 + - - +
99A TRP* 3.8 24.4 - - + +
101A LYS* 1.3 77.5 - - - +
103A LEU* 1.3 56.2 + - - +
105A GLU* 4.5 1.1 - - - -
106A HIS* 2.9 44.9 + - + +
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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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11A LEU* 3.6 26.2 - - + -
75A TYR* 3.8 34.3 - - + -
81A ALA* 3.5 28.9 - - + -
83A ILE* 3.9 11.2 - - + -
99A TRP 2.9 16.0 + - - +
100A VAL 3.4 5.8 - - - +
101A LYS 3.0 0.4 - - - -
102A GLU* 1.3 78.5 - - - +
104A LYS* 1.3 58.1 + - - +
107A GLY* 3.1 31.5 + - - +
111A ILE* 4.6 19.5 - - + +
113A MET* 3.7 25.6 - - - -
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Residues in contact with LYS 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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100A VAL* 2.9 24.5 + - + +
101A LYS* 3.0 6.3 + - - +
103A LEU* 1.3 76.0 - - - +
105A GLU* 1.3 57.8 + - - +
107A GLY 4.9 4.6 - - - +
111A ILE* 6.2 2.7 - - + -
113A MET* 4.3 23.1 - - + -
139A SER 4.9 0.6 + - - -
140A ILE* 3.5 45.5 + - - +
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Residues in contact with GLU 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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76A ARG* 5.3 1.7 + - - -
101A LYS 3.1 13.6 + - - +
102A GLU* 3.9 2.0 - - - +
104A LYS* 1.3 80.0 - - - +
106A HIS* 1.3 82.9 + - + +
107A GLY 3.8 1.6 - - - -
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Residues in contact with HIS 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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72A PRO* 5.5 4.7 - - + -
75A TYR* 3.3 35.3 - - + +
76A ARG* 3.2 40.6 + - - +
102A GLU* 2.9 21.8 + - + +
105A GLU* 1.3 95.7 - - + +
107A GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 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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75A TYR* 4.1 12.3 - - - -
76A ARG* 5.3 2.5 - - - -
103A LEU* 3.1 23.1 + - - +
104A LYS* 4.9 5.0 - - - +
105A GLU 5.2 0.5 - - - -
106A HIS* 1.3 80.2 + - - +
108A PRO* 1.3 78.9 - - - +
109A GLU* 3.4 2.9 + - - -
111A ILE* 5.2 2.2 - - - -
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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