Contacts of the helix formed by residues 90 - 108 (chain F) in PDB entry 3L73
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 LEU 90 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ASP* 3.0 17.5 + - - +
37F LEU* 4.1 23.1 - - + -
43F VAL* 4.2 16.4 - - + -
46F ALA* 3.8 39.5 - - + +
47F LEU* 3.8 26.9 - - + -
50F LEU* 3.8 14.8 - - + -
58F ARG* 5.3 1.1 - - - +
89F TYR* 1.3 89.4 - - + +
91F GLU* 1.3 66.3 + - - +
92F PRO* 3.2 4.3 - - - -
93F TYR* 3.0 8.5 + - + +
94F LEU* 3.0 25.3 + - + +
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Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ASN* 3.6 25.0 + - - +
380C TYR* 4.2 13.2 - - + -
33F ARG* 2.7 31.4 + - - +
34F ASP* 2.8 15.1 + - - +
88F PRO* 3.6 14.8 - - + +
90F LEU* 1.3 72.0 - - - +
92F PRO* 1.3 69.0 - - + +
94F LEU* 3.5 10.5 + - + +
95F LYS* 3.0 54.5 + - + +
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Residues in contact with PRO 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F PRO* 3.1 19.1 - - + +
89F TYR 4.0 6.1 - - - +
90F LEU 3.3 4.0 - - - -
91F GLU* 1.3 95.0 - - + +
93F TYR* 1.3 72.4 + - + +
95F LYS* 3.5 6.3 + - + +
96F GLU* 3.5 17.2 + - - +
99F ARG* 5.4 0.9 + - - -
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Residues in contact with TYR 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ALA* 4.2 19.3 - - + +
49F ARG* 3.4 45.3 + - + +
50F LEU* 4.0 10.1 - - + -
51F PRO* 3.1 30.4 - - + +
54F LEU* 5.0 3.8 - - + +
89F TYR 3.8 24.2 - - - -
90F LEU* 3.0 7.2 + - + +
92F PRO* 1.3 80.9 - - + +
94F LEU* 1.3 67.6 + - - +
96F GLU* 3.1 8.4 + - - +
97F VAL* 3.0 24.2 + - - +
135O TRP* 3.8 23.3 - + - -
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Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LYS* 6.1 4.5 - - + -
380C TYR* 5.4 7.4 - - + -
37F LEU* 3.8 29.8 - - + -
42F ASP* 3.8 30.3 - - + +
43F VAL* 3.9 23.6 - - + +
46F ALA* 3.8 12.2 - - + +
90F LEU* 3.0 18.5 + - + +
91F GLU* 3.8 10.3 - - + +
93F TYR* 1.3 76.2 - - - +
95F LYS* 1.3 64.1 + - + +
97F VAL* 3.3 4.5 + - - +
98F ILE* 3.1 39.9 + - + +
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Residues in contact with LYS 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F GLU* 3.0 46.8 + - + +
92F PRO* 3.8 6.1 - - + +
93F TYR 3.2 0.4 - - - -
94F LEU* 1.3 76.6 - - + +
96F GLU* 1.3 57.0 + - - +
98F ILE* 3.4 11.6 + - + +
99F ARG* 3.1 42.1 + - - +
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Residues in contact with GLU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ARG* 4.1 6.3 - - - +
92F PRO 3.5 8.5 + - - +
93F TYR* 3.1 10.4 + - - +
95F LYS* 1.3 75.8 - - - +
97F VAL* 1.3 57.8 + - - +
99F ARG* 2.8 41.7 + - - +
100F GLU* 2.7 55.2 + - - +
133O ARG* 2.9 38.2 + - - +
135O TRP* 5.7 1.8 - - + -
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ASP* 3.8 39.0 - - + +
45F GLU* 3.9 19.5 - - + -
46F ALA* 4.1 13.5 - - - +
49F ARG* 3.2 32.1 - - - +
93F TYR 3.0 13.0 + - - +
94F LEU* 3.3 9.8 + - - +
96F GLU* 1.3 76.1 - - - +
98F ILE* 1.3 58.2 + - - +
100F GLU* 3.6 11.0 + - - +
101F ARG* 3.1 25.3 + - + +
104F ARG* 4.8 2.6 + - - +
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F ASP* 3.6 25.4 - - + +
94F LEU* 3.1 35.1 + - + +
95F LYS* 3.7 11.7 - - + +
96F GLU 3.1 0.6 - - - -
97F VAL* 1.3 74.5 - - - +
99F ARG* 1.3 60.8 + - - +
101F ARG* 3.3 18.7 + - - +
102F LEU* 2.9 47.3 + - + +
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Residues in contact with ARG 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F PRO 5.4 0.4 + - - -
95F LYS* 3.1 21.0 + - - +
96F GLU* 2.8 49.0 + - - +
98F ILE* 1.3 76.0 - - - +
100F GLU* 1.3 57.6 + - - +
102F LEU* 3.4 9.7 + - + +
103F GLU* 3.0 27.3 + - - +
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Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ARG* 2.7 38.9 + - - -
96F GLU* 2.7 25.5 + - - +
97F VAL* 3.7 8.1 - - - +
99F ARG* 1.3 75.5 - - - +
101F ARG* 1.3 64.8 + - - +
103F GLU* 3.3 14.2 + - - +
104F ARG* 3.1 42.1 + - - +
76O THR* 5.1 3.7 - - - +
81O SER* 5.8 7.0 - - - -
133O ARG* 3.0 27.9 + - - -
135O TRP* 5.3 0.2 + - - -
136O GLU* 5.0 4.5 - - - +
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Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ASP* 2.4 45.1 + - - +
97F VAL* 3.1 15.4 + - + +
98F ILE* 3.5 17.5 - - - +
100F GLU* 1.3 80.3 - - - +
102F LEU* 1.3 72.2 + - - +
104F ARG* 3.2 29.3 + - - +
105F GLU* 2.7 65.7 + - + +
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ILE* 2.9 39.5 + - + +
99F ARG* 3.8 7.6 - - + +
101F ARG* 1.3 90.2 - - - +
103F GLU* 1.3 66.3 + - - +
105F GLU* 3.9 14.1 - - + +
106F ALA* 3.0 26.3 + - - +
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Residues in contact with GLU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ARG 3.0 13.8 + - - +
100F GLU* 3.4 15.3 - - - +
101F ARG 3.1 0.4 - - - -
102F LEU* 1.3 78.2 - - - +
104F ARG* 1.3 65.0 + - - +
106F ALA* 3.6 4.1 - - - +
107F TRP* 2.9 30.3 + - + +
81O SER* 2.5 35.0 + - - -
83O PHE* 4.1 20.6 - - + +
84O ARG* 3.8 26.1 + - - +
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Residues in contact with ARG 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F VAL* 4.8 2.6 + - - +
100F GLU* 3.1 29.7 + - - +
101F ARG* 3.3 39.3 - - - +
103F GLU* 1.3 78.7 - - - +
105F GLU* 1.3 67.0 + - + +
107F TRP* 3.0 2.4 + - - +
108F ASN* 2.8 34.6 + - - +
289N HIS* 4.7 15.0 + - - -
83O PHE* 3.5 47.4 - - + +
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Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ARG* 2.7 63.3 + - + +
102F LEU* 3.9 14.9 - - + +
104F ARG* 1.3 75.4 - - + +
106F ALA* 1.3 62.6 + - - +
108F ASN* 3.5 11.4 + - - +
109F LYS* 3.3 32.2 + - - +
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Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU 3.0 20.0 + - - +
103F GLU* 3.6 4.7 - - - +
105F GLU* 1.3 77.5 - - - +
107F TRP* 1.3 60.9 + - - +
109F LYS* 3.3 29.9 + - + +
110F LYS* 3.3 12.4 + - - +
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Residues in contact with TRP 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLU* 2.9 23.6 + - + +
104F ARG 3.0 3.8 + - - +
106F ALA* 1.3 72.6 - - - +
108F ASN* 1.3 56.8 + - - +
109F LYS 3.1 5.2 - - - -
110F LYS* 3.1 34.8 + - + +
83O PHE* 3.7 16.6 - + + -
84O ARG* 3.6 38.4 - - + -
87O ARG* 3.6 39.8 - - + +
88O GLY* 3.7 30.1 - - - -
91O ALA* 4.7 8.9 - - + +
122O TYR* 4.7 2.5 - - - -
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Residues in contact with ASN 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ARG* 2.8 34.0 + - - +
105F GLU* 3.5 8.0 + - - +
106F ALA 3.3 0.2 - - - -
107F TRP* 1.3 74.7 - - - +
109F LYS* 1.3 63.2 + - - +
110F LYS* 4.4 1.9 - - - +
83O PHE* 4.1 1.8 - - - -
87O ARG* 2.8 37.7 + - - +
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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
------------------------------------------------------------
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