Contacts of the helix formed by residues 86 - 104 (chain F) in PDB entry 5A2Q
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 LYS 86 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16732 U 3.9 4.0 + - - +
16742 G 3.4 23.1 - - - +
16752 A 3.4 21.6 + - - +
51F HIS* 3.6 33.2 - - + +
70F GLU* 3.9 19.4 + - - +
73F THR* 3.8 22.6 - - + +
74F ASN* 2.6 30.4 + - - +
77F MET* 3.5 24.9 - - + -
84F GLY 3.2 4.8 + - - -
85F LYS* 1.3 72.5 - - - +
87F LEU* 1.3 66.4 + - + +
88F MET 3.2 0.7 - - - -
89F THR* 2.9 27.8 + - - -
90F VAL* 3.5 4.5 + - + -
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Residues in contact with LEU 87 (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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15912 C 3.2 35.0 - - - +
15922 C 4.1 17.3 - - - -
16732 U 5.2 6.1 - - - +
16742 G 4.7 10.3 - - - +
51F HIS* 5.2 5.4 - - + +
85F LYS* 3.5 0.8 - - - +
86F LYS* 1.3 84.3 - - + +
88F MET* 1.3 65.4 + - - +
89F THR 3.0 2.2 - - - -
90F VAL* 3.0 21.5 + - + +
91F ARG* 2.8 25.5 + - - +
44Q PRO* 4.6 17.0 - - + -
46Q THR* 5.7 3.1 - - - +
47Q LEU* 4.5 17.3 - - + -
78Q VAL* 4.4 22.0 - - + -
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Residues in contact with MET 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15352 U 3.4 44.4 - - - +
15362 G 3.8 10.3 - - - +
15912 C 3.8 26.4 + - - +
15922 C 4.0 27.2 + - - +
82F ASN* 5.6 2.2 - - + +
85F LYS* 4.1 31.0 + - + +
86F LYS 3.2 0.2 - - - -
87F LEU* 1.3 76.5 - - - +
89F THR* 1.3 57.1 + - - +
91F ARG* 3.4 30.1 - - - +
92F ILE* 3.0 33.6 + - - +
104Z ARG* 4.4 9.9 - - - +
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Residues in contact with THR 89 (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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15352 U 4.5 4.2 + - - -
73F THR* 3.1 47.5 + - + +
76F MET* 3.4 33.1 + - + +
77F MET* 4.2 3.1 + - - +
85F LYS 4.5 4.7 + - - -
86F LYS* 2.9 15.4 + - - -
88F MET* 1.3 75.1 - - - +
90F VAL* 1.3 53.9 + - - -
91F ARG 3.0 5.2 - - - -
92F ILE* 2.9 5.6 + - + +
93F VAL* 2.5 43.6 + - + +
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Residues in contact with VAL 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F PHE* 3.8 7.6 - - + -
49F LEU* 6.3 0.9 - - + -
50F PRO* 3.6 39.3 - - + -
51F HIS* 4.5 13.7 - - + +
73F THR* 3.7 14.4 - - + -
86F LYS* 3.5 5.3 + - + +
87F LEU* 3.3 35.4 - - + +
89F THR* 1.3 76.3 - - - +
91F ARG* 1.3 57.2 + - - +
93F VAL* 4.6 5.8 - - - +
94F LYS* 3.2 22.8 + - - +
46Q THR* 4.0 23.4 - - + +
47Q LEU* 5.0 6.7 - - + -
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Residues in contact with ARG 91 (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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15352 U 4.0 22.4 + - - -
15362 G 5.8 0.2 + - - -
15922 C 4.8 4.0 - - - +
87F LEU 2.8 15.6 + - - +
88F MET* 3.4 34.5 - - - +
90F VAL* 1.3 78.1 - - - +
92F ILE* 1.3 83.7 + - - +
94F LYS* 3.0 26.1 + - - +
95F HIS* 3.2 28.4 - - - +
168F THR* 4.2 22.2 - - - +
170F ALA* 6.0 0.4 - - - +
46Q THR* 4.6 8.7 - - + +
103Z HIS* 3.4 44.9 + - + +
104Z ARG* 5.8 3.4 - - - +
106Z GLN* 4.4 8.5 - - - +
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Residues in contact with ILE 92 (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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15352 U 3.5 33.7 - - + +
76F MET* 5.1 9.0 - - + -
88F MET 3.0 16.9 + - - +
89F THR* 2.9 9.9 + - - +
91F ARG* 1.3 99.9 - - - +
93F VAL* 1.3 69.0 + - + +
94F LYS 3.2 0.2 + - - -
95F HIS* 3.4 4.8 + - - -
96F ALA* 3.1 22.2 + - - +
169F ILE* 3.9 41.7 - - + +
170F ALA* 4.1 15.3 - - + +
173F LEU* 4.8 9.0 - - + -
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Residues in contact with VAL 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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20F PHE* 4.4 6.7 - - + -
50F PRO* 5.4 0.7 - - + -
69F VAL* 4.0 14.8 - - + -
72F LEU* 4.8 9.6 - - + -
73F THR* 3.9 15.5 - - - +
76F MET* 4.0 18.4 - - + -
89F THR* 2.5 43.2 + - + +
90F VAL* 4.6 3.8 - - - -
92F ILE* 1.3 72.4 - - + +
94F LYS* 1.3 59.4 + - - +
96F ALA* 4.0 6.2 - - + +
97F PHE* 3.3 50.2 + - + -
173F LEU* 5.0 2.0 - - + -
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Residues in contact with LYS 94 (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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20F PHE* 3.5 40.2 - - + +
49F LEU* 6.2 1.2 - - - +
90F VAL 3.2 15.8 + - - +
91F ARG* 3.0 16.8 + - - +
93F VAL* 1.3 81.7 - - - +
95F HIS* 1.3 72.0 + - + +
96F ALA 3.4 0.2 + - - -
97F PHE* 3.6 2.6 + - - +
98F GLU* 3.3 44.3 + - - +
45Q ARG 4.8 4.6 + - - -
46Q THR* 4.3 29.2 + - + +
49Q TYR* 6.4 0.2 - - - -
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Residues in contact with HIS 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 ARG* 3.2 38.2 + - + +
92F ILE* 3.4 2.4 + - - +
94F LYS* 1.3 88.0 - - + +
96F ALA* 1.3 59.9 + - - +
98F GLU* 4.0 3.8 + - - -
99F ILE* 3.1 32.6 + - - +
170F ALA* 3.7 18.4 - - + -
101Z SER* 4.6 14.7 - - - -
102Z LYS 5.1 0.2 - - - -
103Z HIS* 3.2 43.2 + - + +
106Z GLN* 3.8 26.2 - - + +
108Z ILE* 3.5 18.3 - - + +
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Residues in contact with ALA 96 (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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92F ILE 3.1 18.5 + - - +
93F VAL* 4.0 5.4 - - + +
94F LYS 3.2 0.4 - - - -
95F HIS* 1.3 76.5 - - - +
97F PHE* 1.3 61.5 + - + +
99F ILE* 3.3 4.3 + - - +
100F ILE* 3.0 36.6 + - + +
170F ALA* 3.9 24.2 - - - +
173F LEU* 4.0 26.0 - - + -
174F ALA* 3.8 3.2 - - - +
177F LEU* 6.3 0.2 - - + -
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Residues in contact with PHE 97 (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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19F LEU* 4.8 0.9 - - + -
20F PHE* 4.3 17.0 - + + -
23F TRP* 3.9 22.6 - + - +
69F VAL* 3.6 15.3 - - + -
72F LEU* 5.0 2.7 - - + -
93F VAL* 3.3 38.8 + - + +
94F LYS 4.0 3.4 - - - +
95F HIS 3.4 0.4 - - - -
96F ALA* 1.3 80.8 - - + +
98F GLU* 1.3 57.3 + - - +
99F ILE 3.1 0.2 - - - -
100F ILE* 2.9 31.2 + - + +
101F HIS* 3.1 15.1 + - - +
108F PRO* 3.6 37.7 - - + +
109F LEU* 3.5 21.3 - - + -
112F LEU* 3.7 27.6 - - + -
177F LEU* 4.7 2.0 - - + -
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Residues in contact with GLU 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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20F PHE* 5.2 4.4 - - + +
22F LYS* 3.2 37.7 + - - +
23F TRP* 3.9 17.3 - - + +
94F LYS* 3.3 42.3 + - - +
95F HIS* 4.6 2.2 + - - -
96F ALA 3.4 0.2 - - - -
97F PHE* 1.3 74.3 - - - +
99F ILE* 1.3 57.4 + - - +
101F HIS* 4.4 2.6 + - - +
102F LEU* 3.3 28.1 + - - +
100Z VAL* 4.0 8.1 - - + +
101Z SER* 3.0 30.5 + - - -
108Z ILE* 4.0 16.7 - - + +
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Residues in contact with ILE 99 (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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95F HIS 3.1 22.2 + - - +
96F ALA 3.5 4.3 - - - +
97F PHE 3.1 0.6 - - - -
98F GLU* 1.3 77.2 - - - +
100F ILE* 1.3 67.1 + - - +
102F LEU* 3.0 23.4 + - - +
103F LEU* 3.4 8.4 + - + +
170F ALA 3.9 1.8 - - - -
171F GLU* 3.7 28.7 - - + +
174F ALA* 3.5 18.8 - - + -
67Z LEU* 3.7 32.5 - - + +
69Z THR* 4.5 10.8 - - + +
106Z GLN* 3.6 24.9 - - - +
108Z ILE* 4.0 14.8 - - + -
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Residues in contact with ILE 100 (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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96F ALA* 3.0 22.7 + - + +
97F PHE* 2.9 23.8 + - + +
99F ILE* 1.3 74.8 - - - +
101F HIS* 1.3 63.4 + - - +
103F LEU* 2.9 13.7 + - - +
104F THR* 3.3 13.6 + - - +
105F GLY 4.1 0.7 + - - -
106F GLU 5.1 1.8 - - - +
108F PRO* 4.2 7.9 - - + -
111F VAL* 3.6 37.0 - - + -
174F ALA* 3.6 21.3 - - + -
177F LEU* 3.5 32.1 - - + -
178F ILE* 4.2 18.2 - - + -
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Residues in contact with HIS 101 (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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23F TRP* 3.4 41.7 - + + -
97F PHE 3.1 4.8 + - - +
98F GLU 4.5 4.3 - - - +
100F ILE* 1.3 78.0 - - - +
102F LEU* 1.3 70.4 + - + +
103F LEU 3.3 0.2 - - - -
105F GLY* 3.2 33.5 - - - +
106F GLU 3.3 28.5 + - - +
107F ASN* 5.2 1.1 - - - -
108F PRO* 4.5 1.3 - - + +
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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 GLU 3.3 22.0 - - - +
99F ILE 3.0 7.8 + - - +
101F HIS* 1.3 88.7 - - + +
103F LEU* 1.3 65.2 + - - +
105F GLY* 4.8 0.9 + - - -
66Z LYS* 4.3 19.1 - - - +
67Z LEU* 4.0 26.9 - - + -
100Z VAL* 4.5 7.4 - - + -
108Z ILE* 3.8 21.5 - - + -
109Z TYR 4.3 1.6 - - - +
110Z THR* 3.2 42.6 - - + +
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Residues in contact with LEU 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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1013 U 4.4 16.2 - - - +
99F ILE* 3.4 7.8 + - + +
100F ILE 2.9 8.9 + - - +
102F LEU* 1.3 81.0 - - - +
104F THR* 1.3 66.2 + - - +
174F ALA* 5.6 2.5 - - + -
175F ASP* 5.9 2.2 - - - +
178F ILE* 3.8 26.5 - - + -
65Z TYR 5.4 1.1 - - - +
66Z LYS* 4.6 15.4 - - + +
67Z LEU* 3.5 49.6 - - + +
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Residues in contact with THR 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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100F ILE* 3.3 6.8 + - - +
103F LEU* 1.3 78.0 - - - +
105F GLY* 1.3 59.4 + - - +
106F GLU* 3.6 39.4 - - + +
111F VAL* 5.2 11.7 - - + +
178F ILE* 3.8 30.8 - - - +
182F LYS* 5.1 7.7 - - - -
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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