Contacts of the helix formed by residues 91 - 106 (chain F) in PDB entry 6ACQ
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 ARG 91 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89F VAL* 2.8 29.6 + - + +
90F GLU* 1.3 75.2 - - - +
92F MET* 1.3 66.4 + - - +
93F ASP* 2.8 40.5 + - - +
94F ILE* 3.3 28.1 + - + +
95F LYS* 3.0 21.0 + - - +
119F LEU* 3.8 3.4 - - - +
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Residues in contact with MET 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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91F ARG* 1.3 71.0 - - - +
93F ASP* 1.3 58.6 + - - +
95F LYS* 3.5 1.6 - - - +
96F LYS* 2.9 52.2 + - + +
119F LEU* 3.6 43.7 - - + +
120F SER 3.8 17.7 - - - +
123F GLU* 3.7 33.9 - - - +
124F VAL* 3.6 25.1 - - - -
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Residues in contact with ASP 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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91F ARG* 2.8 48.5 + - - +
92F MET* 1.3 77.9 + - - +
94F ILE* 1.3 72.2 + - - -
96F LYS* 3.6 9.2 + - - +
97F GLN* 3.5 18.4 + - - +
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Residues in contact with ILE 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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88F ALA* 5.1 5.8 - - + -
89F VAL* 4.5 20.0 - - + +
91F ARG* 3.3 45.3 + - + +
93F ASP* 1.3 85.8 + - - +
95F LYS* 1.3 63.8 + - + +
97F GLN* 3.2 8.1 + - - +
98F ILE* 3.1 41.2 + - + +
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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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86F GLU* 3.1 42.6 + - - +
87F ALA* 5.9 0.2 - - - +
88F ALA* 4.3 3.0 + - - -
89F VAL 3.2 24.6 + - - -
90F GLU* 2.7 27.9 + - - -
91F ARG 3.0 11.9 + - - +
92F MET* 3.5 7.0 - - - +
94F ILE* 1.3 80.8 - - - +
96F LYS* 1.3 63.5 + - - +
98F ILE* 3.6 5.0 + - - +
99F PHE* 3.0 41.1 + - + -
114F SER* 3.7 5.1 + - - +
116F THR* 3.6 15.3 - - - +
119F LEU* 3.7 19.1 - - + -
124F VAL* 4.5 17.3 - - + -
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Residues in contact with LYS 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 MET* 2.9 43.9 + - + +
93F ASP* 3.9 8.5 - - - +
94F ILE 3.3 0.2 - - - -
95F LYS* 1.3 77.7 - - - +
97F GLN* 1.3 57.1 + - - +
99F PHE* 3.8 3.2 - - - +
100F ALA* 2.9 30.3 + - - +
123F GLU* 3.8 32.0 + - - +
124F VAL* 4.4 10.5 - - - -
127F ALA* 3.5 29.2 - - + +
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Residues in contact with GLN 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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93F ASP 3.5 10.4 + - - +
94F ILE* 3.2 12.7 + - - +
95F LYS 3.1 0.2 - - - -
96F LYS* 1.3 77.7 - - - +
98F ILE* 1.3 58.2 + - + +
100F ALA* 3.0 9.2 + - - +
101F ASP* 2.8 60.0 + - - +
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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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7F ILE* 4.3 19.3 - - + -
30F ARG* 5.9 3.6 - - - +
75F LEU* 5.0 6.9 - - + +
86F GLU* 4.1 15.5 - - + -
88F ALA* 4.0 27.1 - - + -
94F ILE* 3.1 21.7 + - + +
95F LYS* 3.7 9.0 - - - +
97F GLN* 1.3 81.1 - - + +
99F PHE* 1.3 66.7 + - + +
101F ASP* 3.2 8.9 + - - +
102F LEU* 2.9 48.6 + - + +
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Residues in contact with PHE 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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86F GLU* 3.7 31.9 - - + -
95F LYS* 3.0 25.4 + - + +
96F LYS* 3.9 3.8 - - - +
98F ILE* 1.3 86.5 - - + +
100F ALA* 1.3 56.6 + - - +
102F LEU* 3.4 9.7 + - + +
103F ASP* 2.9 28.6 + - - +
112F LEU* 3.6 42.5 - - + +
113F ALA 3.7 26.7 - - - -
114F SER* 4.0 8.7 - - - -
124F VAL* 3.5 26.9 - - + +
128F THR* 3.6 18.1 - - + +
134F VAL* 4.0 15.3 - - + -
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Residues in contact with ALA 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 LYS 2.9 19.2 + - - +
97F GLN* 3.0 12.5 + - - +
99F PHE* 1.3 75.4 - - - +
101F ASP* 1.3 67.3 + - - +
103F ASP* 3.4 6.7 + - - +
104F ASN* 3.3 28.0 + - - +
127F ALA* 3.5 21.9 + - + +
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Residues in contact with ASP 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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75F LEU* 3.8 24.0 - - + +
97F GLN* 2.8 45.1 + - - +
98F ILE* 3.5 9.2 - - - +
100F ALA* 1.3 72.8 - - - +
102F LEU* 1.3 57.9 + - - +
104F ASN* 3.0 10.3 + - - +
105F ILE* 2.9 36.2 + - + +
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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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7F ILE* 4.4 5.4 - - + -
75F LEU* 3.9 31.9 - - + +
78F ALA* 4.2 20.0 - - + -
84F VAL* 3.7 24.5 - - + -
86F GLU* 5.6 1.3 - - + -
98F ILE* 2.9 38.1 + - + +
99F PHE* 3.7 14.4 - - + +
101F ASP* 1.3 75.4 - - - +
103F ASP* 1.3 63.0 + - - +
105F ILE* 4.3 3.8 - - + -
106F CYS* 3.0 37.0 + - - +
112F LEU* 4.0 22.7 - - + -
130F ARG* 4.1 0.3 + - - -
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Residues in contact with ASP 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 PHE 2.9 17.3 + - - +
100F ALA* 3.5 8.4 - - - +
101F ASP 3.2 0.2 - - - -
102F LEU* 1.3 78.0 - - - +
104F ASN* 1.3 66.1 + - - +
106F CYS 3.9 0.9 - - - +
112F LEU* 4.2 2.2 - - + +
128F THR* 3.5 13.4 - - + -
129F LYS* 2.8 40.4 + - - +
130F ARG* 2.8 49.8 + - - +
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Residues in contact with ASN 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 ALA* 3.3 18.1 + - - +
101F ASP* 3.0 10.0 + - - +
103F ASP* 1.3 85.2 - - - +
105F ILE* 1.3 66.7 + - + +
106F CYS 4.2 2.6 - - - +
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Residues in contact with ILE 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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75F LEU* 3.5 47.8 - - + +
76F ASN* 4.0 22.4 - - - +
79F ALA* 3.5 39.7 - - + +
101F ASP* 2.9 23.9 + - + +
102F LEU* 3.9 7.9 - - + +
104F ASN* 1.3 80.6 - - + +
106F CYS* 1.3 66.2 + - - +
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Residues in contact with CYS 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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78F ALA* 3.8 30.5 - - - -
79F ALA* 3.4 7.2 - - - +
84F VAL* 4.4 3.8 - - - -
102F LEU* 3.0 38.2 + - - +
103F ASP 3.9 2.8 - - - +
104F ASN 4.2 1.9 - - - +
105F ILE* 1.3 83.8 - - - +
107F LYS* 1.3 69.7 + - - +
108F PRO* 3.8 0.5 - - - +
110F THR* 3.5 29.6 - - - +
112F LEU* 4.4 1.6 - - - -
130F ARG* 3.0 14.7 + - - +
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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