Contacts of the helix formed by residues 86 - 105 (chain C) in PDB entry 3K9L
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 ASN 86 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 5.7 0.7 - - - +
12C GLY 4.7 10.0 - - - +
13C GLY 5.7 1.4 - - - +
14C VAL* 4.7 2.9 - - - +
83C ALA* 3.1 19.8 + - + +
84C ILE 3.4 1.4 - - - -
85C ASN* 1.3 81.8 - - - +
87C THR* 1.3 61.3 + - - +
88C LYS* 3.4 14.6 - - - +
89C SER* 2.6 60.0 + - - +
90C PHE* 3.4 3.6 + - - +
124C THR* 3.6 0.6 + - - -
125C VAL* 4.5 1.1 - - - -
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Residues in contact with THR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASN* 1.3 71.9 - - - +
88C LYS* 1.3 65.0 + - - +
90C PHE* 3.0 8.1 + - + +
91C GLU* 2.9 44.3 + - + +
124C THR* 3.2 31.6 + - - +
125C VAL* 4.2 11.7 - - + -
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASN* 3.4 10.1 - - - +
87C THR* 1.3 77.9 - - - +
89C SER* 1.3 58.0 + - - +
91C GLU* 3.1 19.9 + - + +
92C ASP* 2.8 60.7 + - - +
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Residues in contact with SER 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 3.9 19.3 + - - +
14C VAL* 3.5 27.8 - - - -
81C VAL 5.0 0.7 - - - +
82C PHE* 3.8 4.4 - - - +
83C ALA 2.9 24.5 + - - -
86C ASN* 2.6 39.3 + - - +
88C LYS* 1.3 72.0 - - - +
90C PHE* 1.3 61.3 + - - +
92C ASP* 3.3 11.8 + - - +
93C ILE* 3.5 15.6 + - - +
96C TYR* 5.7 0.2 - - - -
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Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PHE* 3.7 35.0 - + + -
86C ASN 3.4 0.2 + - - -
87C THR* 3.0 12.4 + - + +
89C SER* 1.3 78.9 + - - +
91C GLU* 1.3 71.4 + - + +
93C ILE* 3.2 20.6 + - - +
94C HIS 4.6 0.3 + - - -
113C LEU* 4.8 0.2 - - + -
125C VAL* 3.8 30.5 - - + -
129C GLN* 3.7 38.6 - - + -
130C ALA* 3.6 23.3 - - + -
133C LEU* 3.6 33.9 - - + +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C THR* 2.9 38.0 + - + +
88C LYS* 3.5 23.7 - - + +
90C PHE* 1.3 84.7 - - + +
92C ASP* 1.3 61.1 + - - +
93C ILE 3.3 1.0 + - - -
94C HIS* 3.8 13.3 + - - +
95C GLN* 4.8 4.2 + - - +
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Residues in contact with ASP 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 3.9 17.3 - - + +
88C LYS* 2.8 51.5 + - - +
89C SER* 3.6 7.9 - - - +
90C PHE 3.2 0.6 - - - -
91C GLU* 1.3 74.7 - - - +
93C ILE* 1.3 62.8 + - - +
94C HIS 3.2 3.1 - - - -
95C GLN* 3.2 24.6 + - + +
96C TYR* 3.0 34.5 + - + -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLY* 5.6 1.1 - - - -
80C CYS* 4.0 19.9 - - + -
81C VAL 3.7 30.7 - - - +
82C PHE* 4.0 7.4 - - + -
89C SER 3.5 8.5 + - - +
90C PHE* 3.2 20.0 + - - +
92C ASP* 1.3 77.4 - - - +
94C HIS* 1.3 64.0 + - - +
96C TYR* 3.2 11.5 + - + +
97C ARG* 3.0 23.0 + - + +
111C MET* 5.8 0.9 - - + -
113C LEU* 4.0 24.5 - - + -
133C LEU* 4.0 20.6 - - + -
137C TYR* 4.0 15.7 - - + -
139C ILE* 6.4 0.2 - - + -
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Residues in contact with HIS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PHE 4.6 0.2 + - - -
91C GLU 3.8 10.1 + - - +
92C ASP 3.2 1.0 - - - -
93C ILE* 1.3 80.1 - - - +
95C GLN* 1.3 67.6 + - + +
97C ARG* 3.4 3.4 + - - +
98C GLU* 3.0 61.5 + - + +
133C LEU* 5.5 0.9 - - + +
137C TYR* 3.3 33.5 + + - +
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLU 4.8 4.1 + - - +
92C ASP* 3.2 24.5 + - + +
94C HIS* 1.3 83.2 - - + +
96C TYR* 1.3 67.5 + - + +
98C GLU* 3.2 8.6 + - - +
99C GLN* 3.0 24.2 + - - +
102C ARG* 5.1 0.9 + - - -
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 4.2 21.5 - - + -
10C GLY* 3.4 40.2 + - - -
11C ALA* 3.5 19.4 + - - +
12C GLY 4.9 0.3 + - - -
60C GLY* 5.0 6.4 + - - -
72C MET* 4.2 2.3 - - + +
80C CYS* 5.0 4.0 - - - -
92C ASP* 3.0 42.3 + - + -
93C ILE* 3.2 13.6 + - + +
95C GLN* 1.3 79.7 - - + +
97C ARG* 1.3 64.1 + - - +
99C GLN* 3.3 21.1 + - - +
100C ILE* 3.0 29.2 + - - +
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Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C CYS* 5.1 0.8 - - - -
93C ILE* 3.0 17.2 + - + +
94C HIS* 3.7 7.2 - - - +
96C TYR* 1.3 78.6 - - - +
98C GLU* 1.3 67.1 + - - +
100C ILE* 3.3 11.2 + - - +
101C LYS* 3.0 57.7 + - + +
107C ASP 3.8 20.0 + - - -
108C ASP* 5.7 1.0 - - - +
109C VAL 6.1 0.2 - - - +
111C MET* 4.0 29.2 - - + +
137C TYR* 3.5 72.3 + - + +
139C ILE* 5.5 2.4 - - - +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C HIS* 3.0 53.1 + - + +
95C GLN* 3.2 8.2 + - - +
97C ARG* 1.3 79.5 + - - +
99C GLN* 1.3 57.7 + - - +
101C LYS* 3.2 35.2 + - - +
102C ARG* 2.9 45.4 + - + +
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Residues in contact with GLN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ASP* 5.8 3.1 - - - +
72C MET* 3.2 30.1 - - - +
95C GLN 3.0 11.9 + - - +
96C TYR* 3.5 24.0 - - - +
97C ARG 3.2 0.2 - - - -
98C GLU* 1.3 77.7 - - - +
100C ILE* 1.3 56.1 + - - +
102C ARG* 3.2 30.3 + - - +
103C VAL* 2.9 34.9 + - + +
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 4.2 9.9 - - + -
72C MET* 3.4 24.2 - - + -
78C PHE* 3.6 60.8 - - + -
80C CYS* 4.1 18.4 - - - -
96C TYR 3.0 16.6 + - - +
97C ARG* 3.6 7.4 - - - +
99C GLN* 1.3 75.7 - - - +
101C LYS* 1.3 56.5 + - + +
103C VAL* 3.9 0.2 - - - -
104C LYS* 2.8 37.3 + - + +
109C VAL* 4.0 17.0 - - + -
111C MET* 4.2 9.0 - - - -
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Residues in contact with LYS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ARG* 3.0 64.0 + - + +
98C GLU* 3.2 27.8 + - - +
99C GLN 3.3 0.2 - - - -
100C ILE* 1.3 73.2 - - + +
102C ARG* 1.3 61.3 + - + +
105C ASP* 2.8 24.4 + - - -
106C SER 3.0 27.5 + - - +
107C ASP* 4.0 34.2 - - - +
109C VAL* 4.7 7.4 - - + +
111C MET* 6.2 0.7 - - - -
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Residues in contact with ARG 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLN 5.1 0.6 + - - -
98C GLU* 2.9 36.6 + - + +
99C GLN* 3.4 42.7 + - - +
101C LYS* 1.3 76.8 - - + +
103C VAL* 1.3 63.1 + - + +
105C ASP* 2.9 28.1 + - - +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASP* 3.9 17.7 - - + +
72C MET* 3.4 39.0 - - + -
73C ARG* 3.2 41.8 - - + +
99C GLN* 2.9 25.4 + - + +
100C ILE 4.1 1.1 - - - +
102C ARG* 1.3 82.7 - - + +
104C LYS* 1.3 59.5 + - - +
105C ASP* 3.1 5.4 + - - +
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Residues in contact with LYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C MET 2.6 28.2 + - - +
73C ARG* 3.2 25.5 + - + -
74C THR 4.2 1.0 + - - -
75C GLY 2.8 26.0 + - - -
76C GLU* 5.1 1.9 - - - +
78C PHE* 4.4 5.2 - - + -
100C ILE* 2.8 35.2 + - + +
103C VAL* 1.3 74.4 - - - +
105C ASP* 1.3 68.0 + - - +
106C SER* 3.0 13.3 + - - +
109C VAL* 4.0 22.9 - - + -
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LYS 2.8 11.5 + - - -
102C ARG* 2.9 16.0 + - - +
103C VAL 3.1 4.6 - - - +
104C LYS* 1.3 79.3 - - - +
106C SER* 1.3 57.1 + - - +
107C ASP* 5.4 1.7 - - - +
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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
------------------------------------------------------------
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