Contacts of the helix formed by residues 80 - 98 (chain C) in PDB entry 4X2Q
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 ASP 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ASP* 3.8 11.9 - - - +
148B GLY* 2.8 33.5 + - - -
498B LYS* 2.9 21.7 + - - +
78C ARG 3.5 3.7 + - - +
79C MET* 1.3 76.7 - - - +
81C ALA* 1.3 66.0 + - - +
82C SER* 3.8 17.3 - - - +
83C GLU* 2.9 27.9 + - + +
84C ARG* 3.4 8.2 + - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO* 4.3 22.0 - - + +
147B ASP* 4.8 1.0 + - - -
498B LYS* 4.2 7.2 - - - +
79C MET 3.6 2.6 + - - -
80C ASP* 1.3 72.2 - - - +
82C SER* 1.3 61.9 + - - +
84C ARG* 3.2 42.4 + - - +
136C ALA* 3.3 34.6 - - - +
137C ASP* 4.0 10.8 - - + -
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Residues in contact with SER 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 4.6 10.6 - - - -
147B ASP* 2.7 37.4 + - - -
80C ASP* 3.8 5.4 - - - +
81C ALA* 1.3 77.1 - - - +
83C GLU* 1.3 59.7 + - - +
85C GLY* 3.6 3.4 + - - -
86C ARG* 3.2 26.6 + - - +
133C ALA 5.4 0.3 - - - +
136C ALA* 5.3 0.2 - - - -
137C ASP* 3.6 30.9 - - - +
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C MET* 3.8 28.5 - - + +
80C ASP* 2.9 23.0 + - + +
82C SER* 1.3 77.2 + - - +
84C ARG* 1.3 61.2 + - - +
85C GLY 3.1 1.8 - - - -
86C ARG* 3.3 18.1 - - + +
87C LEU* 2.9 35.9 + - + +
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B SER* 4.2 19.8 - - - -
76C TRP* 3.7 47.5 + - + -
79C MET* 3.8 29.6 + - + -
80C ASP 3.4 2.9 + - - +
81C ALA* 3.2 35.5 + - - +
83C GLU* 1.3 77.2 - - - +
85C GLY* 1.3 59.9 + - - +
87C LEU* 3.7 4.5 + - - +
88C LEU* 3.3 25.4 + - - +
136C ALA* 4.3 8.0 + - + +
139C ILE* 5.6 1.6 - - - +
158C PRO* 5.9 0.4 - - - +
183C LEU 3.4 6.8 + - - +
184C CYS 2.6 37.4 + - - -
185C CYS 4.5 5.5 + - - -
186C GLY* 3.3 17.4 - - - +
213C PHE* 5.2 0.3 - - - -
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Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA 3.4 7.3 + - - -
82C SER 3.6 4.5 + - - -
83C GLU 3.1 0.4 - - - -
84C ARG* 1.3 79.1 - - - +
86C ARG* 1.3 52.5 + - - +
88C LEU* 3.0 2.8 + - - -
89C ASP* 2.7 31.8 + - - +
133C ALA* 3.2 38.2 - - - +
136C ALA* 3.6 9.7 - - - +
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Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP* 4.8 0.8 + - - -
93A ASP* 5.6 1.2 + - - -
130A ARG* 3.2 51.4 - - - +
82C SER 3.2 16.9 + - - +
83C GLU* 3.0 23.1 + - + +
85C GLY* 1.3 78.7 - - - +
87C LEU* 1.3 58.8 + - + +
89C ASP* 3.1 36.3 + - - +
90C LYS* 2.9 43.2 + - - +
93C ASP* 5.3 4.4 + - - -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TRP* 4.1 8.1 - - + -
79C MET* 3.8 33.4 - - + -
83C GLU* 2.9 19.7 + - + +
84C ARG* 4.1 3.4 - - - +
86C ARG* 1.3 75.9 - - + +
88C LEU* 1.3 58.4 + - - +
90C LYS* 4.0 4.3 - - + +
91C LEU* 3.3 17.5 + - - +
211C ALA* 3.4 26.1 - - - +
212C GLY* 3.8 23.3 - - - +
213C PHE* 3.3 34.9 - - + -
214C PRO* 4.0 10.5 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ARG 3.3 17.4 + - - +
85C GLY* 3.0 10.2 + - - +
87C LEU* 1.3 76.6 - - - +
89C ASP* 1.3 61.9 + - - +
91C LEU* 3.4 9.5 + - + +
92C ALA* 3.3 19.8 + - - +
129C PHE* 3.8 39.2 - - + +
132C TYR* 3.7 28.3 - - + +
133C ALA* 3.8 10.3 - - + +
180C ALA* 3.9 22.2 - - + +
183C LEU* 4.0 26.9 - - + -
184C CYS* 3.9 15.0 - - - +
213C PHE* 4.5 1.6 - - + -
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Residues in contact with ASP 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP* 2.9 27.2 - - - +
130A ARG* 5.2 0.2 - - - -
85C GLY 2.7 19.3 + - - +
86C ARG* 3.1 30.4 + - - +
88C LEU* 1.3 71.6 - - - +
90C LYS* 1.3 62.5 + - - +
92C ALA* 3.2 14.1 + - - +
93C ASP* 3.3 17.2 + - - +
129C PHE 5.1 0.2 - - - -
130C ARG* 3.2 36.7 + - - +
133C ALA* 3.7 10.0 - - + +
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ARG* 2.9 29.3 + - - +
87C LEU* 4.4 6.7 - - + +
89C ASP* 1.3 73.4 - - - +
91C LEU* 1.3 64.5 + - - +
93C ASP* 3.3 36.3 + - + +
94C LEU* 3.3 18.8 + - + +
210C GLU 6.1 0.4 - - - -
211C ALA* 4.0 27.6 - - + +
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU 3.3 18.4 + - - +
88C LEU* 3.5 10.3 - - + +
89C ASP 3.2 0.8 - - - -
90C LYS* 1.3 75.8 - - - +
92C ALA* 1.3 61.6 + - - +
94C LEU* 3.3 4.5 + - - +
95C VAL* 3.1 26.8 + - + +
129C PHE* 3.8 35.9 - - + -
179C ILE* 5.2 4.5 - - + -
204C MET* 3.9 19.3 - - + -
207C LEU* 3.9 37.7 - - + +
208C ILE* 4.0 15.0 - - + -
211C ALA* 4.2 4.2 - - - +
213C PHE* 4.1 19.7 - - + -
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Residues in contact with ALA 92 (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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88C LEU 3.3 9.4 + - - +
89C ASP 3.2 11.1 + - - +
90C LYS 3.2 0.4 - - - -
91C LEU* 1.3 77.9 - - - +
93C ASP* 1.3 59.1 + - - +
95C VAL* 3.3 7.9 + - - +
96C GLU* 2.9 30.0 + - - +
126C ILE* 4.3 9.6 - - + +
129C PHE* 4.0 15.2 - - + +
130C ARG* 3.5 37.3 + - + +
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 5.7 1.2 + - - -
86C ARG* 5.3 4.7 + - - -
89C ASP* 3.3 8.7 + - - +
90C LYS* 3.3 37.3 + - + +
92C ALA* 1.3 78.2 - - - +
94C LEU* 1.3 61.0 + - + +
96C GLU* 3.3 5.4 + - - +
97C ARG* 2.8 29.0 + - - +
130C ARG* 2.9 20.1 + - - +
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Residues in contact with LEU 94 (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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90C LYS* 3.5 18.6 - - + +
91C LEU* 3.3 6.7 + - - +
92C ALA 3.2 0.6 - - - -
93C ASP* 1.3 76.1 - - + +
95C VAL* 1.3 61.0 + - - +
97C ARG* 3.5 20.1 - - - +
98C ASP* 2.9 35.2 + - - +
207C LEU* 3.2 46.2 - - + +
210C GLU* 3.4 34.8 - - - +
211C ALA* 3.7 23.3 - - + +
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Residues in contact with VAL 95 (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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91C LEU 3.1 16.4 + - - +
92C ALA* 3.8 8.1 - - - +
94C LEU* 1.3 76.5 - - - +
96C GLU* 1.3 57.7 + - - +
98C ASP 3.3 1.7 - - - +
99C ARG* 3.1 27.5 + - - +
102C LEU* 3.8 19.5 - - + -
122C LEU* 3.9 10.5 - - + +
125C VAL* 4.0 15.9 - - + -
126C ILE* 3.7 20.4 - - + -
129C PHE* 4.5 9.9 - - + -
172C LEU* 5.4 0.2 - - + -
204C MET* 3.8 23.3 - - + -
207C LEU* 3.8 16.4 - - + -
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Residues in contact with GLU 96 (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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92C ALA 2.9 18.1 + - - +
93C ASP* 3.5 8.1 - - - +
95C VAL* 1.3 75.4 - - - +
97C ARG* 1.3 65.7 + - - +
99C ARG* 3.3 42.6 + - - +
126C ILE* 3.9 28.6 - - + +
130C ARG* 4.7 11.5 + - - +
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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
----------------------------------------------------------
93C ASP 2.8 20.2 + - - +
94C LEU* 3.3 20.6 + - + +
96C GLU* 1.3 74.1 - - - +
98C ASP* 1.3 91.4 + - - +
99C ARG 3.5 2.8 + - - -
100C ALA* 4.9 2.9 + - - +
203C TYR* 4.9 0.8 + - - -
207C LEU* 4.0 4.2 - - - +
210C GLU* 3.0 41.0 + - - -
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Residues in contact with ASP 98 (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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94C LEU 2.9 12.2 + - - +
95C VAL 3.3 3.8 - - - -
97C ARG* 1.3 119.9 + - - +
99C ARG* 1.3 61.7 + - - +
100C ALA* 3.3 2.7 - - - +
101C VAL* 3.6 20.1 - - + +
102C LEU* 3.2 28.1 + - + +
203C TYR* 2.7 30.5 + - + +
207C LEU* 3.4 10.4 - - + +
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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