Contacts of the helix formed by residues 86 - 104 (chain C) in PDB entry 1EJI
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 THR 86 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LYS* 4.1 10.8 - - - -
73C TYR 4.3 0.9 - - - +
74C SER* 3.7 29.2 - - - -
81C ARG* 3.8 20.5 - - + +
83C TYR 4.3 11.5 + - - +
84C GLY* 4.3 7.7 - - - -
85C GLY* 1.3 79.9 + - - +
87C GLU* 1.3 56.2 + - - +
88C PHE 3.2 2.7 - - - -
89C ILE* 3.8 11.0 - - + -
90C ASP* 2.7 54.2 + - - -
378D GLU* 5.7 0.2 + - - -
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLY* 3.2 6.4 - - - -
86C THR* 1.3 79.3 + - - +
88C PHE* 1.3 106.4 + - + +
90C ASP* 3.6 8.0 - - - +
91C GLU* 3.3 24.8 + - - +
94C MSE 5.6 0.2 - - - +
43D ARG* 5.8 1.6 - - - -
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Residues in contact with PHE 88 (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 LEU* 6.1 0.2 - - - -
86C THR 3.2 0.2 - - - -
87C GLU* 1.3 102.8 - - + +
89C ILE* 1.3 69.3 + - - +
90C ASP 2.9 1.3 - - - -
91C GLU* 2.9 29.4 + - - +
92C LEU* 2.9 14.4 + - - +
36D ILE* 3.7 9.8 - - + +
39D LYS* 3.4 58.3 - - + -
40D GLU* 3.3 38.2 + - + +
43D ARG* 3.9 22.0 - - + -
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 3.5 32.1 - - + -
72C LYS* 3.6 35.9 - - + -
74C SER* 3.5 17.0 - - - +
81C ARG* 4.0 8.5 - - - +
86C THR* 3.3 15.8 + - - +
88C PHE* 1.3 76.0 - - - +
90C ASP* 1.3 57.5 + - - +
92C LEU* 3.4 6.4 + - + +
93C GLU* 2.9 28.8 + - + +
306C ASN* 2.9 37.0 - - + +
40D GLU* 4.5 12.8 + - - +
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Residues in contact with ASP 90 (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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78C PRO* 3.7 15.2 - - + +
79C GLY 4.6 4.0 + - - -
81C ARG* 2.9 39.6 + - - +
86C THR* 2.7 34.7 + - - +
87C GLU* 3.6 8.2 + - - +
89C ILE* 1.3 75.5 - - - +
91C GLU* 1.3 64.8 + - - +
94C MSE 2.9 43.8 + - + +
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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
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87C GLU* 3.3 15.9 + - - +
88C PHE* 2.9 37.4 + - - +
90C ASP* 1.3 80.1 - - - +
92C LEU* 1.3 58.6 + - - +
94C MSE 3.8 10.9 - - + +
95C LEU* 2.9 31.7 + - - +
36D ILE* 3.8 19.6 - - + +
39D LYS* 3.3 26.6 + - - -
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Residues in contact with LEU 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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69C LEU* 3.7 30.7 - - + -
88C PHE 2.9 8.5 + - - +
89C ILE* 3.5 10.1 - - + +
91C GLU* 1.3 80.1 - - - +
93C GLU* 1.3 63.1 + - - +
95C LEU* 3.2 5.0 + - + +
96C CYS* 3.0 21.3 + - - +
306C ASN* 3.6 30.7 - - + +
309C ILE* 4.5 7.6 - - + +
310C ALA* 3.8 23.8 - - + +
313C ALA* 4.6 11.4 - - + -
33D VAL* 4.6 14.6 - - + -
36D ILE* 4.1 20.6 - - + +
37D ILE* 6.3 0.9 - - + -
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Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 4.5 1.0 - - - -
78C PRO* 3.5 23.8 - - + +
81C ARG* 2.6 36.7 + - - +
89C ILE* 2.9 22.1 + - + +
90C ASP 4.0 2.2 - - - +
92C LEU* 1.3 74.1 - - - +
94C MSE 1.3 57.1 + - - +
96C CYS* 3.4 2.4 + - - +
97C GLN* 2.9 45.7 + - + +
115C VAL* 3.6 20.7 + - + +
116C GLN* 3.3 27.8 + - - +
304C PRO* 5.2 0.7 - - - +
306C ASN* 5.0 2.1 - - - +
309C ILE* 4.6 20.4 - - + +
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Residues in contact with MSE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PRO* 4.0 25.4 - - + -
87C GLU 5.6 0.2 - - - +
90C ASP* 2.9 40.7 + - + +
91C GLU* 3.9 10.1 - - + +
93C GLU* 1.3 73.5 - - - +
95C LEU* 1.3 60.8 + - - +
97C GLN* 3.3 14.3 + - - +
98C LYS* 2.9 30.0 + - - +
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Residues in contact with LEU 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 GLU 2.9 18.3 + - - +
92C LEU* 3.5 5.6 - - + +
94C MSE 1.3 76.9 - - - +
96C CYS* 1.3 58.4 + - - +
98C LYS* 3.1 27.4 + - - +
99C ARG* 2.8 67.5 + - - +
313C ALA* 5.0 2.5 - - + -
32D GLU* 3.7 26.9 - - + +
33D VAL* 3.9 18.2 - - + -
36D ILE* 4.1 16.6 - - + -
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Residues in contact with CYS 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 LEU 3.0 15.9 + - - +
93C GLU 3.7 4.0 - - - +
95C LEU* 1.3 74.8 - - - +
97C GLN* 1.3 65.3 + - - +
99C ARG* 3.4 2.6 + - - +
100C ALA* 2.9 24.4 + - - +
115C VAL* 4.0 14.8 - - + -
309C ILE* 3.7 24.2 - - + -
312C VAL* 3.6 31.6 - - - -
313C ALA* 3.7 26.0 - - + +
316C LEU* 3.6 4.4 - - - +
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Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 5.8 3.4 - - - -
78C PRO* 4.8 8.0 - - - +
93C GLU* 2.9 42.6 + - - +
94C MSE 3.6 18.9 - - - +
95C LEU 3.3 0.2 - - - -
96C CYS* 1.3 75.5 - - - +
98C LYS* 1.3 62.8 + - - +
100C ALA* 3.3 8.6 + - - +
101C LEU* 3.3 24.8 + - - +
113C VAL* 3.6 30.5 + - + +
114C ASN* 4.7 3.0 - - - +
115C VAL* 4.2 17.8 - - + +
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Residues in contact with LYS 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 MSE 2.9 17.9 + - - +
95C LEU* 3.3 28.4 - - - +
97C GLN* 1.3 76.3 - - - +
99C ARG* 1.3 65.5 + - - +
100C ALA 3.2 0.5 + - - -
101C LEU* 3.2 7.4 + - - +
102C GLN* 3.1 55.2 + - + +
32D GLU* 5.0 5.8 + - - -
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Residues in contact with ARG 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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95C LEU* 2.8 51.5 + - + +
96C CYS* 3.9 1.6 - - - +
98C LYS* 1.3 75.0 - - - +
100C ALA* 1.3 57.9 + - - +
102C GLN* 3.7 14.7 - - - +
103C ALA* 3.0 31.4 + - - +
313C ALA* 2.9 35.2 + - - +
316C LEU* 3.4 13.9 - - + +
317C LYS* 3.6 16.4 - - - +
320C MSE 3.9 21.5 - - + +
30D ASP* 2.5 40.2 + - - -
32D GLU* 3.1 25.9 + - - +
33D VAL* 3.9 4.6 - - - +
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Residues in contact with ALA 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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96C CYS 2.9 17.5 + - - +
97C GLN* 3.5 8.1 - - - +
98C LYS 3.1 0.2 - - - -
99C ARG* 1.3 79.0 - - - +
101C LEU* 1.3 63.0 + - - +
102C GLN 3.4 0.5 + - - -
104C TYR* 3.4 27.2 + - - -
113C VAL* 4.1 7.9 - - + -
115C VAL* 4.9 1.3 - - + -
266C MSE 4.1 11.2 - - - -
268C PHE* 3.9 24.0 - - + -
316C LEU* 3.2 17.5 - - + +
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Residues in contact with LEU 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 GLN 3.3 6.7 + - - +
98C LYS* 3.2 9.0 + - - +
100C ALA* 1.3 75.9 - - - +
102C GLN* 1.3 65.6 + - + +
104C TYR 3.5 1.0 + - - -
105C HIS 3.3 2.1 + - - -
106C LEU* 2.8 63.7 + - + +
108C PRO* 3.7 26.7 - - + -
111C TRP* 3.5 31.9 - - + +
112C GLY* 4.3 4.7 - - - +
113C VAL* 3.3 30.5 - - + -
268C PHE* 3.9 3.6 - - + -
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Residues in contact with GLN 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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98C LYS* 3.1 49.6 + - + +
99C ARG* 3.7 14.9 - - - +
101C LEU* 1.3 75.4 - - + +
103C ALA* 1.3 54.7 + - - +
104C TYR 2.6 1.9 + - - -
105C HIS* 2.5 37.0 + - - +
106C LEU 5.4 0.4 - - - -
320C MSE 3.9 20.9 - - - +
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Residues in contact with ALA 103 (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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99C ARG 3.0 16.2 + - - +
100C ALA 3.8 3.6 - - - +
101C LEU 3.5 0.2 - - - -
102C GLN* 1.3 76.2 - - - +
104C TYR* 1.3 65.1 + - + +
105C HIS* 3.4 8.9 + - - -
237C ALA* 3.7 30.7 - - + +
316C LEU* 3.8 24.0 - - + +
319C ALA* 5.1 2.2 - - + -
320C MSE 3.8 25.6 - - + +
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Residues in contact with TYR 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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100C ALA 3.4 14.8 + - - +
101C LEU 3.5 1.4 + - - -
102C GLN 2.6 4.6 + - - -
103C ALA* 1.3 86.4 - - + +
105C HIS* 1.3 70.9 + - - +
106C LEU* 3.2 30.2 + - + +
229C MSE 3.3 33.3 - - + +
233C SER 2.9 30.9 + - - -
236C VAL* 4.0 11.9 - - + -
237C ALA* 3.7 20.1 - - + +
245C PHE* 3.6 22.3 - + + +
259C LEU* 3.6 16.1 - - - +
266C MSE 4.9 3.1 - - + +
268C PHE* 3.9 17.5 - + - -
316C LEU* 4.6 9.9 - - + -
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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