Contacts of the helix formed by residues 79 - 93 (chain C) in PDB entry 3E4U
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 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.2 7.6 - - - +
77C GLU 3.4 5.4 + - - +
78C ILE* 1.3 80.8 - - - +
80C PRO* 1.3 70.9 - - + +
81C GLU* 4.6 6.1 - - + +
82C GLY 3.6 0.9 + - - +
83C PHE 3.4 11.3 + - - -
104C ALA* 2.8 42.2 - - - +
107C ALA* 4.9 5.7 - - - +
108C THR* 3.7 12.1 + - - -
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Residues in contact with PRO 80 (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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38C VAL* 3.5 30.3 - - + +
41C GLU* 4.7 17.7 - - + +
43C PHE* 3.7 19.1 - - + -
78C ILE 4.0 4.5 - - - +
79C ASN* 1.3 82.9 - - + +
81C GLU* 1.3 61.2 + - + +
82C GLY 3.1 2.0 - - - -
83C PHE* 3.2 1.0 + - - +
84C CYS* 2.9 33.2 + - - +
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Residues in contact with GLU 81 (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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79C ASN* 5.2 4.3 - - + -
80C PRO* 1.3 81.9 - - + +
82C GLY* 1.3 58.8 + - - +
84C CYS* 4.0 6.2 + - - +
85C ILE* 3.6 24.4 + - - +
98C ARG* 4.5 10.5 + - - +
100C GLY 3.6 8.7 - - - +
101C ASN* 3.2 36.1 + - + +
104C ALA* 5.0 7.0 - - + -
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Residues in contact with GLY 82 (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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79C ASN 3.6 4.7 + - - -
80C PRO 3.1 0.6 - - - -
81C GLU* 1.3 79.5 - - - +
83C PHE* 1.3 63.8 + - - +
85C ILE* 3.3 5.2 + - - +
86C LEU* 3.2 24.3 + - - +
104C ALA* 4.1 19.5 - - - +
105C VAL* 4.1 11.9 - - - -
108C THR* 3.6 18.9 + - - -
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Residues in contact with PHE 83 (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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36C ILE* 3.8 15.9 - - + -
38C VAL* 4.1 14.6 - - + -
43C PHE* 3.8 40.4 - + + -
50C LEU* 4.8 0.4 - - + -
57C PHE* 3.6 39.3 - + - -
74C LEU* 3.6 22.0 - - + -
79C ASN 3.4 13.8 + - - +
80C PRO* 3.2 7.2 + - + +
82C GLY* 1.3 71.5 - - - +
84C CYS* 1.3 57.2 + - - +
86C LEU* 3.1 3.2 + - + +
87C LEU* 2.7 56.9 + - + +
90C MET* 4.8 3.8 - - + -
108C THR* 3.7 18.4 + - + -
112C LEU* 4.1 9.9 - - + -
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Residues in contact with CYS 84 (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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43C PHE* 3.6 28.4 - - + -
80C PRO 2.9 18.3 + - - +
81C GLU* 4.1 7.6 - - - +
83C PHE* 1.3 75.9 - - - +
85C ILE* 1.3 63.2 + - - +
87C LEU* 4.6 1.8 - - - -
88C ASP* 2.8 44.8 + - - +
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Residues in contact with ILE 85 (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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81C GLU 3.6 14.1 + - - +
82C GLY 3.3 7.3 + - - +
83C PHE 3.1 0.8 - - - -
84C CYS* 1.3 82.7 - - + +
86C LEU* 1.3 58.9 + - - +
88C ASP* 3.6 5.3 + - - +
89C PHE* 3.0 23.9 + - - +
94C ARG 4.9 1.2 - - - +
95C LEU* 4.6 7.2 - - + +
96C ASN* 3.2 33.9 + - + +
98C ARG* 3.4 22.2 - - - +
101C ASN* 2.8 40.6 - - + +
105C VAL* 3.5 26.5 - - + -
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Residues in contact with LEU 86 (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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82C GLY 3.2 8.0 + - - +
83C PHE* 3.1 7.7 + - + +
85C ILE* 1.3 73.5 - - - +
87C LEU* 1.3 61.0 + - - +
89C PHE* 3.0 5.6 + - + +
90C MET* 2.8 42.7 + - + +
95C LEU* 4.7 4.9 - - + -
105C VAL* 4.2 11.0 - - + +
108C THR* 3.5 11.2 - - + -
109C ALA* 3.4 28.5 - - + +
112C LEU* 3.2 30.7 - - + -
114C MET* 3.7 22.3 - - + +
117C VAL* 3.8 28.9 - - + -
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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
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26C ARG* 3.7 24.5 - - - +
43C PHE* 3.9 35.0 - - + -
44C ARG 4.0 12.1 - - - +
45C ALA* 4.0 12.3 - - + -
50C LEU* 3.6 30.7 - - + -
83C PHE* 2.7 33.7 + - + +
84C CYS* 4.1 4.0 - - - +
86C LEU* 1.3 72.5 - - - +
88C ASP* 1.3 64.0 + - - +
90C MET* 3.3 13.2 + - - +
91C TYR* 3.3 31.2 + - + -
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Residues in contact with ASP 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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26C ARG* 3.8 26.9 + - - +
84C CYS* 2.8 36.6 + - - +
85C ILE* 3.8 6.5 - - - +
87C LEU* 1.3 79.5 - - - +
89C PHE* 1.3 53.0 + - - +
91C TYR 3.2 1.0 + - - -
92C THR* 2.4 46.8 + - + +
94C ARG 4.3 2.2 - - - +
96C ASN* 6.5 1.1 - - + -
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Residues in contact with PHE 89 (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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85C ILE 3.0 14.0 + - - +
86C LEU* 3.0 9.5 + - - +
88C ASP* 1.3 75.9 - - - +
90C MET* 1.3 65.6 + - - +
93C SER* 3.1 27.3 + - - -
94C ARG 3.4 21.9 + - - +
95C LEU* 3.8 26.2 - - + -
114C MET* 3.8 22.2 - - + -
116C HIS* 6.4 0.9 - - + -
117C VAL* 3.7 22.2 - - + -
11D PHE* 3.2 40.4 - + - -
14D HIS* 3.4 41.5 - + - -
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Residues in contact with MET 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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19C LEU* 3.6 13.3 - - - +
49C VAL* 4.3 8.2 - - + +
50C LEU* 3.6 32.3 - - + -
53C CYS* 3.9 23.0 - - + -
54C SER* 4.9 3.8 - - - -
57C PHE* 4.4 16.8 - - + -
83C PHE* 4.8 3.6 - - + -
86C LEU* 2.8 30.1 + - + +
87C LEU* 3.3 20.4 + - + +
89C PHE* 1.3 72.3 - - - +
91C TYR* 1.3 60.9 + - + +
112C LEU* 4.4 11.4 - - + -
114C MET* 3.9 34.8 - - + -
14D HIS* 3.1 25.4 - - - -
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Residues in contact with TYR 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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19C LEU* 3.3 32.3 - - + +
20C LEU* 4.5 1.2 + - - -
22C LEU* 3.6 19.3 - - + -
23C ASN* 3.5 43.3 - - - +
26C ARG* 3.2 37.5 - - - +
45C ALA* 3.8 2.8 - - + -
46C HIS* 2.8 48.3 + + - +
49C VAL* 3.6 33.3 - - + +
87C LEU* 3.3 31.1 + - + +
88C ASP 3.2 2.1 + - - +
89C PHE 3.1 0.6 - - - -
90C MET* 1.3 80.8 - - + +
92C THR* 1.3 57.3 + - - +
93C SER 3.8 0.4 - - - -
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Residues in contact with THR 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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19C LEU* 5.6 0.4 - - - -
20C LEU* 6.3 0.9 - - + +
23C ASN* 2.8 35.2 - - - +
26C ARG* 5.0 2.7 - - - +
88C ASP* 2.4 36.9 + - + +
91C TYR* 1.3 77.2 - - + +
93C SER* 1.3 65.8 + - - +
94C ARG* 2.9 36.9 + - - +
10D GLN* 4.7 4.3 + - - +
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Residues in contact with SER 93 (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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19C LEU* 3.9 6.9 - - - +
89C PHE* 3.1 22.9 + - - -
91C TYR 3.8 0.2 - - - -
92C THR* 1.3 76.7 - - - +
94C ARG* 1.3 58.6 + - - +
9D ILE 3.9 0.2 - - - +
10D GLN* 3.0 9.7 - - - +
11D PHE 2.6 50.6 + - - -
14D HIS* 3.1 27.6 + - - +
15D ALA* 3.7 10.9 + - - +
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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
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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