Contacts of the helix formed by residues 77 - 90 (chain D) in PDB entry 3QEL
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 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C TYR* 3.8 0.4 - - - +
329C CYS 3.0 28.5 - - - +
330C VAL* 3.6 1.3 - - - -
331C GLY* 3.0 20.8 + - - -
332C ASN 3.7 11.9 - - - +
333C THR* 3.9 7.4 - - + +
75D GLU* 3.6 4.7 - - - +
76D THR* 1.3 78.9 - - - +
78D PRO* 1.3 78.0 - - + +
79D LYS* 3.2 11.4 + - - +
80D SER* 2.7 45.4 + - - -
81D ILE* 3.0 21.7 + - - +
111D ILE* 4.5 0.7 - - - -
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Residues in contact with PRO 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ALA* 6.3 0.2 - - + -
79C CYS* 4.6 9.4 - - - -
110C THR* 4.9 16.4 - - + +
113C PHE* 3.8 46.2 - - + -
114C TYR* 4.0 7.2 - - + +
329C CYS* 4.9 2.0 - - + -
77D ASP* 1.3 89.4 - - + +
79D LYS* 1.3 57.2 + - - +
81D ILE* 3.9 0.5 - - - +
82D ILE* 2.9 47.5 + - + +
111D ILE* 4.1 20.8 - - + -
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Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LEU* 3.8 20.1 - - + +
79C CYS* 3.9 25.0 - - + +
80C GLU* 3.0 42.5 + - + +
329C CYS* 3.7 15.5 - - + +
330C VAL* 4.3 20.0 - - + -
77D ASP* 3.2 8.6 + - - +
78D PRO* 1.3 80.2 - - - +
80D SER* 1.3 54.8 + - - +
82D ILE* 4.6 0.7 - - - -
83D THR* 2.7 54.0 + - - +
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Residues in contact with SER 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C VAL* 4.2 11.8 - - - +
73D MET* 4.4 4.3 - - - -
75D GLU* 3.5 32.1 - - - +
77D ASP* 2.7 37.4 + - - -
79D LYS* 1.3 73.1 - - - +
81D ILE* 1.3 58.3 + - - +
83D THR* 3.8 5.3 - - - +
84D ARG* 2.9 33.4 + - - +
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Residues in contact with ILE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D MET* 4.0 16.4 - - + -
76D THR* 3.6 34.1 - - + +
77D ASP 3.0 13.6 + - - +
78D PRO 4.0 1.8 - - - +
80D SER* 1.3 75.1 - - - +
82D ILE* 1.3 61.6 + - - +
84D ARG* 4.1 0.7 - - - +
85D ILE* 3.3 31.3 + - + +
99D PHE* 4.2 11.4 - - + -
108D ILE* 4.2 23.3 - - + -
111D ILE* 3.9 24.7 - - + -
112D LEU* 4.0 26.7 - - + -
115D ILE* 4.0 5.6 - - + -
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE* 4.5 11.0 - - + +
75C ALA* 4.3 24.5 - - + -
76C LEU* 3.9 30.3 - - + +
79C CYS* 6.5 0.2 - - - -
78D PRO* 2.9 33.9 + - + +
79D LYS* 3.9 2.7 - - - +
81D ILE* 1.3 73.9 - - - +
83D THR* 1.3 62.3 + - - +
85D ILE* 3.9 0.3 - - - +
86D CYS* 3.0 42.4 + - - +
111D ILE* 4.3 6.5 - - + -
114D PHE* 4.3 14.6 - - + -
115D ILE* 3.6 28.7 - - + -
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Residues in contact with THR 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LEU* 3.8 17.6 - - - +
79D LYS* 2.7 37.8 + - - +
80D SER* 3.8 4.9 - - - +
82D ILE* 1.3 75.4 - - - +
84D ARG* 1.3 62.9 + - + +
86D CYS* 4.9 2.0 - - - -
87D ASP* 3.0 40.6 + - - +
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ILE* 5.6 5.6 - - + -
71D VAL* 3.5 26.1 - - + +
72D ALA* 2.7 29.9 + - - +
73D MET* 3.7 31.4 - - + +
80D SER 2.9 18.6 + - - +
81D ILE 4.1 1.3 - - - +
83D THR* 1.3 78.7 - - + +
85D ILE* 1.3 61.3 + - + +
87D ASP* 4.1 3.2 - - - +
88D LEU* 3.1 33.8 + - + +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ILE* 3.7 29.4 - - + -
73D MET* 6.1 0.4 - - + -
81D ILE* 3.3 22.6 + - + +
82D ILE 4.1 1.6 - - - +
84D ARG* 1.3 77.3 - - + +
86D CYS* 1.3 66.0 + - - +
88D LEU* 3.4 6.1 + - - +
89D MET* 3.2 37.8 + - + +
97D VAL* 5.0 13.5 - - + -
99D PHE* 4.8 1.3 - - + -
112D LEU* 3.8 22.9 - - + -
115D ILE* 3.7 38.4 - - + -
121D THR* 6.4 0.7 - - + -
123D ILE* 4.5 7.4 - - + -
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Residues in contact with CYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE* 5.0 4.3 - - - -
76C LEU* 5.6 5.2 - - + -
82D ILE* 3.0 34.2 + - + +
83D THR* 4.3 1.6 - - - +
85D ILE* 1.3 81.1 - - - +
87D ASP* 1.3 63.7 + - - +
89D MET* 3.0 9.2 + - - +
90D SER* 2.9 26.3 + - - -
115D ILE* 5.7 3.4 - - - -
119D THR* 5.0 3.6 - - - -
320D SER* 5.4 0.7 - - - -
321D CYS* 2.0 51.7 - - + -
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Residues in contact with ASP 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D THR* 3.0 32.3 + - - +
84D ARG* 4.1 4.7 - - - +
86D CYS* 1.3 77.0 - - - +
88D LEU* 1.3 63.1 + - - +
89D MET 2.9 5.9 + - - -
90D SER* 3.1 22.6 + - - +
91D ASP* 3.3 18.2 + - - +
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA* 5.3 9.6 - - + -
40D ILE* 6.1 3.1 - - + -
71D VAL* 5.6 9.2 - - + -
84D ARG* 3.1 25.9 + - + +
85D ILE* 3.9 6.7 - - - +
86D CYS 3.4 0.2 - - - -
87D ASP* 1.3 75.6 - - - +
89D MET* 1.3 55.7 + - - +
91D ASP* 3.8 8.6 + - - +
92D ARG* 3.3 11.6 + - - +
94D ILE* 3.3 28.8 - - + +
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Residues in contact with MET 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ILE* 3.2 29.3 + - - +
86D CYS* 3.0 9.8 + - - +
87D ASP 2.9 0.8 - - - -
88D LEU* 1.3 77.5 - - + +
90D SER* 1.3 55.7 + - - +
91D ASP 2.9 11.3 + - - +
92D ARG 3.3 9.9 - - - +
93D LYS* 5.0 1.7 - - - -
94D ILE* 3.9 27.3 + - + +
97D VAL* 5.8 1.6 - - - -
119D THR* 3.9 24.2 - - + -
121D THR* 4.0 20.4 - - - +
317D PRO* 6.0 0.4 - - + -
318D LYS* 3.9 31.2 - - + +
319D SER* 3.5 12.1 - - - +
320D SER* 4.6 1.6 - - - +
321D CYS* 3.6 27.1 - - - -
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D CYS 2.9 9.9 + - - -
87D ASP* 3.1 20.2 + - - +
89D MET* 1.3 73.1 - - - +
91D ASP* 1.3 69.7 + - - +
319D SER 3.4 16.6 + - - -
320D SER* 4.8 8.5 - - - -
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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