Contacts of the helix formed by residues 71 - 89 (chain C) in PDB entry 5D4P
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 PRO 71 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C LEU* 4.1 10.3 - - + -
33C VAL* 6.1 0.7 - - - -
69C ALA 4.6 0.2 - - - +
70C VAL* 1.3 95.1 - - + +
72C GLU* 1.3 66.1 + - - +
73C GLU* 3.1 21.1 - - - +
74C LEU* 2.9 42.1 + - + +
75C VAL* 3.7 0.9 + - - +
106C PHE* 3.3 30.3 - - + +
107C ARG* 3.7 27.4 - - + +
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Residues in contact with GLU 72 (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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8C PRO 5.7 0.4 + - - -
9C LEU* 5.3 2.9 - - - +
10C LYS* 2.9 48.5 + - + +
70C VAL 3.7 0.8 + - - -
71C PRO* 1.3 72.4 - - - +
73C GLU* 1.3 70.6 + - - +
74C LEU 3.0 1.6 + - - -
75C VAL* 3.2 21.7 + - - +
76C GLY 4.5 1.6 + - - -
107C ARG* 5.0 1.6 - - - +
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Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO* 3.5 12.8 - - + +
72C GLU* 1.3 86.5 + - - +
74C LEU* 1.3 74.5 + - + +
76C GLY 4.9 0.2 - - - -
77C PRO* 3.4 19.6 - - - +
107C ARG* 3.6 26.0 + - - +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA* 3.7 29.4 - - + +
32C GLY* 3.9 20.9 - - - +
33C VAL* 4.0 16.8 - - + +
70C VAL* 4.2 8.1 - - + -
71C PRO* 2.9 32.5 + - + +
73C GLU* 1.3 94.9 - - + +
75C VAL* 1.3 65.9 + - - +
76C GLY 3.4 0.2 - - - -
77C PRO* 3.3 8.4 - - + +
78C LEU* 3.0 27.1 + - + +
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Residues in contact with VAL 75 (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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6B LEU* 4.3 14.1 - - + -
10C LYS* 3.5 41.5 - - + -
12C LEU* 4.4 7.9 - - + -
70C VAL* 4.0 14.4 - - + -
71C PRO 4.1 0.9 - - - +
72C GLU* 3.2 16.2 + - - +
74C LEU* 1.3 77.7 - - - +
76C GLY* 1.3 66.0 + - - +
78C LEU* 3.7 5.4 - - - +
79C LEU* 3.0 44.8 + - + +
95C VAL* 4.6 11.2 - - + -
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Residues in contact with GLY 76 (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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4B ILE* 4.9 5.8 - - - +
72C GLU 4.5 1.6 + - - -
73C GLU 4.5 1.0 + - - -
75C VAL* 1.3 82.1 - - - +
77C PRO* 1.3 68.5 - - - +
79C LEU* 3.3 6.4 + - - +
80C GLU* 3.1 29.0 + - - +
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Residues in contact with PRO 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 5.7 0.5 - - - +
31C ALA* 5.8 6.5 - - + -
73C GLU 3.4 19.5 - - - +
74C LEU* 3.3 13.2 - - + +
76C GLY* 1.3 87.6 - - - +
78C LEU* 1.3 65.1 + - + +
80C GLU* 3.4 11.0 + - + +
81C GLY* 3.0 19.2 + - - -
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Residues in contact with LEU 78 (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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12C LEU* 3.9 28.9 - - + -
27C LEU* 4.1 21.2 - - + +
28C LEU* 4.0 20.0 - - + -
31C ALA* 3.4 28.7 - - + -
33C VAL* 3.7 24.0 - - + -
70C VAL* 4.3 12.1 - - + -
74C LEU* 3.0 22.7 + - + +
75C VAL 3.3 4.0 + - - +
77C PRO* 1.3 77.6 - - - +
79C LEU* 1.3 57.3 + - - +
81C GLY* 3.1 3.3 + - - -
82C PHE* 2.8 40.0 + - + -
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Residues in contact with LEU 79 (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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4B ILE* 4.6 16.6 - - + +
6B LEU* 3.4 43.7 - - + -
101B GLY* 6.0 1.1 - - - +
204B BCT 4.0 20.6 + - - +
12C LEU* 5.1 7.2 - - + -
75C VAL* 3.0 28.5 + - + +
76C GLY* 3.8 5.8 - - - +
78C LEU* 1.3 77.8 - - + +
80C GLU* 1.3 57.4 + - - +
82C PHE* 3.5 5.8 - - + +
83C GLN* 2.8 30.7 + - - +
93C VAL* 3.8 31.9 - - + -
95C VAL* 4.4 6.7 - - + -
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Residues in contact with GLU 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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4B ILE* 4.4 21.1 + - + +
76C GLY 3.1 18.6 + - - +
77C PRO* 3.7 11.6 - - + +
78C LEU 3.2 0.2 - - - -
79C LEU* 1.3 75.9 - - - +
81C GLY* 1.3 57.9 + - - +
83C GLN* 3.3 14.8 + - - +
84C PRO* 3.0 25.6 - - - +
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Residues in contact with GLY 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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23C PHE* 4.6 8.7 - - - -
27C LEU* 3.5 27.4 - - - +
30C ARG* 5.9 0.2 + - - -
77C PRO 3.0 13.9 + - - -
78C LEU 3.1 4.9 + - - -
80C GLU* 1.3 78.3 - - - +
82C PHE* 1.3 55.6 + - - +
84C PRO* 3.3 14.3 - - - +
85C PHE 4.5 2.3 + - - -
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Residues in contact with PHE 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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204B BCT 4.8 4.0 - - - +
12C LEU* 5.4 3.4 - - + -
14C ILE* 4.0 36.8 - - + -
16C LEU* 4.8 3.6 - - + -
23C PHE* 4.8 4.3 - + - -
24C ALA* 4.0 37.0 - - + -
27C LEU* 3.5 25.1 - - + -
28C LEU* 4.2 12.8 - - + -
78C LEU* 2.8 33.2 + - + +
79C LEU* 3.5 9.0 - - + +
81C GLY* 1.3 75.6 - - - +
83C GLN* 1.3 65.0 + - - +
84C PRO 3.4 0.4 - - - -
85C PHE* 3.1 14.1 + + + +
86C PHE* 3.0 51.0 + + + +
93C VAL* 4.9 7.4 - - + -
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Residues in contact with GLN 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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4B ILE* 4.7 13.9 - - - +
204B BCT 3.9 23.7 + - - +
79C LEU 2.8 16.2 + - - +
80C GLU* 3.3 13.1 + - - +
82C PHE* 1.3 78.2 - - - +
84C PRO* 1.3 72.9 - - + +
86C PHE* 4.0 0.7 - - - +
87C GLU* 3.0 43.2 + - - +
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Residues in contact with PRO 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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23C PHE* 6.5 0.4 - - + -
80C GLU 3.0 17.0 - - - +
81C GLY* 3.3 13.9 - - - +
83C GLN* 1.3 92.5 - - + +
85C PHE* 1.3 59.8 - - - +
87C GLU* 3.4 13.4 + - + +
88C ALA* 3.1 22.7 + - - +
204C BCT 4.8 3.0 + - - -
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Residues in contact with PHE 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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16C LEU* 3.4 31.0 - - + -
20C HIS* 3.6 41.3 - + + -
23C PHE* 3.4 41.8 - + + -
81C GLY 4.5 0.4 + - - +
82C PHE* 3.1 15.7 + + + +
83C GLN 3.1 1.0 - - - -
84C PRO* 1.3 80.1 - - - +
86C PHE* 1.3 81.4 + + - +
87C GLU 3.1 0.2 - - - -
88C ALA* 2.9 5.9 + - - +
89C HIS* 2.7 65.1 + + + +
90C SER 5.0 0.2 - - - -
204C BCT 4.1 15.2 + - - -
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Residues in contact with PHE 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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102B ARG* 3.2 34.3 + - - +
204B BCT 4.6 10.3 - - - +
14C ILE* 3.8 21.5 - - + -
15C ILE 3.7 6.7 - - - -
16C LEU* 4.1 1.8 - - + -
82C PHE* 3.0 44.3 + + + +
83C GLN 4.6 0.2 - - - +
85C PHE* 1.3 89.8 - + - +
87C GLU* 1.3 62.3 + - - +
88C ALA 3.1 1.8 - - - -
89C HIS 3.2 14.6 - - - +
90C SER 3.5 17.7 - - - -
91C GLY* 3.4 33.7 - - - -
92C VAL 3.7 2.0 - - - -
93C VAL* 3.3 30.1 - - + -
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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
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102B ARG* 5.3 1.1 - - - +
83C GLN* 3.0 40.8 + - + +
84C PRO* 3.4 12.3 - - - +
86C PHE* 1.3 78.1 - - - +
88C ALA* 1.3 57.8 + - - +
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Residues in contact with ALA 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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84C PRO 3.1 10.9 + - - +
85C PHE 2.9 8.1 + - - +
87C GLU* 1.3 79.4 - - - +
89C HIS* 1.3 75.1 + - + +
204C BCT 4.5 10.1 - - - +
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Residues in contact with HIS 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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102B ARG* 5.1 0.5 + - - -
17C GLU* 5.4 1.0 + - - -
20C HIS* 3.2 39.0 + + + +
85C PHE* 2.7 50.8 + + + +
86C PHE* 3.2 22.9 - - - +
87C GLU 3.8 0.2 - - - -
88C ALA* 1.3 84.9 + - + +
90C SER* 1.3 66.1 + - - +
91C GLY 3.9 1.0 + - - +
204C BCT 3.0 28.6 + - - -
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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