Contacts of the helix formed by residues 73 - 87 (chain x) in PDB entry 5JPQ
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 GLY 73 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14822 C 3.4 21.1 - - - -
14832 A 5.1 0.7 - - - -
16082 U 3.8 19.5 - - - -
16092 U 3.0 12.9 + - - -
71x GLY 3.2 1.3 + - - +
72x GLY* 1.3 73.7 - - - -
74x HIS* 1.3 66.7 + - - +
76x SER* 3.1 4.2 - - - -
77x GLN* 2.9 21.6 + - - +
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Residues in contact with HIS 74 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14812 C 3.0 39.0 - - + +
14822 C 3.7 6.2 + - - -
15262 A 6.2 0.2 - - - +
16082 U 4.1 2.7 + - - +
16092 U 3.1 4.7 + - - +
41x PRO* 4.9 15.0 - - + -
73x GLY* 1.3 64.5 - - - -
75x VAL* 1.3 58.1 + - - +
76x SER 2.6 16.3 + - - -
77x GLN* 2.6 19.3 + - - +
78x VAL* 3.0 9.5 + - - -
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Residues in contact with VAL 75 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16092 U 3.5 10.4 + - - +
16102 G 3.3 33.9 - - - +
41x PRO* 5.7 1.3 - - - +
74x HIS* 1.3 78.5 - - - +
76x SER* 1.3 63.6 + - - +
78x VAL* 3.5 11.6 - - + +
79x TYR* 2.9 23.0 + - - +
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Residues in contact with SER 76 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16082 U 4.7 5.2 - - - -
16092 U 2.8 30.2 + - - -
16102 G 5.1 0.2 + - - -
13x LYS* 4.1 10.8 - - - +
14x LYS* 5.0 2.9 - - - -
16x ALA* 3.7 20.5 - - - +
73x GLY 3.1 12.1 - - - -
74x HIS 2.6 3.4 + - - -
75x VAL* 1.3 75.9 - - - +
77x GLN* 1.3 66.9 + - - -
79x TYR* 2.9 5.4 + - - +
80x ALA* 2.9 18.0 + - - +
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Residues in contact with GLN 77 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14822 C 6.2 3.1 - - - -
16x ALA* 3.8 5.0 - - - +
69x VAL* 5.2 5.4 - - + +
70x THR* 5.4 7.6 - - - +
71x GLY 4.3 12.8 - - - +
73x GLY 2.9 10.0 + - - +
74x HIS* 2.6 13.0 + - - +
76x SER* 1.3 75.6 - - - +
78x VAL* 1.3 54.7 + - - +
80x ALA* 2.6 29.2 + - - +
81x ILE* 2.9 16.1 + - - +
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Residues in contact with VAL 78 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41x PRO* 5.6 12.1 - - + +
44x LEU 5.6 5.4 - - - +
47x LYS 5.5 0.3 - - - +
48x VAL* 5.4 7.9 - - + +
74x HIS 3.0 7.1 + - - +
75x VAL* 3.5 17.5 - - + +
77x GLN* 1.3 77.8 - - - +
79x TYR* 1.3 63.1 + - - +
80x ALA 3.1 0.2 + - - -
81x ILE* 3.6 7.2 + - - +
82x ARG* 3.3 17.2 + - - +
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Residues in contact with TYR 79 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13x LYS* 4.1 12.8 - - + +
75x VAL 2.9 13.4 + - - +
76x SER* 3.5 8.5 - - - +
78x VAL* 1.3 75.9 - - - +
80x ALA* 1.3 58.7 + - - +
82x ARG* 2.9 24.4 - - - +
83x GLN* 3.8 4.7 + - - +
115x THR* 4.6 3.5 - - - -
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Residues in contact with ALA 80 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11x GLY 3.9 6.5 - - - +
12x LYS 5.2 0.2 - - - -
13x LYS* 3.7 17.9 - - + +
16x ALA* 4.2 0.2 - - + -
17x THR 4.1 10.8 - - - +
18x ALA* 3.3 26.0 - - + +
69x VAL* 5.2 0.7 - - + -
76x SER 2.9 10.0 + - - +
77x GLN* 2.6 21.8 + - - +
79x TYR* 1.3 67.6 - - - +
81x ILE* 1.3 55.7 + - - +
82x ARG 2.7 15.1 + - - -
83x GLN* 3.2 5.1 + - - +
84x ALA* 2.9 19.9 + - - +
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Residues in contact with ILE 81 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18x ALA* 3.3 5.5 - - - +
31x VAL* 5.3 13.7 - - + -
48x VAL* 5.9 6.3 - - + -
69x VAL* 4.5 12.3 - - + +
77x GLN 2.9 11.4 + - - +
78x VAL* 3.9 9.9 - - - +
80x ALA* 1.3 71.8 - - - +
82x ARG* 1.3 58.1 + - - +
84x ALA* 2.9 24.8 - - + +
85x ILE* 3.0 12.5 + - - +
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Residues in contact with ARG 82 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47x LYS 3.9 20.6 - - - +
48x VAL* 5.3 5.6 - - - +
51x PRO* 4.3 10.4 - - + +
78x VAL 3.3 9.7 + - - +
79x TYR* 2.9 24.0 - - - +
80x ALA 2.7 1.0 + - - -
81x ILE* 1.3 76.9 - - - +
83x GLN* 1.3 70.5 + - - +
85x ILE* 3.2 10.9 + - - +
86x ALA* 3.9 3.3 + - - +
115x THR* 3.7 17.3 - - - -
116x LEU* 5.2 0.3 + - - +
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Residues in contact with GLN 83 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11x GLY* 4.9 11.7 - - - +
79x TYR 3.8 3.1 + - - +
80x ALA* 3.2 6.1 + - - +
82x ARG* 1.3 78.6 - - - +
84x ALA* 1.3 68.0 + - - +
85x ILE 2.8 2.3 + - - -
86x ALA 3.1 0.7 + - - -
87x LYS* 2.8 31.5 + - + -
115x THR* 2.9 39.1 - - - +
116x LEU* 3.8 6.7 - - - +
118x ILE 5.9 0.2 - - - -
119x ALA* 6.4 1.1 - - + -
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Residues in contact with ALA 84 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10x PHE 4.8 2.2 - - - +
11x GLY* 4.7 6.5 + - - +
18x ALA* 3.3 28.9 - - + -
19x VAL 4.6 7.2 - - - +
20x ALA* 4.1 13.3 - - - +
80x ALA 2.9 15.0 + - - +
81x ILE* 2.9 21.8 - - - +
83x GLN* 1.3 74.6 - - - +
85x ILE* 1.3 64.3 + - - +
87x LYS* 3.6 13.8 - - - +
88x GLY* 3.9 0.7 + - - -
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Residues in contact with ILE 85 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48x VAL 5.6 1.6 - - - +
51x PRO* 4.2 14.4 - - + -
52x LEU 5.6 1.3 - - - +
81x ILE 3.0 7.7 + - - +
82x ARG 3.8 7.9 - - - +
83x GLN 2.8 3.0 + - - -
84x ALA* 1.3 76.6 - - - +
86x ALA* 1.3 58.7 + - - +
87x LYS 3.0 1.3 - - - -
88x GLY* 2.8 22.5 + - - -
89x LEU* 3.0 8.7 + - - -
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Residues in contact with ALA 86 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51x PRO* 4.7 15.7 - - + +
82x ARG 3.9 3.0 + - - +
83x GLN 3.1 3.6 + - - +
85x ILE* 1.3 72.0 - - - +
87x LYS* 1.3 56.0 + - - +
88x GLY 2.8 11.2 + - - -
89x LEU* 3.5 17.9 + - + +
90x VAL* 3.6 17.3 + - - +
105x LEU* 6.5 0.4 - - + -
109x PHE* 4.7 17.9 - - + -
116x LEU* 3.9 21.6 - - + +
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Residues in contact with LYS 87 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10x PHE* 4.3 18.8 - - + +
11x GLY* 5.6 4.0 - - - +
20x ALA* 4.4 1.0 - - - +
83x GLN* 2.8 32.9 + - + +
84x ALA* 3.6 7.8 - - - +
85x ILE 3.5 1.6 - - - -
86x ALA* 1.3 74.4 - - - +
88x GLY* 1.3 53.9 + - - +
90x VAL 4.0 6.6 - - - +
116x LEU* 4.3 12.0 - - - +
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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