Contacts of the helix formed by residues 88 - 108 (chain B) in PDB entry 4PKO
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 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ALA* 3.9 3.4 - - - +
87B ASP* 1.3 85.1 + - - +
89B THR* 1.3 64.3 + - - +
90B THR 3.3 2.7 - - - -
91B THR* 3.7 18.0 - - - -
92B ALA* 3.0 25.8 + - - +
499B VAL* 4.4 18.6 - - - -
503B ALA* 3.9 4.0 - - - +
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASP* 3.8 5.3 + - - +
53B GLY* 3.5 9.1 + - - -
54B VAL* 3.3 35.5 + - + -
78B ALA* 3.9 7.1 - - - -
81B ALA* 3.6 10.5 - - - -
82B ASN* 3.5 44.9 - - + +
86B GLY 4.6 4.5 - - - +
87B ASP* 4.4 7.2 - - - -
88B GLY* 1.3 78.8 + - - +
90B THR* 1.3 70.6 + - - +
92B ALA* 3.6 3.5 + - - +
93B THR* 3.3 24.1 + - - -
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.4 38.8 - - + +
28B LYS* 4.6 2.7 - - - -
30B THR* 3.4 12.6 + - - +
31B LEU* 4.0 28.7 - - + -
51B LYS 4.7 0.9 + - - -
53B GLY* 3.3 23.0 + - - -
88B GLY* 4.5 0.2 - - - -
89B THR* 1.3 76.1 + - - +
91B THR* 1.3 66.8 + - - +
93B THR* 3.0 12.5 + - - -
94B VAL* 3.1 15.2 + - + +
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.4 17.2 - - + +
88B GLY* 3.4 19.9 + - - -
89B THR 3.4 0.4 - - - -
90B THR* 1.3 78.4 - - - +
92B ALA* 1.3 61.4 + - - +
94B VAL* 3.4 5.6 + - - +
95B LEU* 3.2 26.1 + - + +
416B GLY* 6.2 1.3 - - - -
419B LEU* 4.7 11.9 - - + -
450B PRO* 4.3 23.9 - - + +
499B VAL* 5.9 1.2 - - - +
500B THR* 5.8 5.4 - - - +
503B ALA* 4.3 10.3 - - + -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 4.2 15.0 - - + +
81B ALA* 4.0 13.2 - - + -
88B GLY 3.0 17.3 + - - +
89B THR 3.7 5.4 - - - +
90B THR 3.2 0.2 - - - -
91B THR* 1.3 77.6 - - - +
93B THR* 1.3 56.4 + - - +
95B LEU* 3.3 2.1 + - - -
96B ALA* 3.0 24.9 + - - +
503B ALA* 3.5 35.6 - - + +
506B TYR* 5.4 0.4 - - + -
507B ALA* 3.3 10.2 - - - +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.3 11.6 - - + +
24B ALA* 3.9 30.1 - - + +
27B VAL* 4.0 22.6 - - + +
74B VAL* 6.4 0.7 - - + -
77B VAL* 4.5 7.3 - - + +
78B ALA* 3.4 23.6 + - - +
89B THR 3.3 11.6 + - - -
90B THR 3.0 9.7 + - - -
92B ALA* 1.3 77.4 - - - +
94B VAL* 1.3 65.9 + - + +
96B ALA* 3.3 7.7 + - + +
97B GLN* 3.0 22.0 + - - +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA* 6.1 0.2 - - - -
28B LYS* 4.1 27.8 - - + -
31B LEU* 4.3 19.7 - - + -
90B THR* 3.1 16.1 + - + +
91B THR* 3.8 8.1 - - - +
92B ALA 3.3 0.2 - - - -
93B THR* 1.3 77.7 - - - +
95B LEU* 1.3 62.4 + - - +
97B GLN* 3.4 13.8 + - - +
98B ALA* 3.1 22.9 + - - +
449B ALA* 3.8 24.7 - - + -
450B PRO* 4.0 14.8 - - + -
453B GLN* 4.0 14.6 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B THR* 3.2 14.9 + - + +
92B ALA 3.4 6.7 - - - +
93B THR 3.3 0.2 - - - -
94B VAL* 1.3 78.1 - - - +
96B ALA* 1.3 62.1 + - - +
98B ALA* 3.4 5.2 + - - +
99B ILE* 3.1 29.6 + - + +
419B LEU* 4.4 17.5 - - + -
446B ALA* 3.7 12.7 - - + +
447B MET* 4.3 8.7 - - + -
450B PRO* 3.3 32.3 - - + -
503B ALA* 3.9 10.5 - - + -
504B LEU* 3.7 47.8 - - + +
507B ALA* 3.7 9.4 - - + -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B VAL* 5.0 5.2 - - + -
77B VAL* 3.8 24.0 - - + -
92B ALA 3.0 12.9 + - - +
93B THR* 3.3 8.7 + - + +
95B LEU* 1.3 77.5 - - - +
97B GLN* 1.3 61.2 + - - +
99B ILE* 3.4 1.9 + - - +
100B ILE* 3.0 35.8 + - + +
507B ALA* 3.5 23.5 - - + +
510B VAL* 4.8 2.7 - - + -
511B ALA* 4.3 4.3 - - + -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 4.8 13.0 - - + +
21B ASN* 3.3 25.3 + - - +
24B ALA* 3.6 22.7 - - + +
25B ASP* 3.5 21.2 + - - -
28B LYS* 3.5 26.6 + - - +
93B THR 3.0 16.1 + - - +
94B VAL* 3.7 10.0 - - - +
96B ALA* 1.3 76.3 - - - +
98B ALA* 1.3 63.6 + - - +
100B ILE* 3.3 5.9 + - - +
101B THR* 3.0 34.8 + - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL 3.1 17.7 + - - +
95B LEU 3.4 2.2 + - - +
97B GLN* 1.3 75.8 - - - +
99B ILE* 1.3 62.6 + - - +
101B THR* 4.0 4.0 - - - -
102B GLU* 3.3 30.4 + - + +
446B ALA* 3.5 24.6 - - + +
449B ALA* 3.7 20.6 - - + -
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.1 20.7 + - + +
96B ALA 3.7 3.1 - - - +
98B ALA* 1.3 76.5 - - - +
100B ILE* 1.3 57.1 + - - +
103B GLY* 3.0 26.7 + - - -
120B ILE* 3.8 35.2 - - + -
124B VAL* 5.5 0.4 - - + -
442B VAL* 3.9 9.7 - - + +
443B ALA* 5.0 8.3 - - + +
446B ALA* 3.8 17.7 - - + -
504B LEU* 4.8 13.7 - - + -
507B ALA 4.3 2.9 - - - +
508B ALA* 4.0 32.1 - - + +
511B ALA* 3.7 17.7 - - + +
512B GLY 4.8 0.7 - - - +
515B ILE* 4.5 2.1 - - + +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 4.6 11.0 - - + -
17B LEU* 4.5 9.6 - - + -
20B VAL* 4.1 15.5 - - + -
74B VAL* 3.5 32.1 - - + -
96B ALA* 3.0 19.1 + - + +
97B GLN* 3.8 4.0 - - - +
99B ILE* 1.3 74.6 - - - +
101B THR* 1.3 57.6 - - - +
103B GLY* 3.4 0.3 + - - -
104B LEU* 3.0 46.7 + - + +
511B ALA* 3.6 24.0 - - + +
514B MET* 3.6 15.5 - - + -
515B ILE* 3.8 14.0 - - + +
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 4.1 23.3 - - + +
21B ASN* 4.5 4.9 + - - -
97B GLN* 3.0 27.5 + - - +
98B ALA* 4.0 5.4 - - - -
99B ILE 3.3 0.2 - - - -
100B ILE* 1.3 78.8 - - - +
102B GLU* 1.3 76.8 + - - +
104B LEU* 3.4 2.8 + - - +
105B LYS* 3.1 27.3 + - - +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 3.3 15.0 + - + +
101B THR* 1.3 85.9 - - + +
103B GLY* 1.3 59.7 + - - +
105B LYS* 3.0 40.4 + - - +
106B ALA* 3.0 27.4 + - - +
442B VAL* 3.6 32.1 - - + +
445B ARG* 2.6 44.6 + - + +
446B ALA* 5.9 2.0 - - + +
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE 3.0 19.1 + - - -
100B ILE 3.7 1.1 - - - -
102B GLU* 1.3 73.8 - - - +
104B LEU* 1.3 59.3 + - - +
106B ALA* 2.8 11.0 + - - +
107B VAL* 2.8 33.3 + - - +
116B LEU* 4.1 2.8 - - - +
442B VAL* 4.1 7.3 - - - +
515B ILE* 4.3 18.6 - - - -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 5.4 0.5 - - - +
13B ARG* 3.3 47.3 - - + +
14B VAL* 5.7 0.2 - - - -
16B MET* 4.3 8.5 - - + -
17B LEU* 3.9 42.2 - - + -
100B ILE* 3.0 28.2 + - + +
101B THR* 4.0 3.6 - - - +
103B GLY* 1.3 73.6 - - - +
105B LYS* 1.3 57.2 + - - +
107B VAL* 3.1 5.0 + - + +
108B ALA* 2.9 30.3 + - - +
515B ILE* 4.2 25.5 - - + +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B THR* 3.1 18.3 + - - +
102B GLU* 3.0 44.8 + - - +
103B GLY 3.1 0.2 - - - -
104B LEU* 1.3 77.9 - - - +
106B ALA* 1.3 61.4 + - - +
108B ALA* 3.5 7.6 + - + +
109B ALA* 3.5 17.0 + - - +
445B ARG* 5.7 1.1 - - - +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLU 3.0 13.6 + - - +
103B GLY* 2.8 13.0 + - - +
105B LYS* 1.3 77.3 - - - +
107B VAL* 1.3 60.0 + - - +
108B ALA 3.4 0.2 - - - -
109B ALA* 3.4 13.3 - - - +
111B MET* 3.4 38.7 + - - +
116B LEU* 4.0 16.2 - - + -
438B VAL* 4.2 15.0 - - + -
442B VAL* 4.9 2.2 - - + -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 4.1 30.5 - - - +
103B GLY 2.8 24.2 + - - +
104B LEU* 3.1 11.4 + - + +
106B ALA* 1.3 74.7 - - - +
108B ALA* 1.3 52.8 + - - +
109B ALA 3.0 4.9 - - - -
110B GLY* 2.7 26.3 + - - -
111B MET 3.9 6.7 + - - +
113B PRO* 3.9 22.9 - - + -
116B LEU* 3.9 15.5 - - + -
515B ILE* 3.8 21.5 - - + +
36C ARG* 4.1 9.7 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 4.0 21.7 + - - +
13B ARG* 5.6 1.7 - - - +
104B LEU 2.9 15.5 + - - +
105B LYS* 3.8 9.2 - - + +
106B ALA 3.4 0.2 - - - -
107B VAL* 1.3 76.2 - - - +
109B ALA* 1.3 57.8 + - - +
110B GLY* 3.1 1.7 + - - -
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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