Contacts of the helix formed by residues 88 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ALA* 5.4 1.1 - - - -
87A ASP* 1.3 84.9 + - - +
89A THR* 1.3 55.0 + - - +
90A THR* 3.3 2.5 - - - -
91A THR* 3.2 20.1 + - - -
92A ALA* 2.7 36.8 + - - +
499A VAL* 4.7 10.5 - - - -
503A ALA* 3.8 6.9 - - - +
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Residues in contact with THR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 5.4 0.4 - - - -
52A ASP* 4.2 2.8 + - - +
53A GLY* 3.8 6.1 + - - -
54A VAL* 3.2 32.1 + - + +
78A ALA* 3.7 25.3 - - - +
81A ALA* 4.3 6.1 - - + -
82A ASN* 3.8 30.5 - - + +
86A GLY 4.7 4.0 - - - +
87A ASP* 4.4 9.4 - - - -
88A GLY* 1.3 80.1 - - - +
90A THR* 1.3 61.4 + - - +
92A ALA* 3.4 6.9 + - - +
93A THR* 2.9 33.9 + - - -
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.2 42.8 - - + +
28A LYS* 4.4 2.2 - - - -
30A THR* 3.3 18.4 + - - +
31A LEU* 3.8 29.2 - - + -
51A LYS 4.7 0.9 + - - -
53A GLY* 3.3 18.0 + - - -
88A GLY* 3.3 0.6 - - - -
89A THR* 1.3 77.4 + - - +
91A THR* 1.3 62.7 + - - +
93A THR* 3.3 2.1 + - - -
94A VAL* 3.0 29.7 + - + +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.6 20.3 - - + +
88A GLY* 3.4 19.9 - - - -
90A THR* 1.3 77.4 - - - +
92A ALA* 1.3 60.1 + - - +
94A VAL* 3.3 6.6 + - - +
95A LEU* 3.1 28.6 + - + +
416A GLY* 5.8 2.7 - - - -
419A LEU* 5.5 6.7 - - + -
450A PRO* 3.6 30.0 - - + +
454A ILE* 6.4 1.6 - - + -
500A THR* 6.2 0.2 - - - +
503A ALA* 5.0 6.3 - - + -
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 4.8 10.5 - - + +
81A ALA* 4.4 11.0 - - + -
88A GLY 2.7 15.8 + - - +
89A THR* 3.7 8.5 - - - +
91A THR* 1.3 68.7 - - - +
93A THR* 1.3 65.1 + - - +
95A LEU* 3.3 4.0 + - - +
96A ALA 3.0 17.2 + - - -
503A ALA* 3.3 42.5 - - + +
507A ALA* 3.2 12.9 - - - +
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Residues in contact with THR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.4 13.9 - - + +
24A ALA* 4.1 29.6 - - + +
27A VAL* 4.4 16.3 - - + +
74A VAL* 5.0 2.2 + - + +
77A VAL* 4.2 7.7 - - + +
78A ALA* 3.3 27.2 + - - +
89A THR 2.9 19.5 + - - -
90A THR 3.7 4.5 - - - -
92A ALA* 1.3 73.4 - - - +
94A VAL* 1.3 67.8 + - + +
96A ALA* 3.0 10.4 + - + +
97A GLN* 3.0 21.8 + - - +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 5.9 0.2 - - + -
28A LYS* 4.0 30.5 - - + +
31A LEU* 4.0 19.3 - - + -
90A THR* 3.0 21.7 + - + +
91A THR* 3.6 8.7 - - - +
92A ALA 3.3 0.2 - - - -
93A THR* 1.3 77.9 - - + +
95A LEU* 1.3 61.9 + - - +
97A GLN* 3.6 10.7 + - - +
98A ALA* 3.2 21.7 + - - +
449A ALA* 3.9 25.8 - - + +
450A PRO* 4.2 2.7 - - + -
453A GLN* 3.9 22.9 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR* 3.1 21.4 + - + +
92A ALA* 3.3 8.1 - - - +
94A VAL* 1.3 74.5 - - - +
96A ALA* 1.3 59.6 + - - +
98A ALA* 3.2 5.6 + - - +
99A ILE* 2.8 40.1 + - + +
419A LEU* 5.0 7.6 - - + -
446A ALA* 3.3 20.2 - - + +
447A MET* 4.0 9.4 - - + -
450A PRO* 3.2 29.6 - - + -
500A THR 5.5 0.2 - - - +
503A ALA* 3.9 9.2 - - + +
504A LEU* 3.6 47.6 - - + +
507A ALA* 3.9 6.5 - - + -
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A VAL* 5.1 6.5 - - + -
77A VAL* 4.1 20.0 - - + -
92A ALA 3.0 12.6 + - - +
93A THR* 3.0 11.4 + - + +
95A LEU* 1.3 76.5 - - - +
97A GLN* 1.3 62.4 + - - +
99A ILE* 3.3 3.0 + - - +
100A ILE* 2.9 36.4 + - + +
507A ALA* 3.6 23.9 - - + +
510A VAL* 5.3 1.6 - - + -
511A ALA* 4.9 2.9 - - + -
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.8 12.1 - - + +
21A ASN* 3.3 25.8 + - - +
24A ALA* 3.9 22.0 - - + +
25A ASP* 2.8 28.2 + - - -
28A LYS* 3.2 28.5 + - - +
93A THR 3.0 11.2 + - - +
94A VAL* 3.8 11.5 - - - +
96A ALA* 1.3 75.7 - - - +
98A ALA* 1.3 65.1 + - - +
100A ILE* 3.9 3.6 - - - +
101A THR* 2.9 34.8 + - - +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL 3.2 11.2 + - - +
95A LEU 3.2 8.6 + - - +
97A GLN* 1.3 82.8 - - - +
99A ILE* 1.3 62.1 + - - +
101A THR* 3.9 3.7 - - - -
102A GLU* 3.4 27.4 + - - +
446A ALA* 3.7 18.3 - - + +
449A ALA* 3.6 24.0 - - + -
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 2.8 30.4 + - + +
96A ALA 3.3 3.3 + - - +
98A ALA* 1.3 74.5 - - - +
100A ILE* 1.3 57.4 + - - +
102A GLU 3.7 0.2 + - - -
103A GLY* 2.9 26.5 + - - -
120A ILE* 4.0 31.4 - - + -
124A VAL* 6.1 0.4 - - + -
442A VAL* 4.0 9.4 - - + +
443A ALA* 5.4 6.5 - - + +
446A ALA* 3.7 20.2 - - + -
504A LEU* 5.2 8.1 - - + +
507A ALA* 4.1 7.0 - - + -
508A ALA* 3.7 36.3 - - + +
511A ALA* 3.7 17.9 - - + -
512A GLY 4.9 0.7 - - - +
515A ILE* 5.0 1.3 - - + +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 4.8 7.2 - - + -
17A LEU* 4.6 8.1 - - + -
20A VAL* 4.3 13.2 - - + -
74A VAL* 3.7 19.5 - - + -
96A ALA* 2.9 22.6 + - + +
97A GLN* 3.9 3.6 - - - +
99A ILE* 1.3 73.6 - - - +
101A THR* 1.3 61.5 + - - +
104A LEU* 2.8 53.5 + - + +
511A ALA* 3.2 27.4 - - + +
514A MET* 3.6 29.6 - - + -
515A ILE* 4.3 10.3 - - + -
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Residues in contact with THR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.2 22.4 - - + +
21A ASN* 4.5 3.8 + - - -
97A GLN* 2.9 31.6 + - - +
98A ALA* 3.9 5.8 - - - -
100A ILE* 1.3 77.8 - - - +
102A GLU* 1.3 76.0 + - + +
104A LEU* 4.2 1.8 - - - +
105A LYS* 3.2 25.8 + - + +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA 3.4 13.6 + - - +
101A THR* 1.3 88.5 - - + +
103A GLY* 1.3 61.5 + - - +
105A LYS* 3.5 30.6 + - - +
106A ALA* 3.1 22.2 + - - +
442A VAL* 3.8 26.8 - - + +
445A ARG* 3.1 42.7 + - + +
446A ALA* 6.2 1.1 - - + +
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE 2.9 20.5 + - - -
100A ILE 3.6 0.9 - - - -
101A THR 3.2 0.2 - - - -
102A GLU* 1.3 74.7 - - - +
104A LEU* 1.3 63.7 + - - +
106A ALA* 3.0 17.4 + - - +
107A VAL* 3.2 15.1 + - - +
116A LEU* 3.9 3.5 - - - +
442A VAL* 4.1 7.5 - - - +
515A ILE* 3.9 23.6 - - - -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 5.5 1.2 - - - +
13A ARG* 3.7 36.1 + - + +
16A MET* 3.7 27.6 - - + -
17A LEU* 4.1 30.3 - - + -
100A ILE* 2.8 34.7 + - + +
101A THR* 4.2 2.5 - - - +
103A GLY* 1.3 72.1 - - - +
105A LYS* 1.3 61.8 + - - +
107A VAL* 3.1 16.0 + - + +
108A ALA* 3.4 11.4 + - - +
515A ILE* 3.6 30.5 - - + +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A THR* 3.2 21.7 + - + +
102A GLU* 3.5 31.5 + - - +
103A GLY 3.1 0.2 - - - -
104A LEU* 1.3 78.2 - - - +
106A ALA* 1.3 60.2 + - - +
108A ALA* 3.3 19.8 + - + +
109A ALA* 3.8 4.5 + - - +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU 3.1 12.9 + - - +
103A GLY* 3.0 12.0 + - - +
105A LYS* 1.3 77.1 - - - +
107A VAL* 1.3 62.4 + - - +
109A ALA* 3.3 19.8 + - - +
111A MET* 3.5 29.1 - - - +
116A LEU* 3.6 21.5 - - + -
438A VAL* 4.5 9.6 - - + -
442A VAL* 5.0 2.2 - - + -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.8 33.2 + - - +
103A GLY 3.2 17.3 - - - +
104A LEU* 3.1 15.4 + - - +
106A ALA* 1.3 75.7 - - - +
108A ALA* 1.3 52.8 + - - +
109A ALA 3.0 4.9 - - - -
110A GLY* 2.7 25.3 + - - -
111A MET 4.2 7.9 - - - +
113A PRO* 4.1 13.5 - - + -
116A LEU* 4.3 11.4 - - + -
515A ILE* 4.0 19.7 - - + +
36B ARG* 3.9 19.5 + - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 4.4 17.5 + - - +
13A ARG* 5.6 1.5 - - - +
104A LEU 3.4 6.6 + - - +
105A LYS* 3.3 15.1 + - + +
106A ALA 3.3 0.6 - - - -
107A VAL* 1.3 78.2 - - - +
109A ALA* 1.3 58.5 + - - +
110A GLY* 3.2 0.7 + - - -
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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
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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