Contacts of the helix formed by residues 6 - 21 (chain A) in PDB entry 5O6I
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 ASN 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLU* 1.3 78.5 - - - +
7A VAL* 1.3 57.4 + - + +
8A SER* 3.3 2.4 + - - +
9A GLY* 3.4 6.2 + - - +
10A ILE* 3.0 45.6 + - - +
58A PHE* 4.3 16.8 - - - -
104A ARG* 4.4 9.1 - - - +
182A LEU 5.6 4.1 - - - +
183A ASN* 6.1 0.3 - - - -
184A PRO* 5.5 2.4 - - - +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 2.6 29.4 + - + +
6A ASN* 1.3 71.6 - - + +
8A SER* 1.3 57.8 + - - +
10A ILE* 3.4 2.9 + - - +
11A SER* 2.8 36.6 + - - +
58A PHE* 4.0 25.8 - - + -
59A LEU* 4.0 21.9 - - + +
62A GLU* 4.1 24.2 - - + +
63A LEU* 5.2 6.3 - - + -
90A TYR* 4.1 6.5 - - - +
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Residues in contact with SER 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 3.2 33.0 + - - +
7A VAL* 1.3 81.1 - - - +
9A GLY* 1.3 60.1 + - - +
11A SER* 3.6 6.8 - - - -
12A ALA* 3.0 29.6 + - - +
90A TYR* 5.3 1.1 - - - -
94A MET* 5.6 0.5 - - - +
102A ASN* 5.4 1.9 + - - -
104A ARG* 5.9 2.4 + - - +
105A GLU* 3.7 31.3 - - - +
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Residues in contact with GLY 9 (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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6A ASN* 3.4 10.7 + - - +
7A VAL 3.3 0.6 - - - -
8A SER* 1.3 83.3 + - - +
10A ILE* 1.3 57.8 + - - +
12A ALA* 3.5 1.0 + - - -
13A TYR* 3.1 24.6 + - - +
104A ARG* 5.3 6.3 - - - -
105A GLU* 5.3 4.5 - - - -
108A ALA* 3.3 20.5 - - - +
182A LEU 5.4 2.5 - - - -
183A ASN* 4.3 15.1 - - - +
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Residues in contact with ILE 10 (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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6A ASN* 3.0 32.4 + - - +
7A VAL* 4.0 3.8 - - - +
9A GLY* 1.3 72.6 - - - +
11A SER* 1.3 66.6 + - - +
13A TYR* 3.4 5.8 + - - +
14A LEU* 2.9 41.6 + - + +
55A LEU* 3.9 36.8 - - + +
58A PHE* 3.5 31.9 - - + -
59A LEU* 4.9 5.6 - - + -
184A PRO* 3.8 22.4 - - + -
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Residues in contact with SER 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL 2.8 22.9 + - - -
8A SER* 3.6 7.4 - - - -
9A GLY 3.3 0.2 - - - -
10A ILE* 1.3 77.2 - - - +
12A ALA* 1.3 56.2 + - - +
14A LEU 3.4 0.2 + - - -
15A LEU* 2.9 28.9 + - - +
59A LEU* 3.5 13.4 - - - +
90A TYR* 2.6 34.7 + - - -
91A PHE* 3.6 11.9 - - - -
94A MET* 3.7 18.8 - - - +
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Residues in contact with ALA 12 (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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8A SER 3.0 17.2 + - - +
9A GLY 3.9 3.8 - - - +
11A SER* 1.3 73.4 - - - +
13A TYR* 1.3 64.8 + - - +
15A LEU* 3.4 8.3 + - - +
16A GLY 3.1 17.5 + - - -
94A MET* 4.4 7.5 - - - -
101A CYS* 5.5 3.8 - - - -
105A GLU* 3.4 36.3 - - + +
108A ALA* 4.0 3.8 - - + -
109A PHE* 3.4 17.9 - - + +
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Residues in contact with TYR 13 (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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9A GLY 3.1 17.2 + - - +
10A ILE 3.7 4.3 - - - +
11A SER 3.3 0.2 - - - -
12A ALA* 1.3 77.2 - - - +
14A LEU* 1.3 65.5 + - + +
16A GLY 3.2 2.4 + - - -
17A LEU* 3.2 40.9 + - + +
51A HIS* 2.8 35.7 + + - -
55A LEU* 3.6 25.4 - - + -
108A ALA* 3.4 16.7 + - + +
111A LYS* 3.7 15.9 - - + -
112A GLY* 3.4 34.1 - - - -
115A VAL* 3.7 20.5 - - + +
184A PRO* 4.1 25.6 - - + -
186A PRO* 3.8 8.6 - - + +
187A PRO* 4.2 0.2 - - - +
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Residues in contact with LEU 14 (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 ILE* 2.9 37.1 + - + +
11A SER 3.8 3.1 - - - +
13A TYR* 1.3 77.3 - - + +
15A LEU* 1.3 52.7 + - - +
17A LEU* 3.1 23.8 + - + +
18A ILE* 2.7 44.2 + - + +
40A ILE* 4.4 4.9 - - + -
52A PHE 4.3 7.0 - - - +
55A LEU* 4.0 17.9 - - + +
56A MET* 3.9 41.3 - - + +
59A LEU* 3.9 20.0 - - + -
91A PHE* 4.1 9.4 - - + -
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Residues in contact with LEU 15 (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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11A SER 2.9 18.0 + - - +
12A ALA* 3.6 7.9 - - - +
13A TYR 3.2 0.4 - - - -
14A LEU* 1.3 77.1 - - - +
16A GLY* 1.3 53.1 + - - +
18A ILE* 4.2 7.4 - - + -
19A ILE* 2.7 57.4 + - + +
24A LEU* 4.8 2.9 - - + -
91A PHE* 3.9 37.6 - - + +
94A MET* 3.8 28.9 - - + +
95A LEU* 4.3 21.1 - - + +
98A ILE* 5.0 5.6 - - + -
109A PHE* 4.0 18.8 - - + -
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Residues in contact with GLY 16 (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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12A ALA 3.1 10.9 + - - -
13A TYR 3.2 3.1 + - - -
15A LEU* 1.3 77.0 - - - +
17A LEU* 1.3 56.1 + - - +
19A ILE* 4.8 0.2 - - - -
20A GLY* 2.9 25.6 + - - -
109A PHE* 3.6 22.5 - - - -
112A GLY 3.6 11.9 - - - +
113A LEU* 3.7 21.9 - - - +
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Residues in contact with LEU 17 (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 TYR* 3.2 33.3 + - + +
14A LEU* 3.1 19.9 + - + +
16A GLY* 1.3 75.8 - - - +
18A ILE* 1.3 55.5 + - - +
21A ASP* 2.7 35.2 + - + +
22A GLY 3.5 2.6 + - - -
40A ILE* 4.0 18.2 - - + +
52A PHE* 3.5 39.5 - - + -
112A GLY* 3.4 21.5 + - - +
115A VAL* 3.7 27.1 - - + -
116A ALA* 4.3 7.2 - - + +
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Residues in contact with ILE 18 (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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14A LEU 2.7 26.6 + - - +
15A LEU* 3.7 4.9 - - + +
17A LEU* 1.3 69.0 - - - +
19A ILE* 1.3 68.5 + - + +
22A GLY 2.9 33.3 + - - -
23A GLY* 3.2 28.3 + - - +
24A LEU* 3.8 19.1 - - + -
38A VAL* 3.5 24.5 - - + -
39A VAL 3.8 8.3 - - - +
40A ILE* 3.6 20.0 - - + -
56A MET* 4.2 6.5 - - + -
91A PHE* 3.7 30.3 - - + -
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Residues in contact with ILE 19 (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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15A LEU* 2.7 44.4 + - + +
16A GLY 4.3 1.8 - - - +
18A ILE* 1.3 78.2 - - + +
20A GLY* 1.3 62.1 + - - +
22A GLY 4.6 2.8 - - - +
23A GLY* 5.5 3.1 - - - -
24A LEU* 4.7 7.6 - - + +
95A LEU* 3.6 37.0 - - + -
109A PHE* 4.6 7.0 - - + -
113A LEU* 4.8 3.6 - - + -
129A ASN* 4.7 5.2 + - - +
131A ASN* 6.0 1.1 - - - +
134A LEU* 3.6 32.1 - - + -
202A MN 4.0 5.4 + - - -
15C G 5.3 0.5 - - - +
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Residues in contact with GLY 20 (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 GLY 2.9 18.4 + - - -
19A ILE* 1.3 79.4 - - - +
21A ASP* 1.3 58.3 + - - +
22A GLY 3.4 0.2 - - - -
113A LEU* 4.3 3.1 - - - +
116A ALA* 3.6 11.2 - - - -
117A GLU* 3.6 20.0 - - - -
202A MN 2.4 27.8 + - - -
15C G 3.1 8.0 + - - +
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Residues in contact with ASP 21 (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* 2.7 16.7 + - + +
20A GLY* 1.3 70.3 - - - -
22A GLY* 1.3 53.8 + - - -
40A ILE* 4.4 5.6 - - + -
41A THR* 2.5 48.2 + - - +
42A GLN* 2.8 19.0 + - - +
52A PHE* 5.7 1.3 - - + -
115A VAL 4.7 0.2 - - - -
116A ALA* 3.2 20.5 - - + +
117A GLU* 3.7 4.5 - - - +
201A MN 2.5 34.5 + - - -
14C A 3.6 12.5 - - - +
15C G 3.5 10.9 - - - +
16D C 3.3 7.4 + - - -
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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