Contacts of the helix formed by residues 14 - 29 (chain I) in PDB entry 6AHU
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 ASP 14 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13I SER* 1.3 86.0 + - - +
15I LEU* 1.3 85.3 + - - +
16I LYS* 3.2 21.0 + - + +
17I ALA* 3.6 6.5 + - + +
18I LEU* 3.2 25.5 + - - +
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Residues in contact with LEU 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ASP* 1.3 85.4 + - - +
16I LYS* 1.3 66.2 + - + +
17I ALA 3.4 0.2 - - - -
18I LEU* 3.9 18.6 - - + -
19I ARG* 3.2 51.5 + - + +
52I VAL* 5.4 3.1 - - + -
57I LEU* 3.8 39.7 - - + -
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Residues in contact with LYS 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ASP* 3.2 16.4 + - + +
15I LEU* 1.3 82.0 - - + +
17I ALA* 1.3 62.5 + - - +
19I ARG* 4.3 5.3 - - - +
20I GLY* 3.4 17.2 + - - -
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Residues in contact with ALA 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ALA* 6.2 0.2 - - - -
13I SER* 3.8 21.8 - - - +
14I ASP* 3.6 7.9 + - + +
16I LYS* 1.3 77.8 - - - +
18I LEU* 1.3 63.8 + - - +
20I GLY* 3.8 1.8 + - - +
21I LEU* 3.6 27.6 + - - +
192I GLU 4.7 13.0 - - - +
194I PRO* 4.9 17.9 - - + +
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Residues in contact with LEU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I LEU* 6.2 2.2 - - + -
11I ALA* 3.4 38.6 - - + +
12I GLY* 5.7 3.6 - - - -
14I ASP 3.2 18.1 + - - +
15I LEU* 4.2 16.2 - - + +
16I LYS 3.3 0.2 - - - -
17I ALA* 1.3 76.7 - - - +
19I ARG* 1.3 66.7 + - + +
21I LEU* 3.3 8.0 + - + +
22I VAL* 3.3 30.6 + - + +
35I ILE* 3.8 33.2 - - + -
52I VAL* 4.2 20.6 - - + -
54I VAL* 5.6 1.6 - - + -
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Residues in contact with ARG 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I LEU* 3.2 41.0 + - + +
16I LYS* 4.5 4.6 - - - +
18I LEU* 1.3 77.8 - - + +
20I GLY* 1.3 60.3 + - - +
22I VAL* 3.3 9.5 + - + +
23I GLU* 3.0 40.5 + - - +
57I LEU* 2.5 44.1 + - - +
58I PHE* 4.5 26.1 - - + +
59I THR* 4.7 14.0 - - - +
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Residues in contact with GLY 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I LYS 3.4 14.6 + - - -
17I ALA* 3.8 3.1 + - - -
18I LEU 3.2 1.2 - - - -
19I ARG* 1.3 80.0 - - - +
21I LEU* 1.3 54.5 + - - +
23I GLU* 4.1 7.3 - - - +
24I THR* 2.6 35.9 + - - -
194I PRO* 4.5 11.1 - - - +
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I LEU* 3.9 19.4 - - + +
11I ALA* 3.8 18.2 - - + -
17I ALA 3.6 15.6 + - - +
18I LEU* 3.3 8.8 + - + +
19I ARG 3.3 0.4 - - - -
20I GLY* 1.3 75.2 - - - +
22I VAL* 1.3 61.9 + - + +
24I THR* 4.0 2.4 - - - -
25I ALA* 3.0 29.3 + - - +
191I ALA* 3.3 40.8 - - + +
192I GLU 4.9 3.6 - - - +
193I ARG 3.5 16.6 - - - +
194I PRO* 3.4 24.2 - - + +
195I LEU 4.4 0.7 - - - +
196I GLU 4.6 3.8 - - - +
197I ILE* 5.2 11.3 - - + +
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Residues in contact with VAL 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I LEU* 5.9 1.1 - - + -
18I LEU* 3.3 25.7 + - + +
19I ARG* 3.3 10.7 + - + +
20I GLY 3.3 0.2 - - - -
21I LEU* 1.3 77.9 - - + +
23I GLU* 1.3 57.8 + - - +
25I ALA* 3.4 4.7 + - - +
26I ALA* 2.8 29.5 + - + +
33I VAL* 5.2 17.2 - - + +
35I ILE* 5.7 5.2 - - + -
58I PHE* 4.0 29.6 - - + -
62I PRO* 5.6 1.6 - - + -
71I ILE* 4.9 12.0 - - + +
73I ILE* 4.9 17.3 - - + -
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Residues in contact with GLU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ARG* 3.0 26.5 + - - +
20I GLY* 4.3 6.6 - - - +
22I VAL* 1.3 77.6 - - + +
24I THR* 1.3 57.3 + - - +
26I ALA* 3.9 6.9 - - - +
27I HIS* 3.2 25.1 + - - +
58I PHE* 5.0 16.7 - - + -
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Residues in contact with THR 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E VAL* 4.7 16.7 - - + +
98E PHE* 5.0 3.1 - - + -
20I GLY 2.6 24.1 + - - -
21I LEU* 4.0 6.1 - - - -
22I VAL 3.2 0.2 - - - -
23I GLU* 1.3 75.6 - - - +
25I ALA* 1.3 63.3 + - - +
27I HIS* 3.1 14.1 + - - +
28I LEU* 3.3 22.0 + - + +
194I PRO 4.2 7.8 + - - +
195I LEU* 4.3 20.0 - - + +
197I ILE* 3.8 24.9 - - + -
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Residues in contact with ALA 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I LEU* 5.3 3.4 - - + -
21I LEU 3.0 19.6 + - - +
22I VAL* 3.9 2.9 - - - +
24I THR* 1.3 72.8 - - - +
26I ALA* 1.3 64.7 + - - +
27I HIS 3.4 0.3 + - - -
28I LEU* 3.5 4.2 + - - -
30I TYR* 3.1 55.0 + - + +
33I VAL* 3.9 25.8 - - + -
71I ILE* 5.2 0.2 - - - -
197I ILE* 5.2 9.4 - - + +
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Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I VAL* 2.8 20.5 + - + +
23I GLU* 3.9 8.3 - - - +
25I ALA* 1.3 76.4 - - - +
27I HIS* 1.3 61.2 + - - +
28I LEU 4.8 1.7 - - - -
62I PRO* 5.5 1.1 - - + -
63I ILE 3.6 22.3 - - - +
64I VAL* 3.3 36.2 - - + +
65I GLN 3.9 1.4 + - - -
71I ILE* 3.7 20.8 - - + +
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Residues in contact with HIS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E GLU* 3.2 23.5 + - - -
14E VAL* 3.6 33.3 - - + +
117E TYR* 3.3 9.7 + + - -
121E GLN* 5.0 11.9 - - + -
23I GLU 3.2 14.3 + - - +
24I THR* 3.1 12.6 + - - +
26I ALA* 1.3 78.9 - - - +
28I LEU* 1.3 70.4 + - + +
65I GLN* 2.5 60.9 + - - +
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Residues in contact with LEU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E GLU* 6.0 0.7 - - - +
14E VAL* 4.8 0.9 - - + -
98E PHE* 3.6 54.1 - - + -
99E ASN 5.8 0.4 - - - +
24I THR* 3.3 18.0 + - + +
25I ALA 3.5 0.8 + - - -
26I ALA 3.4 1.5 - - - -
27I HIS* 1.3 96.5 - - + +
29I GLY* 1.3 60.4 + - - +
30I TYR* 4.1 12.1 - - + -
65I GLN* 4.7 5.6 + - - +
66I GLY* 5.8 2.4 + - - -
197I ILE* 4.1 11.2 - - + -
198I ARG 3.4 25.4 - - - +
199I GLY* 3.9 2.0 - - - -
200I PRO* 3.7 24.1 - - + +
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Residues in contact with GLY 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I PHE* 4.0 6.1 - - - +
5I ALA* 3.4 16.4 - - - +
26I ALA 5.5 1.1 - - - -
27I HIS 4.0 0.2 - - - -
28I LEU* 1.3 81.5 - - - +
30I TYR* 1.3 66.2 + - - +
31I SER* 3.6 3.8 + - - -
64I VAL* 5.3 5.8 - - - -
66I GLY* 6.5 1.1 - - - -
200I PRO* 3.7 18.2 - - - +
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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