Contacts of the helix formed by residues 15 - 24 (chain D) in PDB entry 6WNX
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 LEU 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D LEU* 2.8 27.2 + - + +
13D GLN* 3.6 19.5 - - + +
14D GLY* 1.3 81.3 - - - +
16D ASP* 1.3 64.9 + - - +
17D HIS* 3.2 17.0 - - + -
18D ILE* 3.1 37.3 + - + +
19D ALA 3.6 2.9 + - - -
87E LEU* 3.8 30.1 - - + +
90E ASN* 3.6 26.0 - - + +
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Residues in contact with ASP 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO* 3.5 33.7 - - + +
14D GLY* 3.4 10.4 + - - +
15D LEU* 1.3 76.0 - - - +
17D HIS* 1.3 64.0 + - - +
19D ALA* 3.1 8.0 + - - +
20D GLU* 3.0 35.6 + - - +
43D ARG* 3.7 25.6 + - - -
44D VAL* 5.1 3.4 - - + +
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Residues in contact with HIS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLY 4.7 3.6 + - - -
15D LEU* 4.1 25.4 - - + -
16D ASP* 1.3 78.3 + - - +
18D ILE* 1.3 86.5 + - + +
20D GLU* 3.2 19.3 + - - +
21D ASN* 2.9 41.0 + - - +
90E ASN* 4.0 11.7 + - - -
98E LEU* 6.5 0.4 - - + -
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Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.8 22.0 - - + -
15D LEU* 3.1 30.9 + - + +
17D HIS* 1.3 89.8 - - + +
19D ALA* 1.3 67.8 + - - +
21D ASN* 2.9 23.5 + - - +
22D ILE* 2.9 13.6 + - + +
86E ILE* 4.1 9.6 - - + -
90E ASN* 3.3 43.3 - - + +
98E LEU* 4.4 10.5 - - + -
102E CYS* 4.1 21.5 - - - -
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 3.9 20.5 - - + +
10D LEU* 3.8 30.7 - - + +
11D PRO* 4.1 13.7 - - + -
15D LEU 3.6 1.4 + - - -
16D ASP 3.1 9.5 + - - +
18D ILE* 1.3 77.6 - - - +
20D GLU* 1.3 61.3 + - - +
22D ILE* 3.3 5.8 + - - +
23D LEU* 3.0 29.7 + - - +
44D VAL* 4.5 7.9 - - + -
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ASP* 3.0 34.6 + - - +
17D HIS* 3.2 15.7 + - - +
19D ALA* 1.3 72.7 - - - +
21D ASN* 1.3 54.4 + - - +
23D LEU* 3.1 5.3 + - - +
24D SER* 2.8 31.9 + - - -
44D VAL* 4.4 10.0 - - + +
48D GLY* 3.2 40.9 - - - +
50D LEU* 3.4 22.4 - - + +
53D LYS* 3.4 21.2 + - - -
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D HIS* 2.9 38.3 + - - +
18D ILE* 2.9 13.4 + - - +
20D GLU* 1.3 70.5 - - - +
22D ILE* 1.3 69.6 + - - +
24D SER* 3.1 22.0 + - - -
25D TYR* 3.4 22.5 - - + +
53D LYS* 5.6 5.2 - - - +
98E LEU* 6.2 2.4 - - - +
102E CYS* 5.2 7.2 - - + -
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE* 5.2 2.0 - - + -
7D ILE* 4.0 18.2 - - + -
10D LEU* 3.9 28.3 - - + -
18D ILE* 2.9 10.2 + - + +
19D ALA* 3.4 7.9 - - - +
20D GLU 3.2 0.2 - - - -
21D ASN* 1.3 78.3 - - - +
23D LEU* 1.3 64.0 + - - +
25D TYR* 3.2 25.5 + - - +
26D LEU* 4.4 1.8 + - + +
86E ILE* 5.1 5.2 - - + -
102E CYS* 3.6 39.3 - - + +
105E VAL* 4.1 31.4 - - + -
106E ALA* 3.9 12.3 - - - +
109E ILE* 4.2 11.7 - - + -
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 3.7 32.8 - - + -
19D ALA 3.0 14.2 + - - +
20D GLU* 3.1 5.8 + - - +
22D ILE* 1.3 77.1 - - + +
24D SER* 1.3 55.9 + - - +
25D TYR 3.0 0.4 - - - -
26D LEU* 3.0 51.4 + - + +
31D LEU* 4.8 8.1 - - + +
34D ALA* 4.7 12.3 - - + -
41D TRP* 4.8 4.9 - - + -
44D VAL* 3.7 29.6 - - + -
45D ILE* 3.8 20.0 - - + -
50D LEU* 3.7 17.6 - - + +
109E ILE* 4.8 2.2 - - + -
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Residues in contact with SER 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU 2.8 13.9 + - - -
21D ASN* 3.1 19.2 + - - -
23D LEU* 1.3 74.8 - - - +
25D TYR* 1.3 58.6 + - - +
26D LEU 3.4 1.3 - - - +
50D LEU* 3.7 13.2 - - - +
53D LYS* 4.6 22.2 + - - +
54D LEU* 5.0 6.0 - - - +
57D ARG* 2.9 35.0 + - - +
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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