Contacts of the helix formed by residues 12 - 24 (chain B) in PDB entry 1D4W
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 SER 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B LYS 3.8 1.0 + - - -
11B ILE* 1.3 81.4 - - - +
13B ARG* 1.3 60.3 - - - +
14B GLU* 3.5 14.0 + - - +
15B THR* 3.0 34.5 + - - +
16B GLY 3.0 22.7 + - - -
32B ARG* 3.8 3.8 - - - -
35B GLU* 3.3 15.0 - - - -
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Residues in contact with ARG 13 (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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12B SER* 1.3 73.0 - - - +
14B GLU* 1.3 74.5 + - - +
16B GLY* 3.1 2.6 + - - -
17B GLU* 2.9 36.1 + - - +
32B ARG* 3.8 26.9 + - - +
35B GLU* 3.1 24.7 + - - +
277D SER* 3.1 32.5 + - - -
279D THR* 3.3 37.5 + - - +
281D PTR 3.8 29.9 + - - -
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Residues in contact with GLU 14 (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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12B SER* 3.8 12.2 - - - +
13B ARG* 1.3 97.7 + - - +
15B THR* 1.3 63.7 + - + +
17B GLU* 3.2 17.5 + - - +
18B LYS* 2.9 44.1 + - - +
35B GLU* 4.5 3.6 - - - +
277D SER* 5.3 1.7 + - - -
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Residues in contact with THR 15 (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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11B ILE* 3.2 30.7 - - + +
12B SER* 3.0 20.4 + - - +
14B GLU* 1.3 77.3 - - + +
16B GLY* 1.3 64.2 + - - +
18B LYS* 3.3 17.3 + - - +
19B LEU* 3.0 33.6 + - - +
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Residues in contact with GLY 16 (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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11B ILE* 3.7 18.8 - - - -
12B SER 3.0 8.5 + - - -
13B ARG 3.1 4.4 + - - -
15B THR* 1.3 82.8 + - - +
17B GLU* 1.3 61.2 + - - +
19B LEU* 3.4 2.8 + - - +
20B LEU* 3.2 31.6 + - - +
30B LEU* 3.9 13.1 - - - +
32B ARG* 5.0 4.5 - - - -
44B CYS* 6.0 1.3 - - - -
51B ILE* 5.4 1.6 - - - -
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Residues in contact with GLU 17 (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* 2.9 23.6 + - - +
14B GLU* 3.2 18.4 + - - +
16B GLY* 1.3 76.1 - - - +
18B LYS* 1.3 60.9 + - + +
20B LEU* 3.2 1.2 + - - +
21B LEU* 2.8 42.6 + - + +
51B ILE* 3.6 29.8 - - + -
277D SER* 3.1 20.0 + - - -
278D LEU* 4.0 20.5 + - - +
279D THR* 2.8 28.3 + - - +
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Residues in contact with LYS 18 (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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14B GLU* 2.9 38.3 + - - +
15B THR* 3.8 15.1 - - - +
17B GLU* 1.3 79.8 - - + +
19B LEU* 1.3 62.2 + - + +
21B LEU* 4.0 8.3 - - + +
22B ALA* 3.1 25.8 + - - +
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Residues in contact with LEU 19 (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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8B HIS* 3.7 33.7 - - + +
11B ILE* 4.2 9.4 - - + -
15B THR* 3.0 23.9 + - - +
16B GLY 3.7 4.5 - - - +
17B GLU 3.2 0.2 - - - -
18B LYS* 1.3 78.0 - - + +
20B LEU* 1.3 65.4 + - - +
22B ALA* 3.7 9.7 + - + +
23B THR* 3.9 12.3 - - - +
30B LEU* 3.9 14.4 - - + -
102B VAL* 4.3 16.1 - - + +
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Residues in contact with LEU 20 (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 GLY 3.2 15.5 + - - +
17B GLU 4.0 2.0 - - - +
19B LEU* 1.3 75.8 - - - +
21B LEU* 1.3 67.6 + - - +
22B ALA 3.0 1.6 - - - -
23B THR* 2.9 25.9 + - - -
28B SER* 4.0 8.5 - - - +
29B TYR 3.8 22.7 - - - +
30B LEU* 3.8 13.9 - - + -
44B CYS* 3.5 40.8 - - + +
46B LEU* 3.7 23.0 - - + +
51B ILE* 3.9 17.5 - - + -
102B VAL* 3.7 24.0 - - + -
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Residues in contact with LEU 21 (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 GLU* 2.8 31.2 + - + +
18B LYS* 4.1 7.4 - - + +
20B LEU* 1.3 76.6 - - - +
22B ALA* 1.3 63.5 + - - +
24B GLY* 3.0 14.4 + - - -
46B LEU* 3.8 26.2 - - + +
49B GLY* 4.0 18.6 - - - +
51B ILE* 4.1 11.2 - - + -
278D LEU* 3.5 27.6 - - + -
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Residues in contact with ALA 22 (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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18B LYS 3.1 18.4 + - - +
19B LEU* 4.0 8.7 - - + +
20B LEU 3.0 1.8 + - - -
21B LEU* 1.3 77.7 - - - +
23B THR* 1.3 62.4 + - + +
24B GLY* 3.5 0.3 + - - -
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Residues in contact with THR 23 (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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19B LEU 3.9 12.1 - - - +
20B LEU 2.9 15.9 + - - +
22B ALA* 1.3 79.9 - - + +
24B GLY* 1.3 62.2 + - - +
25B LEU* 3.0 18.7 + - - +
28B SER* 2.8 28.0 + - - +
100B TYR* 6.2 0.7 - - + -
102B VAL* 4.0 15.7 - - + -
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Residues in contact with GLY 24 (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 LEU 3.8 0.2 + - - -
21B LEU 3.0 15.7 + - - -
22B ALA 3.3 0.4 - - - -
23B THR* 1.3 77.0 + - - +
25B LEU* 1.3 58.2 + - - +
26B ASP* 4.0 2.5 + - - +
46B LEU* 4.1 7.9 - - - -
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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