Contacts of the helix formed by residues 10 - 22 (chain B) in PDB entry 5ZJS
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 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ASN 3.7 1.4 + - - -
9B PHE* 1.3 75.4 - - - +
11B LYS* 1.3 59.5 + - - +
12B GLN* 2.8 21.5 + - - +
13B ALA* 2.9 30.0 + - - +
14B SER* 3.4 8.3 + - - -
43B GLY 5.6 2.6 + - - -
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Residues in contact with LYS 11 (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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9B PHE 3.6 2.7 + - - -
10B SER* 1.3 70.6 - - - +
12B GLN* 1.3 56.7 + - - +
13B ALA 3.5 0.2 - - - -
14B SER* 3.5 11.8 + - - -
15B GLU* 3.1 27.0 - - - +
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Residues in contact with GLN 12 (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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10B SER* 2.8 11.8 + - - +
11B LYS* 1.3 79.3 - - - +
13B ALA* 1.3 61.0 + - - +
15B GLU* 3.5 7.8 + - - +
16B ILE* 3.0 38.9 + - + +
41B LYS 5.2 8.0 + - - +
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Residues in contact with ALA 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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9B PHE* 4.2 17.9 - - + -
10B SER* 2.9 20.9 + - - +
12B GLN* 1.3 79.6 - - - +
14B SER* 1.3 58.8 + - - +
16B ILE* 3.3 12.9 - - - +
17B LEU* 3.0 35.6 + - + +
42B CYS* 3.9 24.3 - - + -
43B GLY 5.1 2.2 - - - +
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Residues in contact with SER 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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9B PHE* 5.1 7.5 - - - +
10B SER 3.4 7.2 + - - -
11B LYS* 3.5 15.2 + - - -
13B ALA* 1.3 78.6 - - - +
15B GLU* 1.3 68.7 + - - +
17B LEU* 3.3 9.3 + - - +
18B ASN* 2.9 41.8 + - - +
52B TRP* 5.4 7.9 - - - +
5D G 5.8 3.4 - - - -
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Residues in contact with GLU 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 LYS 3.1 19.5 - - - +
12B GLN* 3.5 8.9 + - - +
13B ALA 3.3 0.8 - - - -
14B SER* 1.3 87.8 + - - +
16B ILE* 1.3 60.2 + - + +
18B ASN* 3.8 13.7 + - - +
19B GLU* 2.9 26.7 + - - +
73B LEU* 6.0 2.3 - - - +
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Residues in contact with ILE 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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12B GLN* 3.0 33.0 - - + +
13B ALA* 3.3 14.8 - - - +
15B GLU* 1.3 72.3 - - + +
17B LEU* 1.3 62.5 + - - +
18B ASN 3.1 1.3 - - - -
19B GLU* 3.7 25.9 - - - +
20B TYR* 2.9 29.6 + - - +
38B LEU* 4.9 7.3 - - + +
41B LYS* 4.4 22.7 - - + +
42B CYS* 3.8 23.6 - - - +
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Residues in contact with LEU 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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9B PHE* 4.6 13.5 - - + -
13B ALA* 3.0 25.1 + - + +
14B SER* 3.3 6.7 + - - +
16B ILE* 1.3 77.7 - - - +
18B ASN* 1.3 55.6 + - - +
20B TYR* 3.8 4.4 - - - +
21B PHE* 2.9 28.1 + - - +
38B LEU* 4.4 12.1 - - + -
42B CYS* 4.1 20.2 - - + -
49B VAL* 4.3 26.7 - - + -
52B TRP* 3.4 56.6 - - + +
53B PHE* 4.3 11.2 - - + -
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Residues in contact with ASN 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 SER* 2.9 30.9 + - - +
15B GLU* 3.8 16.1 + - - +
17B LEU* 1.3 74.7 - - - +
19B GLU* 1.3 60.9 + - - +
20B TYR 3.1 1.6 - - - -
21B PHE* 4.2 1.3 - - - +
22B TYR* 2.9 61.0 + - + +
52B TRP* 3.2 24.3 - - - -
56B LYS* 4.5 4.3 - - - -
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Residues in contact with GLU 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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15B GLU 2.9 18.0 + - - +
16B ILE* 3.3 25.8 + - - +
18B ASN* 1.3 77.1 - - - +
20B TYR* 1.3 58.8 + - - +
23B SER* 3.1 26.5 + - - -
74B TYR* 5.3 2.5 - - - +
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Residues in contact with TYR 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 ILE 2.9 16.8 + - - +
17B LEU* 3.8 4.7 - - - +
19B GLU* 1.3 79.0 - - + +
21B PHE* 1.3 67.7 + - - +
23B SER 3.3 5.0 + - - -
24B HIS* 2.7 62.7 + + + +
28B PRO 4.8 5.2 - - - -
29B TYR 3.8 5.0 + - - -
30B PRO* 3.2 34.6 - - + +
31B SER 4.5 0.9 + - - -
34B ALA* 4.8 11.7 - - + +
38B LEU* 4.1 28.0 - - + -
53B PHE* 3.3 35.9 - + + -
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Residues in contact with PHE 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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13A TRP* 5.1 6.3 - + - -
17B LEU 2.9 20.7 + - - +
18B ASN* 3.3 4.0 + - - +
20B TYR* 1.3 81.9 - - - +
22B TYR* 1.3 83.2 + + - +
24B HIS* 2.9 29.2 + - - +
25B LEU* 3.5 4.7 + - - -
28B PRO* 4.2 21.9 - - + +
52B TRP* 4.1 8.3 - + + -
53B PHE* 4.2 21.5 - + + -
56B LYS* 3.8 33.0 - - + -
57B ARG* 4.3 9.2 - - + -
60B TYR* 3.6 49.8 - + + -
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Residues in contact with TYR 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 ASN* 2.9 54.0 + - + +
19B GLU* 5.7 0.2 - - - -
21B PHE* 1.3 98.8 - + - +
23B SER* 1.3 58.4 + - - +
24B HIS 3.3 0.4 - - - -
25B LEU* 4.3 11.1 + - + +
56B LYS* 3.6 11.0 + - - -
60B TYR* 4.1 10.7 - + - -
68B GLN* 2.7 49.6 + - + +
71B ALA* 3.2 33.3 - - + +
72B ASN* 3.5 23.3 + - - +
73B LEU 5.6 0.7 - - - +
74B TYR* 3.6 16.7 - - + +
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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