Contacts of the helix formed by residues 15 - 25 (chain B) in PDB entry 6W4E
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 GLY 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY 3.2 2.6 - - - -
14B VAL* 1.3 80.0 - - - +
16B LYS* 1.3 60.6 + - - +
18B ALA* 3.7 0.2 - - - +
19B LEU* 2.9 38.4 + - - +
81B VAL* 4.8 0.4 - - - -
116B ASN* 3.7 1.8 - - - -
201B GSP 3.0 43.2 + - - -
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Residues in contact with LYS 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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8B VAL* 2.8 43.6 + - + +
9B VAL* 3.5 30.0 - - - +
10B GLY* 3.7 8.2 + - - +
11B ALA 4.0 14.4 - - - -
14B VAL* 3.4 19.1 - - + -
15B GLY* 1.3 76.4 - - - +
17B SER* 1.3 57.8 + - - +
19B LEU* 4.1 2.7 - - - +
20B THR* 2.7 32.4 + - - -
57B ASP* 3.2 18.6 + - - +
58B THR* 2.6 29.6 + - - -
59B ALA 4.4 5.9 + - - -
60B GLY 5.2 0.2 - - - +
81B VAL* 4.1 9.0 - - + -
201B GSP 2.7 12.9 + - - +
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 1.3 72.7 - - - +
18B ALA* 1.3 53.9 + - - +
20B THR* 3.2 3.5 + - - -
21B ILE* 2.7 54.8 + - - +
29B VAL* 5.9 0.4 - - - -
33B ASP 4.6 0.8 + - - -
35B THR* 2.7 6.2 + - - +
40B TYR* 5.7 4.0 + - - -
57B ASP* 2.6 4.7 + - - +
201B GSP 2.4 32.5 + - - -
202B MG 1.7 33.0 - - - -
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Residues in contact with ALA 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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15B GLY 3.7 2.7 - - - +
17B SER* 1.3 76.7 - - - +
19B LEU* 1.3 56.1 + - - +
21B ILE* 4.0 2.3 - - - +
22B GLN* 3.0 35.0 + - - +
27B HIS 4.7 0.9 - - - +
28B PHE* 4.1 17.0 - - + -
29B VAL* 4.4 13.9 - - + +
146B ALA* 4.2 3.8 - - + -
201B GSP 2.8 49.9 + - + +
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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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15B GLY 2.9 17.7 + - - +
16B LYS* 4.1 3.4 - - - +
18B ALA* 1.3 74.0 - - - +
20B THR* 1.3 65.6 + - - +
22B GLN* 3.3 14.1 + - - +
23B LEU* 3.3 13.9 + - - +
79B LEU* 6.2 1.3 - - + -
81B VAL* 3.7 34.5 - - + -
114B VAL* 4.0 15.0 - - + -
116B ASN* 3.6 29.4 - - + +
144B THR* 4.2 7.4 - - + -
146B ALA* 3.9 12.3 - - + -
152B VAL* 3.9 29.2 - - + +
156B PHE* 3.8 16.4 - - + -
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Residues in contact with THR 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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8B VAL* 4.1 17.2 - - - +
16B LYS 2.7 21.4 + - - -
17B SER* 3.2 5.6 + - - -
19B LEU* 1.3 76.3 - - - +
21B ILE* 1.3 59.6 + - - +
23B LEU* 3.0 4.3 + - - +
24B ILE* 2.8 40.6 + - + +
40B TYR* 3.6 33.0 - - + -
55B ILE* 3.8 24.9 - - + +
57B ASP* 4.8 5.2 - - + +
156B PHE* 3.8 11.6 - - + -
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Residues in contact with ILE 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 SER* 2.7 39.6 + - - +
18B ALA* 4.1 3.4 - - - +
20B THR* 1.3 73.0 - - - +
22B GLN* 1.3 55.6 + - - +
24B ILE* 4.4 4.0 - - - +
25B GLN* 2.8 41.8 + - + +
26B ASN 2.9 4.9 + - - -
27B HIS* 3.5 37.9 - - + +
29B VAL* 4.1 21.5 - - + -
40B TYR* 4.7 21.1 - - + +
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Residues in contact with GLN 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 ALA 3.0 19.1 + - - +
19B LEU* 3.5 8.1 - - - +
20B THR 3.2 0.4 - - - -
21B ILE* 1.3 77.0 - - - +
23B LEU* 1.3 56.3 + - - +
26B ASN* 3.0 27.4 - - - +
27B HIS 3.5 22.7 - - - +
28B PHE* 3.8 19.0 - - + +
146B ALA* 3.1 28.2 + - + +
147B LYS 3.8 7.1 + - - -
149B ARG* 2.8 52.2 + - + +
152B VAL* 4.8 9.4 - - + -
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Residues in contact with LEU 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 3.3 9.2 + - - +
20B THR 3.0 7.7 + - - +
22B GLN* 1.3 80.5 - - - +
24B ILE* 1.3 63.9 + - + +
26B ASN* 3.5 10.6 + - - +
42B LYS* 3.3 42.3 - - + -
44B VAL* 6.1 1.1 - - + -
53B LEU* 4.6 6.7 - - + -
55B ILE* 4.0 15.9 - - + -
149B ARG* 3.9 6.1 - - - +
152B VAL* 4.5 2.0 - - + +
153B ASP* 4.3 34.5 - - - +
156B PHE* 3.7 46.7 - - + -
157B TYR* 5.5 4.3 - - + -
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Residues in contact with ILE 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 THR* 2.8 23.6 + - + +
21B ILE* 4.3 2.9 - - - +
23B LEU* 1.3 82.0 - - + +
25B GLN* 1.3 70.3 + - + +
26B ASN* 3.6 7.3 + - - -
40B TYR* 3.7 45.8 - - + -
41B ARG 4.2 8.7 - - - +
42B LYS* 3.8 37.3 + - + +
55B ILE* 4.0 13.0 - - + -
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Residues in contact with GLN 25 (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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21B ILE* 2.8 21.0 + - + +
24B ILE* 1.3 87.5 - - + +
26B ASN* 1.3 71.5 - - - +
27B HIS* 2.9 39.4 + - + +
40B TYR* 6.3 2.6 - - + -
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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