Contacts of the helix formed by residues 20 - 28 (chain B) in PDB entry 4YET
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 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B MET 4.2 1.8 - - - -
16B ILE* 4.3 8.1 - - - -
17B PRO 5.4 1.1 + - - -
18B HIS 4.3 0.2 - - - -
19B ILE* 1.3 77.0 - - - +
21B GLU* 1.3 65.5 + - - +
22B GLU* 3.4 9.7 + - - +
23B THR* 3.0 18.0 + - - -
24B LEU* 3.1 23.0 + - - +
166B ILE* 4.5 0.2 - - - +
167B ASP* 2.5 35.7 + - - -
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Residues in contact with GLU 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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12B MET* 3.2 27.0 + - + +
13B ARG* 2.6 51.8 + - + +
16B ILE* 4.2 11.1 - - + +
20B SER* 1.3 73.8 - - - +
22B GLU* 1.3 59.1 + - - +
24B LEU* 3.2 2.6 + - - +
25B SER* 2.8 31.7 + - - -
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Residues in contact with GLU 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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169A LYS* 3.3 21.3 + - - -
20B SER* 3.2 9.2 + - - +
21B GLU* 1.3 80.6 - - - +
23B THR* 1.3 62.3 + - - +
25B SER* 3.2 6.4 + - - -
26B PHE* 3.1 48.2 + - + -
166B ILE* 3.5 24.7 - - + +
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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 ILE* 3.6 18.4 - - + -
20B SER* 3.0 10.5 + - - -
21B GLU 3.3 0.2 - - - -
22B GLU* 1.3 77.4 - - - +
24B LEU* 1.3 54.8 + - + +
26B PHE* 3.2 1.6 + - - +
27B HIS* 2.7 51.6 + - + +
162B HIS 4.4 4.7 - - - +
163B ALA 3.6 24.0 + - - +
164B TYR 5.4 0.7 - - - -
166B ILE* 3.6 20.4 + - + +
167B ASP* 2.6 32.5 + - - +
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Residues in contact with LEU 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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8B LEU* 4.3 7.4 - - + -
10B TYR* 4.1 11.7 - - + -
11B GLY 4.1 1.6 - - - +
12B MET* 3.5 42.1 - - + +
15B LEU* 4.0 31.6 - - + -
19B ILE* 4.0 18.2 - - + +
20B SER 3.1 15.5 + - - +
21B GLU 3.9 5.2 - - - +
23B THR* 1.3 77.2 - - + +
25B SER* 1.3 64.2 + - - +
27B HIS* 4.4 1.6 - - - +
28B TYR* 2.9 29.5 + - - +
29B GLY 3.5 0.2 + - - -
78B TRP* 3.5 34.1 - - + -
81B MET* 5.3 0.2 - - + -
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Residues in contact with SER 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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12B MET* 3.7 21.4 - - - +
21B GLU* 2.8 20.8 + - - -
22B GLU* 3.4 9.4 - - - -
24B LEU* 1.3 76.9 - - - +
26B PHE* 1.3 65.3 + - - +
29B GLY* 3.0 25.8 + - - -
30B LYS* 3.6 3.1 + - - +
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Residues in contact with PHE 26 (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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165A TYR* 4.0 13.9 - - - +
169A LYS* 3.7 39.5 - - + -
170A ASN* 3.5 27.1 - - - -
22B GLU* 3.1 40.3 + - + +
23B THR 4.0 1.3 - - - +
25B SER* 1.3 84.5 - - - +
27B HIS* 1.3 60.8 + - - +
30B LYS* 2.9 41.2 + - + +
31B HIS* 3.0 14.4 + - + -
166B ILE* 4.0 10.8 - - + -
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Residues in contact with HIS 27 (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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165A TYR* 5.5 0.2 - - - -
23B THR* 2.7 32.2 + - + +
24B LEU 4.4 0.2 - - - +
26B PHE* 1.3 73.9 - - - +
28B TYR* 1.3 57.8 + - - +
31B HIS* 3.4 7.9 - - + +
32B HIS* 2.9 26.5 + - - +
74B HIS* 3.2 13.9 + + - -
77B TYR* 3.5 24.0 + + - -
78B TRP* 3.5 16.8 - + + -
158B ASP* 2.8 17.2 + - - -
162B HIS* 3.2 18.8 + + - +
163B ALA* 3.6 26.6 + - + -
300B FE 2.2 26.9 - - - -
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Residues in contact with TYR 28 (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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5B LEU* 3.5 32.4 + - + +
6B PRO 2.8 28.7 + - - -
7B ALA* 3.4 5.4 - - - -
8B LEU* 3.3 42.0 + - + -
12B MET* 3.9 19.3 - - + -
24B LEU* 2.9 14.8 + - - +
27B HIS* 1.3 78.9 - - - +
29B GLY* 1.3 64.1 + - - +
30B LYS 3.3 0.4 + - - -
32B HIS* 3.5 10.0 - - - +
33B ALA* 3.1 28.9 + - - +
78B TRP* 3.5 33.1 - + + -
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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