Contacts of the strand formed by residues 30 - 37 (chain A) in PDB entry 4C8B
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ARG* 4.0 2.2 - - - -
27A GLY* 3.3 27.6 + - - +
28A ALA 3.3 4.0 + - - -
29A SER* 1.3 79.7 - - - +
31A THR* 1.3 65.0 + - - -
32A VAL* 5.0 1.6 - - - +
47A LYS* 5.6 4.7 - - - +
48A HIS 3.6 11.0 - - - -
49A LEU* 4.3 2.2 - - - -
50A HIS* 4.4 14.8 - - - -
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.7 22.2 - - + -
25A SER 3.4 14.1 - - - +
26A ARG* 4.5 4.9 - - - +
30A GLY* 1.3 75.3 - - - -
32A VAL* 1.3 65.6 + - - +
33A SER* 3.6 16.8 - - - +
47A LYS* 3.4 2.5 - - - +
48A HIS* 3.0 53.2 + - + +
50A HIS* 4.2 15.6 + - - -
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 2.9 34.7 + - + +
25A SER* 2.8 29.5 + - - +
27A GLY* 5.1 4.5 - - - +
30A GLY 5.0 3.1 - - - +
31A THR* 1.3 75.4 - - - +
33A SER* 1.3 67.6 + - - +
45A ALA* 4.7 1.1 - - + -
46A VAL 3.4 7.2 - - - +
47A LYS* 4.6 16.8 - - + -
165A PHE* 4.1 25.4 - - + -
1000A 0LI 3.9 40.4 - - + +
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Residues in contact with SER 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.4 10.5 - - - -
22A ARG 3.3 16.6 - - - -
23A TYR* 4.3 3.3 + - - -
24A LEU* 3.7 6.3 - - - -
31A THR* 3.6 7.1 - - - +
32A VAL* 1.3 77.0 + - - +
34A SER* 1.3 63.4 + - - +
45A ALA* 3.4 3.8 - - - +
46A VAL* 2.8 43.6 + - - +
48A HIS* 2.7 28.8 + - - -
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP 3.4 1.1 + - - +
21A LEU* 3.1 7.3 - - - +
22A ARG* 2.8 53.5 + - - +
24A LEU* 3.5 21.5 - - - +
33A SER* 1.3 74.2 - - - +
35A ALA* 1.3 62.0 + - - +
43A GLN* 5.8 4.8 + - - -
44A VAL 3.4 8.5 - - - -
45A ALA* 4.6 0.4 - - - +
97A TYR* 4.1 19.5 - - - -
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.3 11.2 - - + -
19A ALA 3.4 13.7 - - - +
20A ASP 3.7 4.5 - - - -
21A LEU* 4.0 18.6 - - + -
34A SER* 1.3 78.9 - - - +
36A ARG* 1.3 64.7 + - - +
43A GLN* 3.3 8.3 + - - +
44A VAL* 2.8 43.9 + - + -
46A VAL* 4.7 6.7 - - + -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS 3.6 0.2 - - - +
18A LEU* 3.6 1.9 - - - -
19A ALA* 2.7 49.6 + - + +
20A ASP* 5.4 8.3 - - + -
35A ALA* 1.3 77.3 - - - +
37A HIS* 1.3 66.1 + - - +
41A ARG* 4.3 19.1 + - - +
42A VAL* 3.5 5.6 - - - +
43A GLN* 3.7 42.0 - - + +
44A VAL* 4.8 0.7 - - - -
291B GLU* 5.9 4.4 + - - -
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Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.0 30.8 - - + +
14A PRO* 5.8 0.4 - - - +
17A LYS* 3.5 21.4 - - + +
18A LEU* 4.4 9.6 - - + -
35A ALA 4.2 0.6 - - - -
36A ARG* 1.3 73.4 - - - +
38A ALA* 1.3 61.3 + - - +
39A ASP* 3.3 16.3 + - + -
40A TRP* 3.2 78.7 + + + -
41A ARG* 3.0 29.6 + - - -
42A VAL* 3.1 13.3 + - + +
44A VAL* 4.5 11.2 - - + +
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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