Contacts of the strand formed by residues 25 - 32 (chain B) in PDB entry 6Y2G
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 THR 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL 3.9 0.5 - - - +
21B THR* 3.4 6.1 - - - +
22B CYS 3.1 27.6 + - - -
23B GLY 3.4 1.0 - - - -
24B THR* 1.4 81.0 + - - +
26B THR* 1.3 62.7 + - - +
27B LEU* 4.8 4.9 - - + -
41B HIS* 4.8 6.3 - - + +
42B VAL* 3.5 33.7 + - + +
44B CYS 3.2 22.0 + - - +
45B THR* 5.2 0.2 - - - -
49B MET* 6.5 0.9 - - + -
621B O6K 4.4 23.6 - - + +
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Residues in contact with THR 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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19B GLN* 3.3 36.3 + - + +
20B VAL 3.5 4.0 - - - -
21B THR* 2.7 29.2 + - - +
24B THR 3.7 5.0 + - - -
25B THR* 1.3 72.4 - - - +
27B LEU* 1.3 68.3 + - - +
119B ASN* 3.6 16.8 - - - +
143B GLY* 4.4 4.5 - - - -
621B O6K 3.3 26.9 - - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLN* 3.8 7.0 - - - +
20B VAL* 3.0 31.9 + - + +
25B THR* 4.8 3.1 - - + -
26B THR* 1.3 78.5 - - - +
28B ASN* 1.3 75.9 + - - +
38B CYS* 4.3 6.5 - - + -
39B PRO* 4.1 16.6 - - + -
41B HIS* 4.2 16.4 - - + +
42B VAL* 3.8 40.4 - - + +
119B ASN 5.5 2.2 - - - +
143B GLY* 4.4 7.9 - - - +
145B CYS* 3.3 33.0 - - + +
621B O6K 4.3 9.0 - - - +
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Residues in contact with ASN 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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17B MET* 4.1 10.1 - - + -
18B VAL 3.4 6.3 - - - +
20B VAL* 4.6 1.3 - - - -
27B LEU* 1.3 85.2 - - - +
29B GLY* 1.3 58.3 + - - +
38B CYS* 3.6 7.4 - - - +
117B CYS* 2.9 28.0 + - - +
119B ASN 3.5 4.2 + - - -
120B GLY* 2.7 34.3 + - - -
143B GLY 2.9 28.0 + - - -
144B SER 3.5 5.7 + - - -
145B CYS 3.0 20.2 + - - +
146B GLY* 3.4 25.8 - - - -
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Residues in contact with GLY 29 (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 MET* 3.6 12.9 - - - +
18B VAL* 2.9 39.4 + - - +
20B VAL* 4.2 2.6 - - - +
28B ASN* 1.3 74.8 - - - +
30B LEU* 1.3 60.4 + - - -
36B VAL* 4.0 13.7 - - - -
37B TYR 3.2 10.5 - - - -
38B CYS* 4.1 3.4 - - - -
146B GLY 5.1 2.0 - - - -
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Residues in contact with LEU 30 (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 VAL* 4.7 1.1 - - + -
16B CYS* 3.7 24.7 - - + -
17B MET* 4.0 18.4 - - - -
29B GLY* 1.3 71.0 - - - -
31B TRP* 1.4 58.6 + - - +
32B LEU* 3.6 25.6 - - + -
36B VAL* 3.2 3.3 - - - -
37B TYR* 2.7 50.1 + - + +
148B VAL* 4.1 12.1 - - + -
159B PHE* 3.9 32.3 - - + -
162B MET* 4.5 10.5 - - + +
177B LEU* 3.4 28.7 - - + -
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Residues in contact with TRP 31 (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 5.0 3.6 - - - -
16B CYS* 2.8 18.9 + - - +
18B VAL* 3.7 25.4 - - + -
29B GLY 4.0 0.4 - - - -
30B LEU* 1.4 69.8 - - - +
32B LEU* 1.3 69.4 + - - +
33B ASP 3.1 23.6 + - - -
35B VAL 3.5 8.1 - - - -
36B VAL* 4.0 17.5 - - + +
70B ALA* 3.7 20.4 - - + -
73B VAL* 6.1 0.7 - - + -
75B LEU* 3.3 28.4 - - + +
91B VAL* 3.9 6.3 - - + +
93B THR* 3.2 28.7 + - - -
94B ALA 3.9 2.0 - - - -
95B ASN* 3.0 57.4 + - + -
96B PRO* 4.3 8.1 - - + -
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Residues in contact with LEU 32 (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 CYS* 3.6 24.5 - - + -
30B LEU* 3.6 28.5 + - + -
31B TRP* 1.3 82.7 - - - +
33B ASP* 1.3 71.5 + - - +
34B ASP 3.2 0.2 + - - -
35B VAL* 3.0 27.0 + - - +
37B TYR* 4.3 9.0 + - + -
98B THR* 4.2 3.4 - - + -
99B PRO* 4.3 10.5 - - + -
101B TYR* 3.7 43.1 + - + +
103B PHE* 3.8 15.3 - - + -
159B PHE* 3.8 17.0 - - + -
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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