Contacts of the strand formed by residues 17 - 22 (chain A) in PDB entry 6Y2E
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 MET 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.5 22.0 - - - +
14A GLU* 3.2 11.7 + - - +
15A GLY 5.1 1.4 - - - +
16A CYS* 1.3 77.4 - - - +
18A VAL* 1.3 63.5 + - - +
28A ASN* 3.9 23.8 - - + -
29A GLY 3.3 19.7 - - - +
30A LEU* 3.9 22.0 - - + +
70A ALA* 4.8 5.5 - - - +
71A GLY 5.2 2.1 + - - -
115A LEU* 4.1 9.0 - - + -
117A CYS* 3.8 28.3 - - + -
120A GLY 3.8 21.0 - - - +
122A PRO* 4.6 4.0 - - + -
146A GLY 4.0 12.6 - - - +
147A SER* 4.7 4.0 - - - -
148A VAL* 4.5 6.5 - - + -
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Residues in contact with VAL 18 (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 MET* 1.3 76.7 - - - +
19A GLN* 1.3 58.7 + - - +
20A VAL* 4.4 0.9 - - + -
28A ASN* 3.4 6.8 - - - +
29A GLY* 2.8 48.1 + - - +
30A LEU 4.3 0.4 - - - +
31A TRP* 3.7 27.4 - - + -
36A VAL* 3.8 24.2 - - + -
68A VAL* 3.9 16.4 - - + -
69A GLN 3.5 10.1 - - - +
70A ALA* 3.7 24.7 - - + +
71A GLY 5.7 0.4 - - - +
120A GLY* 3.4 12.0 - - - -
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Residues in contact with GLN 19 (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 VAL* 1.3 73.1 - - - +
20A VAL* 1.3 61.0 + - - +
21A THR* 4.2 11.2 + - - +
26A THR* 3.4 28.4 + - - +
27A LEU 3.7 4.5 - - - +
67A LEU 3.6 1.0 - - - +
68A VAL* 3.3 8.0 - - - +
69A GLN* 2.9 63.8 + - + +
119A ASN* 3.6 44.6 + - - +
120A GLY* 3.8 3.2 - - - -
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Residues in contact with VAL 20 (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 VAL* 4.4 1.8 - - + -
19A GLN* 1.3 76.2 - - - +
21A THR* 1.3 69.2 + - - +
26A THR* 3.3 2.8 + - - -
27A LEU* 2.8 41.7 + - + +
29A GLY* 4.1 17.0 - - - +
36A VAL* 3.9 27.6 - - + -
38A CYS* 4.0 17.7 - - + -
42A VAL* 3.9 22.2 - - + +
66A PHE* 4.6 4.7 - - + -
67A LEU 3.4 5.6 - - - +
68A VAL* 4.4 6.7 - - + -
89A LEU* 4.2 13.9 - - + -
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Residues in contact with THR 21 (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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19A GLN* 4.2 12.5 + - - -
20A VAL* 1.3 75.8 - - - +
22A CYS* 1.3 60.9 + - - +
23A GLY 3.5 21.5 - - - +
24A THR 5.4 0.4 - - - -
25A THR 3.3 10.3 - - - +
26A THR* 3.5 18.0 + - - -
65A ASN 3.5 1.2 - - - +
66A PHE* 3.5 4.7 - - - -
67A LEU* 2.8 59.4 + - + +
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Residues in contact with CYS 22 (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 THR* 1.3 72.7 - - - +
23A GLY* 1.3 65.2 + - - +
24A THR* 3.1 4.2 + - - +
25A THR* 3.1 17.4 + - - +
42A VAL* 3.5 25.7 - - + +
43A ILE* 4.2 6.9 - - - -
61A LYS* 3.6 41.2 + - - -
65A ASN* 3.5 14.1 - - - +
66A PHE* 3.6 30.7 - - + -
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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