Contacts of the strand formed by residues 21 - 26 (chain y) in PDB entry 6QXT
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 HIS 21 (chain y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17y TYR* 3.6 3.6 - - - +
18y LYS* 2.9 38.0 + - - +
19y ASN* 3.8 6.1 - - + +
20y ASN* 1.3 78.7 - - - +
22y LEU* 1.3 64.7 + - - +
23y ILE* 3.5 2.6 + - - +
32y MET* 5.1 11.4 - - + -
33y ILE 3.8 8.3 - - - +
34y HIS* 4.9 1.3 - - - +
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Residues in contact with LEU 22 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16y SER 3.6 7.4 - - - +
17y TYR* 4.8 2.2 - - - +
20y ASN 4.5 0.2 + - - -
21y HIS* 1.3 70.7 - - - +
23y ILE* 1.3 61.2 + - - +
24y PHE* 3.8 2.5 + - + +
32y MET* 3.3 5.2 - - - -
33y ILE* 2.9 47.2 + - + +
34y HIS 5.6 2.0 - - - +
35y LEU* 5.0 6.4 - - + +
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Residues in contact with ILE 23 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14y LYS 3.5 1.7 - - - +
15y LEU* 3.3 6.9 - - - +
16y SER* 2.9 51.8 + - - +
18y LYS* 5.5 7.2 - - + +
21y HIS 3.5 3.5 + - - +
22y LEU* 1.3 69.9 - - - +
24y PHE* 1.3 59.2 + - - +
25y ARG* 4.0 2.5 + - + +
31y GLU 3.9 4.0 - - - -
32y MET* 4.7 4.9 - - + +
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Residues in contact with PHE 24 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13y SER* 5.5 4.0 - - - -
14y LYS 3.6 5.2 - - - +
15y LEU* 4.8 3.8 - - + +
22y LEU* 3.8 2.5 + - + +
23y ILE* 1.3 72.1 - - - +
25y ARG* 1.3 59.7 + - - +
26y ASN 4.2 1.0 + - - -
29y LYS 4.5 0.2 - - - +
30y THR* 3.6 2.8 - - - -
31y GLU* 2.9 46.5 + - + +
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Residues in contact with ARG 25 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ILE* 5.6 2.8 - - - +
118F ASP* 6.1 5.2 - - + -
13y SER* 3.1 6.8 - - - -
14y LYS* 2.9 49.0 + - + +
23y ILE* 5.3 2.7 - - + +
24y PHE* 1.3 72.5 - - - +
26y ASN* 1.3 60.3 + - - +
29y LYS 4.4 1.8 - - - -
30y THR* 4.5 10.3 - - - +
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Residues in contact with ASN 26 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ILE* 5.8 2.2 - - - -
11y ILE* 5.6 6.1 - - + -
12y HIS 4.0 15.5 - - - +
13y SER* 4.2 5.6 - - - +
24y PHE 4.2 0.6 - - - -
25y ARG* 1.3 77.1 - - - +
27y SER* 1.3 67.2 + - - +
28y TYR* 3.2 6.9 - - + +
29y LYS 3.1 27.3 + - - +
30y THR* 5.6 0.3 - - - -
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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