Contacts of the strand formed by residues 17 - 22 (chain F) in PDB entry 6QY3
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 17 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15F ASN 3.3 9.4 - - - +
16F LEU* 1.3 79.5 - - - +
18F THR* 1.3 59.3 + - - -
182F LEU* 5.6 6.7 + - - -
185F THR* 4.2 15.7 - - - -
186F LYS 5.4 0.2 - - - +
192F VAL* 3.4 12.8 - - - -
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Residues in contact with THR 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU 5.4 2.0 - - - -
14F VAL* 4.5 25.1 - - - -
15F ASN 4.9 1.6 - - - -
16F LEU 4.9 0.4 - - - -
17F GLY* 1.3 74.2 - - - -
19F VAL* 1.3 57.0 + - - +
20F LEU* 3.8 2.5 + - - +
192F VAL 2.9 12.8 + - - +
193F LEU* 3.4 5.5 - - - -
194F PHE* 2.8 33.2 + - - +
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Residues in contact with VAL 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F THR* 1.3 72.0 - - - +
20F LEU* 1.3 60.6 + - - +
21F VAL* 4.0 0.4 - - - -
194F PHE* 3.9 12.1 - - + -
200F ILE* 6.3 2.5 - - + -
203F ILE* 6.0 3.6 - - + -
204F GLN 4.1 11.1 + - - +
205F GLN* 3.2 21.1 - - + +
206F PHE* 2.9 27.6 + - - +
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F THR* 3.8 2.4 + - - +
19F VAL* 1.3 71.8 - - - +
21F VAL* 1.3 59.9 + - - +
22F ILE* 4.1 0.9 + - - +
193F LEU* 6.2 2.5 - - + -
194F PHE 2.7 18.9 + - - +
195F LEU* 3.3 6.5 - - + +
196F GLU* 3.0 24.4 + - - +
206F PHE* 3.7 10.5 - - + +
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Residues in contact with VAL 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F VAL 4.0 0.8 + - - -
20F LEU* 1.3 72.3 - - - +
22F ILE* 1.3 58.6 + - - +
23F GLU 4.0 1.3 + - - +
196F GLU* 3.2 11.4 - - + +
197F PRO 5.0 1.1 - - - +
198F ARG 4.4 3.4 - - - +
199F GLN* 4.2 30.3 - - + +
205F GLN* 5.4 7.6 - - + -
206F PHE 2.9 14.7 + - - +
207F ILE* 4.5 7.6 - - + -
208F LEU* 2.9 30.0 + - - +
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Residues in contact with ILE 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU 4.1 0.8 + - - -
21F VAL* 1.3 70.4 - - - +
23F GLU* 1.3 62.5 + - - +
24F ASP 3.2 8.6 + - - +
27F VAL* 5.2 4.5 - - + -
28F PHE* 3.9 28.5 - - + +
31F LEU* 6.4 0.2 - - + -
196F GLU 3.0 8.5 + - - +
197F PRO* 2.9 25.7 - - - +
208F LEU* 4.1 10.3 - - + -
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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