Contacts of the strand formed by residues 409 - 414 (chain A) in PDB entry 6T8G
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 VAL 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A PHE 3.6 0.2 - - - +
369A GLU* 4.2 1.2 - - - -
370A ILE* 3.1 50.6 + - + +
372A PRO* 4.2 14.3 - - + +
378A VAL* 3.7 33.7 - - + -
381A ILE* 5.4 11.0 - - + -
399A VAL* 5.3 4.3 - - + -
400A VAL* 3.7 11.0 - - - +
401A GLU 3.9 16.6 - - - +
403A ILE* 5.0 1.6 - - - -
408A THR* 1.3 80.2 - - - +
410A GLY* 1.3 60.9 + - - +
411A ILE* 6.2 0.2 - - + -
390B ARG* 4.1 17.0 - - + +
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Residues in contact with GLY 410 (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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367A ARG* 4.2 11.0 - - - -
368A PHE 3.5 8.7 - - - -
369A GLU* 5.1 0.9 - - - -
399A VAL* 3.5 6.1 - - - +
400A VAL* 2.6 52.7 + - - +
403A ILE* 5.3 0.4 - - - -
408A THR 4.3 0.2 + - - -
409A VAL* 1.3 78.1 - - - +
411A ILE* 1.3 64.3 + - - -
412A GLU* 3.9 0.4 - - - -
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Residues in contact with ILE 411 (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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343A LEU* 3.8 18.6 - - + -
347A LEU* 4.3 4.0 - - + -
366A THR 3.4 1.9 - - - +
367A ARG 3.3 3.1 - - - -
368A PHE* 2.9 41.4 + - + -
370A ILE* 3.7 28.3 - - + -
381A ILE* 4.8 14.1 - - + -
388A LEU* 3.8 26.2 - - + -
397A VAL* 3.7 22.7 - - + -
398A ARG 4.2 2.0 - - - -
399A VAL* 4.9 3.4 - - + +
409A VAL* 4.2 0.4 + - + -
410A GLY* 1.3 74.1 - - - +
412A GLU* 1.3 62.0 + - - +
413A ILE* 3.7 24.7 - - + -
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Residues in contact with GLU 412 (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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365A ILE* 4.2 20.8 - - + +
366A THR 3.4 4.0 - - - +
367A ARG* 3.3 24.8 + - + +
397A VAL* 3.6 20.3 - - - +
398A ARG* 2.8 65.3 + - + +
400A VAL* 3.3 24.7 - - + +
411A ILE* 1.3 73.4 - - - +
413A ILE* 1.3 60.8 + - - +
414A PRO* 4.1 3.0 - - - +
447A ILE* 3.7 11.0 - - - +
690A ARG* 3.6 14.3 + - - +
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Residues in contact with ILE 413 (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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339A MET* 3.9 11.2 - - + -
343A LEU* 4.5 2.0 - - + -
365A ILE* 4.2 0.7 - - - -
366A THR* 2.8 38.7 + - - +
368A PHE* 3.6 29.2 - - + -
392A LEU* 3.8 28.0 - - + -
394A VAL* 3.7 29.8 - - + -
397A VAL* 3.7 18.8 - - + -
411A ILE* 3.7 15.5 - - + -
412A GLU* 1.3 76.5 - - - +
414A PRO* 1.3 70.7 - - + +
415A ASN 3.6 0.2 + - - -
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Residues in contact with PRO 414 (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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364A VAL* 3.4 8.3 - - + +
365A ILE* 3.7 21.3 - - + -
394A VAL* 3.6 18.5 - - + +
395A ILE* 3.7 28.2 - - + +
396A SER* 3.3 22.2 - - - +
412A GLU 4.1 3.1 - - - +
413A ILE* 1.3 90.9 - - + +
415A ASN* 1.3 69.4 + - - +
416A GLU* 3.7 1.2 + - - +
673A LEU* 4.7 17.9 - - + -
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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