Contacts of the strand formed by residues 409 - 414 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369E GLU* 5.1 0.2 - - - -
370E ILE* 2.8 48.0 + - + +
372E PRO* 4.1 11.7 - - + -
378E VAL* 4.3 23.1 - - + -
381E ILE* 4.9 12.6 - - + -
399E VAL* 4.4 14.4 - - + -
400E VAL 3.5 14.1 - - - +
401E GLU 4.8 1.8 - - - +
403E ILE* 4.3 1.1 - - - -
408E THR* 1.3 79.6 - - - +
410E GLY* 1.3 65.7 + - - +
411E ILE* 3.3 1.2 + - + -
390F ARG* 3.7 32.1 - - - +
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Residues in contact with GLY 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E ARG* 4.8 10.3 - - - -
368E PHE 4.4 3.6 - - - -
369E GLU* 5.1 1.3 - - - -
398E ARG 3.8 0.2 - - - +
399E VAL* 3.3 5.2 - - - +
400E VAL* 2.5 55.9 + - - +
403E ILE* 3.6 17.1 - - - +
409E VAL* 1.3 70.5 - - - +
411E ILE* 1.3 60.7 + - - +
412E GLU* 4.2 0.9 - - - -
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Residues in contact with ILE 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E LEU* 4.4 14.6 - - + -
347E LEU* 4.3 20.0 - - + -
366E THR 3.7 0.5 - - - +
367E ARG* 3.5 1.4 - - - -
368E PHE* 2.6 44.7 + - + +
370E ILE* 3.7 31.0 - - + -
381E ILE* 4.7 10.8 - - + -
388E LEU* 4.6 11.2 - - + -
397E VAL* 3.7 23.6 - - + -
398E ARG 3.6 3.1 - - - +
399E VAL* 4.8 12.8 - - + -
409E VAL* 3.3 5.0 + - + +
410E GLY* 1.3 75.6 - - - +
412E GLU* 1.3 62.5 + - - +
413E ILE* 4.2 15.0 - - + -
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Residues in contact with GLU 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E ILE* 3.8 24.2 - - + -
366E THR 3.4 3.6 - - - -
367E ARG* 4.2 23.9 + - + -
396E SER 4.8 0.2 - - - +
397E VAL* 3.3 8.0 - - - +
398E ARG* 3.0 39.9 + - + +
400E VAL* 3.8 26.9 - - + +
411E ILE* 1.3 79.4 - - - +
413E ILE* 1.3 61.8 + - - +
414E PRO* 4.3 1.6 - - - +
447E ILE* 3.7 15.8 - - - +
690E ARG* 3.0 39.3 + - - +
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Residues in contact with ILE 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E MET* 5.3 13.9 - - + -
343E LEU* 3.7 20.6 - - + -
365E ILE* 4.0 2.5 - - - -
366E THR* 2.7 42.1 + - - +
368E PHE* 3.6 31.4 - - + -
392E LEU* 3.7 15.7 - - + -
394E VAL* 3.7 22.9 - - + -
397E VAL* 3.8 14.6 - - + -
411E ILE* 4.2 4.9 - - + -
412E GLU* 1.3 78.6 - - - +
414E PRO* 1.3 80.1 - - + +
415E ASN* 4.6 0.8 + - - +
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Residues in contact with PRO 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364E VAL* 3.8 2.9 - - + +
365E ILE* 3.8 16.5 - - + -
394E VAL* 4.3 17.8 - - + +
395E ILE* 4.3 15.0 - - + -
396E SER 3.9 22.9 - - - +
397E VAL* 5.1 0.2 - - - -
412E GLU 4.3 1.8 - - - +
413E ILE* 1.3 102.0 - - + +
415E ASN* 1.3 69.4 + - - +
673E LEU* 3.7 32.5 - - + -
690E ARG* 6.2 0.2 - - - +
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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