Contacts of the strand formed by residues 422 - 426 (chain E) in PDB entry 3TMH
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 422 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A LEU* 6.2 2.2 - - + -
400E GLY* 5.5 4.5 - - - -
401E SER 4.1 12.6 - - - +
402E PHE* 4.3 9.6 - - + -
420E GLU 3.8 11.2 - - - +
421E ASP* 1.3 72.6 - - - +
423E ILE* 1.3 72.9 + - - +
424E ILE* 3.8 5.2 + - + +
432E LEU* 5.1 7.6 - - + -
454E VAL* 3.1 4.6 - - - -
455E CYS* 2.9 42.2 + - + +
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Residues in contact with ILE 423 (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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390E PHE* 5.3 0.7 - - + -
392E LEU* 3.7 33.2 - - + -
400E GLY* 5.8 0.3 - - - -
401E SER* 3.1 22.3 + - - +
403E ILE* 4.3 17.7 - - + -
421E ASP 4.5 0.7 - - - +
422E VAL* 1.3 78.3 - - - +
424E ILE* 1.3 63.9 + - - +
425E GLU 4.3 3.1 - - - +
426E VAL* 4.1 14.8 - - + -
431E VAL* 3.8 25.7 - - + +
432E LEU* 3.3 16.8 - - - +
439E VAL* 4.9 2.7 - - + -
443E ILE* 4.7 7.0 - - + -
452E LEU* 4.4 19.1 - - + -
453E LEU 4.0 5.2 - - - +
454E VAL* 4.1 12.6 - - + -
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Residues in contact with ILE 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 4.4 8.5 - - + -
396A ARG 4.3 0.4 - - - +
397A GLY 4.3 13.5 - - - -
398A LEU* 3.7 34.8 - - + -
422E VAL* 4.2 7.0 - - + +
423E ILE* 1.3 76.9 - - - +
425E GLU* 1.3 61.3 + - + +
429E VAL 3.3 1.0 - - - +
430E ASN* 3.4 22.4 - - - +
431E VAL* 3.0 29.2 + - - -
432E LEU* 3.8 14.5 + - + -
453E LEU* 2.9 37.5 + - + +
454E VAL 4.1 9.2 - - - +
455E CYS* 4.0 15.7 - - + -
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Residues in contact with GLU 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ARG 4.8 5.8 - - - +
397A GLY* 5.2 1.9 - - - -
651D GLN* 5.3 5.6 + - - +
423E ILE* 4.8 0.7 - - - -
424E ILE* 1.3 93.9 - - + +
426E VAL* 1.3 62.5 + - - +
428E GLY* 3.3 30.5 - - - +
429E VAL 2.8 17.6 - - - +
430E ASN* 4.1 11.5 + - - +
451E THR 3.6 0.9 - - - +
452E LEU* 3.4 8.3 - - - +
453E LEU* 2.9 52.5 + - + +
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Residues in contact with VAL 426 (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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423E ILE* 4.1 7.6 - - + -
425E GLU* 1.3 75.8 - - - +
427E ASN* 1.3 79.6 + - - +
429E VAL* 2.8 25.7 + - - +
431E VAL* 4.0 29.2 - - + -
439E VAL* 4.3 10.1 - - + -
442E ARG* 4.4 12.7 + - + +
443E ILE* 3.9 22.2 - - + +
450E VAL* 3.8 24.2 - - + -
451E THR 3.8 2.0 - - - -
452E LEU* 3.6 15.9 - - + -
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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