Contacts of the strand formed by residues 365 - 370 (chain D) 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 ILE 365 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360D HIS 5.4 0.4 - - - +
362D GLY* 3.1 20.7 + - - +
364D VAL* 1.3 85.8 - - + +
366D THR* 1.3 72.6 + - - +
367D ARG* 3.7 17.7 - - + +
412D GLU* 4.0 19.3 - - + +
413D ILE 3.3 17.9 - - - +
414D PRO* 4.2 9.0 - - + -
415D ASN* 3.1 7.5 - - - +
447D ILE* 3.7 42.4 - - + +
673D LEU* 4.5 2.5 - - + -
690D ARG* 3.4 38.1 - - - +
692D HIS* 4.8 2.7 - - - +
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Residues in contact with THR 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D TYR* 5.0 0.5 - - - -
336D LEU* 4.1 10.1 - - + +
359D VAL* 3.8 12.1 - - + -
360D HIS 4.0 3.6 - - - -
361D PRO* 3.7 24.2 - - + +
365D ILE* 1.3 75.2 + - - +
367D ARG* 1.3 62.9 + - - +
368D PHE* 3.4 31.9 + - + -
411D ILE 3.8 0.5 - - - +
413D ILE* 2.7 32.1 + - - +
415D ASN* 2.5 33.7 + - - -
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Residues in contact with ARG 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D VAL* 3.7 0.5 - - - -
360D HIS* 3.0 49.8 + - + +
365D ILE* 3.7 13.0 - - + +
366D THR* 1.3 70.6 - - - +
368D PHE* 1.3 74.7 + - - +
369D GLU* 4.0 13.2 + - + +
398D ARG* 5.2 0.4 - - - +
400D VAL* 4.0 18.8 - - - +
403D ILE* 3.4 31.6 - - - +
410D GLY* 4.3 4.8 - - - -
411D ILE 3.6 7.4 - - - +
412D GLU* 2.4 32.8 + - + +
447D ILE* 3.5 31.8 - - + +
690D ARG* 5.9 1.4 - - - +
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Residues in contact with PHE 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D LEU* 5.0 2.2 - - + -
339D MET* 3.9 40.8 - - + -
340D SER* 4.6 2.9 - - - -
343D LEU* 3.9 18.8 - - + -
356D VAL* 5.0 7.9 - - + -
358D SER 4.0 3.4 - - - +
359D VAL* 3.6 25.6 - - + -
366D THR* 3.6 29.2 - - + -
367D ARG* 1.3 81.3 - - - +
369D GLU* 1.3 67.1 + - - +
370D ILE* 4.1 8.2 - - + +
409D VAL 3.7 2.6 - - - +
410D GLY* 3.7 0.7 - - - -
411D ILE* 2.7 41.4 + - + +
413D ILE* 3.6 33.7 - - + -
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Residues in contact with GLU 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D VAL* 4.1 4.0 - - - +
357D ASP* 3.2 25.3 + - - +
358D SER* 2.9 32.7 + - - +
360D HIS* 3.8 18.9 + - + -
367D ARG* 3.9 9.6 - - - -
368D PHE* 1.3 76.9 - - - +
370D ILE* 1.3 63.3 + - - +
403D ILE* 4.7 18.8 - - + +
406D LYS* 2.8 43.8 + - - +
408D THR* 3.8 19.8 + - + +
409D VAL 4.4 2.2 - - - -
410D GLY* 4.9 1.6 - - - -
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Residues in contact with ILE 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D LEU* 3.8 12.8 - - + -
347D LEU* 4.7 0.4 - - + -
354D VAL* 3.6 33.9 - - + -
355D SER 3.7 8.3 - - - +
356D VAL* 4.5 9.0 - - + -
357D ASP* 4.3 0.4 - - - -
368D PHE* 4.1 4.5 - - + +
369D GLU* 1.3 81.2 - - - +
371D GLN* 1.3 63.7 + - - +
372D PRO* 3.2 29.2 - - + +
381D ILE* 6.5 0.9 - - + -
408D THR* 3.3 12.0 - - - -
409D VAL* 3.2 39.5 + - + +
411D ILE* 3.7 32.8 - - + -
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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