Contacts of the strand formed by residues 365 - 370 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360F HIS 5.5 0.2 - - - +
362F GLY* 3.2 21.0 + - - -
363F PRO* 5.4 0.2 - - - +
364F VAL* 1.3 87.8 - - + +
366F THR* 1.3 74.6 + - - +
367F ARG* 3.6 17.3 - - + +
412F GLU* 3.7 27.4 - - + -
413F ILE 3.3 13.9 - - - +
414F PRO* 3.8 20.0 - - + -
415F ASN* 3.2 11.8 - - - +
447F ILE* 3.7 37.7 - - + +
673F LEU* 4.4 1.3 - - + -
690F ARG* 3.8 27.1 - - - +
692F HIS* 4.9 1.1 - - + +
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Residues in contact with THR 366 (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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331F TYR* 4.9 3.5 - - - -
336F LEU* 4.2 10.7 - - + +
359F VAL* 3.7 22.4 - - + -
360F HIS 3.3 17.0 - - - +
361F PRO* 3.7 17.5 - - + +
362F GLY 3.8 1.0 + - - -
365F ILE* 1.3 78.4 + - - +
367F ARG* 1.3 64.8 + - - +
368F PHE* 3.3 32.9 - - + -
413F ILE 3.0 15.5 + - - +
415F ASN* 2.8 26.9 + - - -
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Residues in contact with ARG 367 (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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359F VAL* 3.5 4.2 - - - -
360F HIS* 2.9 62.4 + - + -
365F ILE* 3.6 7.7 - - + +
366F THR* 1.3 73.9 - - - +
368F PHE* 1.3 61.3 - - - +
369F GLU* 3.8 14.8 + - - +
400F VAL* 5.2 3.6 - - - +
403F ILE* 3.9 43.3 - - + +
406F LYS* 5.7 3.4 - - - +
410F GLY* 5.1 1.8 - - - -
411F ILE 3.6 10.5 - - - +
412F GLU* 2.7 38.1 + - + +
447F ILE* 3.4 28.0 - - + +
690F ARG* 6.2 0.6 - - - +
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Residues in contact with PHE 368 (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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336F LEU* 4.5 8.3 - - + -
339F MET* 3.6 33.0 - - + -
340F SER* 4.1 18.8 - - - -
343F LEU* 4.5 13.9 - - + -
356F VAL* 5.1 6.7 - - + -
358F SER 3.8 3.1 - - - -
359F VAL* 4.0 27.1 - - + -
366F THR* 3.3 36.8 - - + -
367F ARG* 1.3 72.3 - - - +
369F GLU* 1.3 65.8 + - - +
370F ILE* 3.4 12.3 + - + +
411F ILE* 2.7 35.7 + - + +
413F ILE* 3.7 37.9 - - + -
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Residues in contact with GLU 369 (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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356F VAL* 4.1 1.2 - - - +
357F ASP* 3.0 27.1 + - + +
358F SER* 2.8 38.1 + - - +
360F HIS* 3.6 17.9 + - + -
367F ARG* 3.7 15.1 + - + +
368F PHE* 1.3 73.1 - - - +
370F ILE* 1.3 61.2 + - - +
403F ILE* 4.5 12.1 - - + +
406F LYS* 3.5 33.0 + - - +
408F THR* 2.6 39.0 + - + +
409F VAL 3.9 5.2 - - - +
410F GLY* 4.6 1.1 - - - -
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Residues in contact with ILE 370 (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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343F LEU* 3.8 22.7 - - + -
347F LEU* 4.5 0.7 - - + -
354F VAL* 3.6 24.5 - - + -
355F SER 3.4 17.0 - - - +
356F VAL* 4.5 8.3 - - + -
368F PHE* 3.6 16.6 - - + +
369F GLU* 1.3 74.1 - - - +
371F GLN* 1.3 68.8 + - - +
372F PRO* 3.3 6.4 - - + +
408F THR* 3.3 5.0 - - - -
409F VAL* 2.7 58.4 + - + +
411F ILE* 3.7 32.1 - - + -
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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