Contacts of the strand formed by residues 415 - 420 (chain B) in PDB entry 1F6A
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 THR 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ARG* 3.6 3.3 - - - -
377B ALA* 2.9 61.4 + - + +
413B GLY 4.4 4.5 - - - +
414B GLU* 1.3 90.0 + - - +
416B TYR* 1.3 68.7 + - - +
417B GLN* 5.6 0.7 - - - +
432B SER* 4.8 6.8 + - - -
433B THR 3.9 0.4 - - - -
434B THR* 2.9 26.9 - - - +
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Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU* 4.4 1.5 - - - +
356B ILE* 3.7 24.9 - - + -
374B TRP* 5.0 3.6 - - + -
375B SER 3.6 4.9 - - - +
376B ARG* 3.3 37.4 + - + -
382B VAL* 5.0 3.8 - - + -
403B LEU* 4.8 9.9 - - + -
405B VAL* 3.2 38.0 - - + +
406B GLY 4.2 3.3 + - - -
409B ASP* 3.7 24.3 - - - +
410B TRP* 3.8 32.9 + + - -
414B GLU* 3.7 18.1 - - + +
415B THR* 1.3 76.1 - - - +
417B GLN* 1.3 61.6 + - - +
432B SER* 3.2 5.2 - - - -
433B THR* 3.0 35.5 + - + +
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Residues in contact with GLN 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LEU* 5.0 0.2 - - - -
373B THR 3.8 0.3 - - - +
374B TRP* 3.7 10.3 - - - -
375B SER* 2.9 48.4 + - - +
376B ARG 6.3 0.2 - - - -
415B THR* 5.6 0.7 - - - +
416B TYR* 1.3 76.6 - - - +
418B CYS* 1.3 65.4 + - - +
419B ARG* 5.1 5.5 - - + +
430B MET* 3.8 32.1 - - - +
431B ARG 3.3 18.4 - - - +
432B SER* 3.9 14.6 - - - +
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Residues in contact with CYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LEU* 4.2 6.7 - - + +
358B CYS* 2.0 52.7 - - + -
372B LEU* 3.3 25.1 - - - -
373B THR 3.9 2.7 - - - -
374B TRP* 4.1 13.6 - - + -
417B GLN* 1.3 72.6 - - - +
419B ARG* 1.3 60.1 + - - +
420B VAL* 4.1 7.4 + - - +
429B LEU 3.8 0.7 - - - +
430B MET* 3.3 6.6 - - - +
431B ARG* 2.8 36.0 + - + +
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ASN 3.4 6.1 - - - +
372B LEU* 4.4 0.4 - - - -
373B THR* 3.0 50.1 + - + +
375B SER* 5.7 2.2 - - - +
417B GLN* 5.1 5.6 - - - +
418B CYS* 1.3 73.3 - - - +
420B VAL* 1.3 65.3 + - - +
421B THR* 4.4 8.8 + - - +
428B ALA* 4.1 19.9 - - + +
429B LEU 3.4 3.8 - - - +
430B MET* 3.8 29.4 - - + +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B VAL* 5.5 0.7 - - + -
338B ALA* 5.0 4.5 - - + -
358B CYS* 4.6 1.1 - - - -
360B VAL* 3.7 33.7 - - + -
363B LEU* 6.2 1.6 - - + -
370B VAL* 5.5 8.1 - - + -
371B ASN 4.0 4.0 - - - -
372B LEU* 4.0 17.9 - - + +
418B CYS* 4.1 11.9 - - - +
419B ARG* 1.3 76.7 - - - +
421B THR* 1.3 66.3 + - - +
425B LEU* 4.5 12.0 - - + +
428B ALA* 4.0 1.2 - - - +
429B LEU* 2.8 58.7 + - + +
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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