Contacts of the strand formed by residues 413 - 418 (chain L) in PDB entry 6C23
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 413 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366L MET* 3.0 26.1 - - - +
380L GLY* 3.8 15.1 - - - -
381L ASN 2.8 18.7 + - - +
384L GLY* 3.2 37.7 - - - +
386L LEU* 4.2 10.1 - - + -
409L CYS* 5.3 1.1 - - + -
412L ALA* 1.3 72.3 - - - +
414L ARG* 1.3 60.0 + - - +
415L GLN 4.0 2.9 - - - +
416L THR* 4.0 9.9 - - + -
427L ALA* 3.7 30.1 - - + +
428L VAL 3.3 21.3 - - - +
429L CYS* 3.7 13.7 - - + -
435L TRP* 5.6 5.2 - - + +
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Residues in contact with ARG 414 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B M3L 2.9 32.8 + - - +
117B PHE* 3.1 28.3 - - - +
95L PRO* 5.5 0.8 - - - +
96L LEU 3.7 20.2 + - - +
97L PHE* 3.7 40.4 - - + +
363L ILE* 3.3 24.9 - - - +
364L TRP 3.5 17.0 + - - -
365L TYR* 3.5 18.2 + - + +
366L MET* 3.6 7.2 - - - +
367L ARG* 2.8 32.5 + - - +
380L GLY 5.4 0.9 + - - -
412L ALA* 3.7 11.4 + - - +
413L ILE* 1.3 76.9 - - - +
415L GLN* 1.3 61.3 + - + +
416L THR* 5.1 0.9 - - - +
428L VAL* 3.6 8.6 + - + -
430L ASP* 4.1 14.1 + - - +
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Residues in contact with GLN 415 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L PHE 3.5 13.9 - - - +
98L GLY* 3.4 21.0 - - - -
99L VAL* 3.6 23.4 + - + +
100L GLN* 3.4 22.6 + - - +
150L CYS* 5.7 0.2 - - - -
365L TYR* 5.2 1.0 + - - -
367L ARG* 3.9 39.6 + - + +
368L PHE 4.6 7.7 + - - +
369L SER* 5.7 1.0 - - - -
413L ILE* 4.0 1.4 - - - +
414L ARG* 1.3 80.7 - - - +
416L THR* 1.3 83.3 + - - +
427L ALA* 3.6 2.8 - - - -
428L VAL* 3.5 25.2 + - + +
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Residues in contact with THR 416 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L VAL* 4.0 3.8 - - - +
100L GLN* 5.1 0.9 + - - -
367L ARG 5.3 0.2 - - - +
368L PHE* 3.7 16.9 - - - +
369L SER* 3.7 10.8 + - - -
378L ALA* 3.2 25.0 - - - +
379L LEU* 3.8 30.1 - - - +
380L GLY 3.9 3.4 - - - +
386L LEU* 4.4 2.9 - - + -
413L ILE* 4.0 12.6 - - + -
414L ARG 5.1 0.7 - - - +
415L GLN* 1.3 94.4 + - - +
417L SER* 1.3 67.3 + - - +
425L LEU* 4.5 2.9 - - - -
426L ILE 3.1 11.0 - - - -
427L ALA* 4.1 7.4 - - + -
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Residues in contact with SER 417 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L VAL* 4.2 22.4 - - - -
100L GLN* 4.3 5.7 + - - -
101L PHE* 3.1 35.2 + - - -
103L TRP* 5.0 3.6 + - - -
369L SER* 3.7 10.1 - - - -
416L THR* 1.3 80.5 + - - +
418L PHE* 1.3 68.7 + - - +
425L LEU* 3.2 7.6 - - - +
426L ILE* 2.9 31.8 + - - -
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Residues in contact with PHE 418 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L PHE* 4.4 17.9 - + - -
101L PHE* 3.0 16.0 - - - -
103L TRP* 3.2 15.1 + - - -
369L SER* 3.7 16.9 + - - -
370L MET* 4.2 1.8 - - - +
371L ASP* 4.0 29.4 - - + -
376L MET* 4.4 19.7 - - + -
377L LEU 4.1 5.4 - - - -
378L ALA* 3.2 47.1 - - + -
388L VAL* 4.6 4.7 - - + -
417L SER* 1.3 77.8 + - - +
419L SER* 1.3 71.8 + - - +
421L ASP 4.2 4.7 - - - +
422L SER* 4.7 12.8 - - - -
424L ILE 3.3 19.7 - - - +
425L LEU* 3.6 13.2 - - + -
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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