Contacts of the strand formed by residues 413 - 418 (chain H) in PDB entry 5LS6
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366H MET* 3.2 18.6 - - - +
367H ARG 4.7 1.9 - - - +
380H GLY* 3.5 36.0 + - - +
381H ASN 3.1 9.5 + - - +
384H GLY* 3.8 17.9 - - - +
385H LYS 3.7 16.8 - - - +
386H LEU* 4.0 12.8 - - + -
409H CYS* 5.0 3.6 - - - -
411H ALA 4.2 7.2 - - - +
412H ALA* 1.3 75.7 - - - +
414H ARG* 1.3 61.7 + - - +
415H GLN* 3.4 21.6 + - - +
416H THR* 4.1 4.0 - - + -
427H ALA* 3.9 16.8 - - + -
428H VAL 3.3 8.7 - - - +
429H CYS* 4.2 9.6 - - - -
435H TRP* 6.3 0.2 - - + -
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Residues in contact with ARG 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H PRO* 5.2 0.2 - - + -
96H LEU 3.5 26.2 - - - +
97H PHE* 3.7 35.4 - - + +
363H ILE* 3.6 4.0 - - - +
364H TRP 3.3 6.6 + - - -
365H TYR* 3.1 21.0 + - + +
366H MET* 3.1 29.0 - - - -
367H ARG* 2.9 27.2 + - - +
412H ALA* 4.9 1.6 - - - +
413H ILE* 1.3 73.0 - - - +
415H GLN* 1.3 61.9 + - - +
428H VAL 3.3 5.8 + - - +
429H CYS 5.0 4.9 - - - -
430H ASP* 2.9 25.7 + - - +
7S M3L 2.9 32.5 + - - +
8S PHE* 3.1 35.2 - - - +
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Residues in contact with GLN 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H PHE 3.9 7.6 - - - +
98H GLY* 3.1 24.2 - - - -
99H VAL* 3.1 26.5 + - + +
100H GLN* 4.4 13.9 + - - +
149H THR* 6.1 0.2 - - - -
195H GLU* 4.0 16.0 + - - -
313H ARG* 4.4 6.9 - - - +
367H ARG* 3.7 33.1 + - + +
368H PHE 5.0 2.0 + - - -
369H SER* 5.3 3.5 - - - -
413H ILE* 3.3 4.2 - - - +
414H ARG* 1.3 81.5 - - - +
416H THR* 1.3 87.0 + - - +
428H VAL* 3.3 26.6 + - + +
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Residues in contact with THR 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H VAL* 3.8 2.5 - - - +
100H GLN* 5.0 0.9 + - - -
367H ARG 4.2 1.6 + - - +
368H PHE 4.2 0.7 - - - -
369H SER* 2.7 41.4 + - - -
378H ALA* 3.4 16.1 + - + +
379H LEU* 4.4 2.0 - - - -
380H GLY 4.0 14.8 - - - +
386H LEU* 3.5 31.0 - - + -
413H ILE* 4.1 5.6 - - + -
415H GLN* 1.3 92.7 + - - +
417H SER* 1.3 65.5 + - - +
425H LEU* 3.9 11.9 - - - -
426H ILE 3.4 6.5 - - - -
427H ALA* 4.3 3.8 - - + -
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Residues in contact with SER 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H VAL* 3.8 27.1 - - - -
100H GLN* 3.7 7.8 + - - -
101H PHE* 3.2 36.5 + - - +
103H TRP* 4.8 2.3 + - - -
369H SER* 3.8 5.6 - - - -
416H THR* 1.3 79.1 - - - +
418H PHE* 1.3 66.4 + - - +
425H LEU* 3.5 3.2 - - - +
426H ILE* 3.0 32.2 + - - -
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Residues in contact with PHE 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H PHE* 4.2 6.7 - + - -
101H PHE* 3.4 7.1 - - - -
103H TRP* 2.8 32.8 + - - -
369H SER* 4.5 3.5 + - - -
370H MET* 3.5 29.0 + - - +
371H ASP* 3.5 18.6 - - + -
376H MET* 3.7 44.0 - - - -
378H ALA* 3.6 28.7 - - + -
388H VAL* 4.2 9.9 - - + -
417H SER* 1.3 75.0 + - - +
419H SER* 1.3 60.4 + - - +
422H SER* 4.7 7.2 - - - -
424H ILE 3.4 15.5 - - - +
425H LEU* 3.5 31.6 - - + -
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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