Contacts of the strand formed by residues 417 - 420 (chain L) in PDB entry 6ULG
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 PHE 417 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368L VAL* 4.0 14.8 - - + -
374L VAL* 3.6 28.0 - - + -
388L PHE* 3.7 36.1 - + + -
391L LEU* 3.8 39.3 - - + -
392L ARG* 3.9 7.4 - - + -
395L LEU* 3.9 16.2 - - + -
400L VAL* 3.6 20.4 - - + -
401L ARG 3.6 2.6 + - - -
402L ILE* 3.7 17.2 - - + +
403L ILE* 2.7 35.7 + - - +
415L CYS* 4.5 0.2 - - - -
416L ASN* 1.3 99.4 + - - +
418L LEU* 1.3 57.8 + - - +
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Residues in contact with LEU 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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373L GLN* 3.7 20.9 - - - +
374L VAL 2.7 16.3 + - - +
375L ILE* 3.9 13.7 - - + -
376L TRP 2.6 33.6 + - - -
388L PHE* 3.3 10.0 - - - -
403L ILE* 3.4 21.3 - - + -
406L SER* 3.6 24.0 - - - +
409L TYR* 4.3 11.4 - - + -
410L GLU* 4.2 11.4 - - + +
415L CYS* 3.6 11.0 - - - -
417L PHE* 1.3 73.3 - - - +
419L GLY* 1.3 58.7 + - - +
420L LEU* 3.8 29.6 - - + -
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Residues in contact with GLY 419 (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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376L TRP* 3.3 9.6 - - - -
384L VAL* 4.9 8.7 - - - -
388L PHE* 3.5 7.9 - - - -
403L ILE 3.2 11.5 + - - -
404L PRO 3.6 11.7 - - - -
405L TYR* 3.3 9.7 - - - -
406L SER* 3.2 25.5 + - - -
418L LEU* 1.3 74.2 - - - +
420L LEU* 1.3 61.4 + - - -
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Residues in contact with LEU 420 (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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375L ILE* 3.7 22.0 - - + -
376L TRP 2.6 15.2 + - - +
377L LYS* 4.5 8.7 - - + -
378L SER* 3.1 26.0 + - - +
405L TYR* 4.9 4.5 - - - -
406L SER* 3.4 16.6 - - - +
408L GLN 3.3 26.0 - - - +
409L TYR* 4.6 4.7 - - + -
418L LEU* 3.8 27.1 - - + -
419L GLY* 1.3 74.0 - - - -
421L SER* 1.3 67.8 + - - +
424L VAL* 3.8 28.9 - - + +
426L ILE* 4.3 14.6 - - + -
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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