Contacts of the strand formed by residues 382 - 386 (chain L) in PDB entry 6R8Y
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 MET 382 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55L VAL* 4.3 23.1 - - + +
56L GLY 3.7 27.2 - - - +
57L LEU* 4.4 2.8 - - - +
58L ALA 4.3 13.2 - - - +
355L ARG* 4.1 13.9 - - - +
365L THR* 4.9 6.5 - - - +
373L ASP* 4.1 9.0 - - - +
374L VAL 4.1 5.8 - - - +
375L PHE* 3.8 27.3 - - + -
381L LYS* 1.3 81.9 - - - +
383L MET* 1.3 76.7 + - - +
384L CYS 4.7 3.1 - - - +
385L GLN* 3.2 35.0 - - - +
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Residues in contact with MET 383 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L LEU* 3.4 32.5 - - + -
58L ALA* 3.2 23.4 - - - +
64L PRO* 4.5 14.5 - - - +
66L CYS* 5.4 7.6 - - - -
95L LEU* 3.9 33.3 - - + +
350L LEU* 5.8 0.7 - - + -
374L VAL 3.1 9.7 + - - +
375L PHE 5.2 1.6 - - - -
376L ASP* 4.7 24.9 - - + +
379L SER* 5.8 2.7 - - - +
381L LYS* 4.9 11.4 - - + +
382L MET* 1.3 85.0 - - - +
384L CYS* 1.3 65.8 + - - +
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Residues in contact with CYS 384 (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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58L ALA* 4.3 7.4 - - - +
95L LEU* 4.8 5.8 - - + +
98L LEU* 4.4 11.2 - - + -
99L ASP* 3.0 32.8 - - - +
102L ARG* 5.1 0.4 - - - -
373L ASP* 3.7 0.9 - - - +
374L VAL* 2.9 41.3 + - + +
382L MET* 4.7 3.2 - - - +
383L MET* 1.3 82.9 - - - +
385L GLN* 1.3 94.8 + - - +
386L LEU* 3.7 24.9 - - - -
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Residues in contact with GLN 385 (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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58L ALA* 4.8 3.8 + - - +
59L GLY* 5.2 20.9 - - - +
60L PRO* 5.0 9.6 - - + +
102L ARG* 4.2 17.2 + - - +
355L ARG* 4.9 4.9 + - - +
365L THR* 5.3 9.1 + - - +
367L TYR 5.4 3.1 - - - +
371L THR* 4.0 19.1 - - - +
372L ILE 3.4 7.0 - - - +
373L ASP* 3.2 21.3 + - - +
382L MET* 3.2 35.0 - - - +
384L CYS* 1.3 91.7 - - - +
386L LEU* 1.3 61.0 + - - +
387L TYR* 3.9 3.4 + - + +
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Residues in contact with LEU 386 (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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98L LEU* 4.0 37.2 - - + +
101L TYR* 4.5 6.3 - - + -
102L ARG* 4.7 7.9 - - - +
371L THR* 2.0 29.2 + - - -
372L ILE* 2.8 36.5 + - + +
374L VAL* 4.4 9.0 - - + -
384L CYS* 3.7 22.2 - - - -
385L GLN* 1.3 69.9 - - - +
387L TYR* 1.3 57.6 + - - +
407L LEU* 4.5 15.9 - - + -
418L TRP* 3.5 40.8 - - + -
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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