Contacts of the strand formed by residues 384 - 388 (chain K) in PDB entry 6R1U
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 SER 384 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383K LYS* 1.3 79.5 - - - +
385K VAL* 1.3 69.6 + - - +
407K LYS* 3.4 24.7 - - - -
619K SER 4.8 0.6 + - - -
620K ALA* 3.5 12.2 - - - +
621K GLN* 3.2 28.0 + - - +
622K LYS* 3.1 24.9 + - - +
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Residues in contact with VAL 385 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383K LYS* 4.4 3.4 - - + -
384K SER* 1.3 85.7 - - - +
386K ILE* 1.3 76.2 + - - +
387K ILE* 4.1 7.4 + - + -
401K LEU* 4.2 19.7 - - + -
406K ILE* 3.9 18.8 - - + -
407K LYS* 2.9 9.7 + - - +
408K VAL* 3.5 5.2 - - + -
409K THR* 3.1 25.3 + - - -
620K ALA* 3.9 1.3 - - - -
622K LYS* 3.2 17.3 - - + +
623K VAL 4.6 0.4 - - - +
624K LEU 4.6 2.0 - - - +
819K ILE* 3.9 35.7 - - + -
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Residues in contact with ILE 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385K VAL* 1.3 74.0 - - - +
387K ILE* 1.3 64.8 + - - +
388K ILE* 4.2 13.9 - - + -
409K THR* 3.4 17.0 - - + +
411K LEU* 3.8 28.3 - - + -
608K VAL* 4.8 1.1 - - + +
610K VAL* 3.9 20.2 - - + -
618K TYR* 3.9 9.2 - - + -
619K SER* 3.6 28.7 - - - +
620K ALA* 3.5 24.5 - - + +
622K LYS 3.0 9.0 + - - +
623K VAL* 3.3 14.5 - - + +
624K LEU 2.8 25.8 + - - -
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Residues in contact with ILE 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385K VAL* 4.3 6.3 - - + -
386K ILE* 1.3 76.7 - - - +
388K ILE* 1.3 60.8 + - - +
389K GLY 3.8 7.0 - - - +
394K GLY* 3.7 30.3 - - - +
397K ALA* 3.8 11.0 - - + -
398K ALA* 3.4 42.0 - - + +
401K LEU* 4.2 7.2 - - + -
408K VAL* 3.7 14.4 - - + -
409K THR 2.7 13.3 + - - +
410K VAL* 3.2 9.3 - - + +
411K LEU* 2.7 33.4 + - - +
624K LEU* 3.6 22.0 - - + +
626K THR* 4.5 0.7 - - + -
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Residues in contact with ILE 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386K ILE* 4.2 6.5 - - + -
387K ILE* 1.3 75.1 - - - +
389K GLY* 1.3 54.8 + - - +
411K LEU* 3.6 3.4 - - + -
598K VAL* 3.9 29.8 - - + -
601K ILE* 3.3 34.1 - - + -
610K VAL* 4.8 2.7 - - + -
623K VAL* 3.7 18.6 - - + -
624K LEU 2.9 17.3 + - - +
625K VAL* 4.3 8.1 - - + -
626K THR* 2.7 36.7 + - - +
627K VAL* 3.8 15.9 + - + -
637K ILE* 4.4 3.1 - - + -
901K FAD 3.6 26.7 - - + +
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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
------------------------------------------------------------
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