Contacts of the strand formed by residues 434 - 438 (chain C) in PDB entry 1RQQ
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 434 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409C TRP* 3.7 35.9 - + + +
423C VAL* 3.9 1.1 - - - -
432C GLY 4.0 3.4 - - - +
433C LEU* 1.3 85.5 - - - +
435C VAL* 1.3 78.2 + - - +
436C ILE* 3.9 20.0 - - + -
448C LEU* 3.3 23.3 - - + -
449C THR 3.2 12.8 - - - +
450C PHE* 3.7 12.1 - - + -
476C PHE* 3.8 24.7 - + - -
479C VAL* 3.6 15.0 - - + -
480C PHE* 4.0 7.6 - + + -
483C LEU* 3.5 29.6 - - + +
475D TRP* 3.8 13.5 - + + -
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Residues in contact with VAL 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C TRP 3.5 5.8 - - - -
411C HIS* 3.6 34.8 - - + +
414C LEU* 4.6 8.3 - - + -
419C ALA* 4.2 16.8 - - + -
422C LEU* 4.3 22.2 - - + -
423C VAL* 4.3 7.4 - - + -
433C LEU* 4.5 1.3 - - + -
434C PHE* 1.3 89.8 - - - +
436C ILE* 1.3 69.2 + - - +
437C ARG* 4.2 2.9 + - + +
447C VAL 3.8 0.2 - - - +
448C LEU* 3.6 3.1 - - - +
449C THR* 2.9 47.6 + - - +
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Residues in contact with ILE 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C TRP* 2.9 39.0 + - + +
410C PHE* 3.5 16.5 - - + -
411C HIS* 2.7 31.4 + - - +
434C PHE* 3.9 9.4 - - + -
435C VAL* 1.3 78.6 - - - +
437C ARG* 1.3 62.1 + - - +
446C CYS* 4.1 18.8 - - + -
447C VAL 3.4 9.9 - - - +
448C LEU* 4.1 10.1 - - + -
461C LEU* 4.4 4.5 - - + -
463C LEU* 4.3 11.0 - - + -
476C PHE* 3.5 40.4 - - + -
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Residues in contact with ARG 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158B PTR 2.7 43.4 + - - -
410C PHE* 4.3 2.7 - - - -
411C HIS* 4.8 2.0 - - + +
412C GLY 3.5 13.7 - - - +
414C LEU* 3.3 27.8 - - + +
416C ARG* 3.0 24.0 - - - +
419C ALA* 3.8 15.9 - - - +
435C VAL* 5.3 2.9 - - + +
436C ILE* 1.3 76.7 - - - +
438C GLN* 1.3 69.6 + - - +
440C GLU* 4.1 3.4 - - - +
446C CYS* 3.1 10.2 - - - +
447C VAL* 2.8 54.0 + - + +
449C THR* 3.0 16.2 + - - +
458C HIS* 2.9 27.9 - - - -
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Residues in contact with GLN 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C PHE* 4.1 17.6 - - + -
412C GLY* 2.9 28.6 + - - +
413C THR* 4.4 22.6 - - + +
414C LEU 4.7 3.3 - - - +
437C ARG* 1.3 85.1 + - - +
439C SER* 1.3 69.9 + - - +
440C GLU* 3.5 3.5 + - - +
444C GLY* 5.5 8.3 - - - +
445C GLU 3.7 7.8 + - - +
446C CYS* 4.3 5.4 - - - +
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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