Contacts of the strand formed by residues 437 - 442 (chain C) in PDB entry 2QLF
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 437 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369C LYS* 3.6 23.8 - - + -
371C ILE* 3.9 25.6 - - + -
423C LEU* 4.7 1.1 - - + -
426C ALA* 4.7 2.7 - - + -
431C HIS* 4.4 11.4 - + + -
436C CYS* 1.3 81.7 - - - +
438C ALA* 1.3 79.6 + - - +
439C CYS* 3.9 23.8 - - + -
466C PHE* 3.4 41.7 - + - -
474C LEU* 3.6 24.2 - - + -
478C PRO 3.0 6.8 + - - +
479C LYS* 3.5 5.6 - - + -
480C LEU* 2.8 29.0 + - - +
481C PHE* 4.0 17.5 - + - -
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Residues in contact with ALA 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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369C LYS 3.0 14.4 + - - +
370C CYS* 4.1 5.8 - - - -
371C ILE 2.9 22.3 + - - -
401C PHE* 4.3 17.7 - - + -
406C PHE* 3.8 27.6 - - + -
437C PHE* 1.3 85.8 - - - +
439C CYS* 1.3 59.5 + - - +
480C LEU* 3.3 16.4 - - + +
482C PHE* 4.6 2.5 - - + -
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Residues in contact with CYS 439 (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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371C ILE* 3.3 16.2 - - + +
373C ILE* 4.7 0.2 - - - -
423C LEU* 4.0 20.9 - - - -
437C PHE* 3.9 11.7 - - + -
438C ALA* 1.3 75.7 - - - +
440C ILE* 1.3 67.3 + - - +
441C LEU* 3.6 29.8 - - - +
480C LEU 2.9 5.3 + - - +
481C PHE* 3.2 31.9 - - + +
482C PHE* 2.8 24.3 + - - +
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Residues in contact with ILE 440 (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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370C CYS* 4.1 16.8 - - - -
371C ILE 2.8 12.1 + - - +
372C ILE* 4.2 11.8 - - + +
373C ILE 3.0 26.7 + - - -
397C LEU* 3.4 38.1 - - + -
401C PHE* 3.7 37.0 - - + -
439C CYS* 1.3 80.1 - - - +
441C LEU* 1.3 66.5 + - - +
442C LEU* 3.5 15.0 + - + -
482C PHE* 3.1 29.4 - - + +
542D VAL* 5.9 0.4 - - + -
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Residues in contact with LEU 441 (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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373C ILE* 3.4 38.1 - - + -
419C MET* 5.4 3.1 - - - -
423C LEU* 5.2 2.0 - - + -
439C CYS* 3.6 20.9 - - - +
440C ILE* 1.3 73.0 - - - +
442C LEU* 1.3 64.5 + - - +
443C SER* 3.9 0.4 - - - -
450C ILE* 4.3 21.5 - - + -
459C ILE* 5.0 3.1 - - + -
462C LEU* 4.0 28.3 - - + -
463C THR* 6.0 0.2 - - + -
481C PHE* 5.2 7.9 - - + -
482C PHE 2.8 10.9 + - - +
483C ILE* 3.6 30.6 - - + +
484C GLN 2.8 30.7 + - - +
485C ALA* 5.1 0.2 - - - +
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Residues in contact with LEU 442 (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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372C ILE* 4.1 12.3 - - + -
373C ILE 3.0 12.6 + - - +
374C ASN* 3.9 16.4 - - - +
375C ASN 2.8 29.5 + - - -
387C ARG* 3.3 9.0 + - - +
390C THR* 3.9 12.1 - - - +
393C ASP* 4.3 6.3 - - + -
394C ALA* 3.9 20.6 - - - +
397C LEU* 3.7 22.9 - - + -
440C ILE* 3.5 25.6 - - + -
441C LEU* 1.3 76.7 - - - +
443C SER* 1.3 63.1 + - - +
484C GLN* 3.5 22.2 - - + -
542D VAL* 4.2 7.2 - - + -
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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