Contacts of the strand formed by residues 425 - 433 (chain C) in PDB entry 5IXM
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 425 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417C GLU* 4.1 7.6 - - - +
418C TYR 3.3 13.7 - - - +
419C ARG* 4.1 15.7 - - + +
423C ASP 5.5 0.4 - - - -
424C ARG* 1.3 75.6 - - - +
426C ILE* 1.3 77.6 + - - +
427C GLN* 3.7 8.7 - - + +
460C THR* 3.2 43.1 - - + +
461C ALA* 3.1 8.5 - - - +
462C SER* 2.9 39.5 + - - +
463C TRP* 3.7 4.2 - - - -
545C LEU* 4.3 10.5 - - - -
552C TYR* 3.4 42.0 - - + +
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Residues in contact with ILE 426 (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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603A C8E 3.6 38.4 - - - +
605A C8E 4.1 23.6 - - - +
416C MET* 4.6 2.4 - - + +
417C GLU* 3.3 4.2 - - - +
418C TYR* 2.9 41.5 + - + +
425C MET* 1.3 81.7 - - - +
427C GLN* 1.3 65.9 + - - +
428C LEU* 4.0 21.3 - - + -
459C THR* 5.2 3.8 - - + -
460C THR 3.5 8.3 - - - +
461C ALA* 4.7 8.5 - - + -
463C TRP* 3.7 28.5 - - + -
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Residues in contact with GLN 427 (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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415C ILE* 3.5 31.2 - - + +
416C MET 3.3 11.0 - - - +
417C GLU* 2.8 24.9 - - + +
425C MET* 3.9 13.0 - - + -
426C ILE* 1.3 76.6 - - - +
428C LEU* 1.3 66.9 + - - +
429C ASN* 4.8 6.5 + - - +
458C GLY 3.6 0.7 - - - +
459C THR* 3.3 6.8 - - - -
460C THR* 2.9 41.2 + - - +
476C TYR* 4.4 15.6 + - - -
552C TYR* 3.2 24.6 - - - -
553C GLN 3.5 13.8 + - - +
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Residues in contact with LEU 428 (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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222A ILE* 4.3 16.6 - - + -
263A VAL* 4.4 8.5 - - + -
603A C8E 3.7 38.8 - - - +
415C ILE* 3.2 8.4 - - - +
416C MET* 2.9 60.9 + - + -
426C ILE* 4.0 15.5 - - + -
427C GLN* 1.3 79.3 - - - +
429C ASN* 1.3 61.6 + - - +
458C GLY 3.3 8.3 - - - +
459C THR* 4.3 13.7 - - + +
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Residues in contact with ASN 429 (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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414C ALA 3.2 12.3 - - - +
415C ILE* 3.9 16.6 - - + +
427C GLN* 4.8 5.8 + - - +
428C LEU* 1.3 78.6 - - - +
430C TYR* 1.3 65.8 + - - +
431C ARG* 3.8 25.2 - - + +
456C GLN* 4.4 5.5 + - - +
457C VAL* 3.5 5.9 - - - +
458C GLY* 2.9 56.9 + - - +
460C THR* 5.6 0.2 + - - -
476C TYR* 3.4 25.1 + - - -
67D VAL 5.3 0.4 + - - -
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Residues in contact with TYR 430 (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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215A LEU* 3.5 30.7 - - + -
412C GLY 5.3 0.4 - - - -
413C ASN* 3.2 6.8 - - - +
414C ALA* 2.9 38.0 + - + +
429C ASN* 1.3 75.6 - - - +
431C ARG* 1.3 68.7 + - - +
432C TYR* 3.7 20.9 - - + +
455C SER* 2.8 28.6 + - - -
456C GLN 3.2 25.4 - - - -
457C VAL* 3.5 22.4 - - + -
479C THR* 4.8 0.2 - - + -
606C C8E 3.6 24.4 - - - -
609C C8E 3.5 35.7 - - - -
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Residues in contact with ARG 431 (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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309C GLN* 6.0 0.4 - - - +
411C LEU* 5.9 0.2 - - - +
412C GLY 3.8 4.3 - - - -
413C ASN* 4.0 28.2 + - + +
429C ASN* 3.8 17.3 - - + +
430C TYR* 1.3 84.0 - - - +
432C TYR* 1.3 61.2 + - - +
454C ILE* 3.6 9.7 - - + +
455C SER* 3.2 6.2 + - - -
456C GLN* 2.9 37.4 + - + +
67D VAL* 3.6 40.1 - - - +
68D SER* 4.3 2.0 - - - -
77D GLU* 2.5 47.2 + - - +
79D GLN* 5.2 3.6 + - - -
105D THR* 3.8 30.7 + - - +
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Residues in contact with TYR 432 (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 LEU* 3.9 36.7 + - + -
410C THR 4.1 7.0 - - - -
411C LEU* 3.5 6.4 - - - +
412C GLY 2.8 40.8 + - - +
430C TYR* 3.7 28.9 - - + -
431C ARG* 1.3 75.2 - - - +
433C ALA* 1.3 64.3 + - - +
434C SER* 3.5 34.7 + - - -
435C PRO* 4.3 6.7 - - + +
454C ILE* 3.1 23.8 - - - -
455C SER* 4.5 3.6 - - - -
480C LYS* 5.0 7.4 - - - -
606C C8E 4.6 6.7 - - - -
609C C8E 3.6 43.3 + - - -
77D GLU* 4.9 2.0 - - - +
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Residues in contact with ALA 433 (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 THR 3.4 7.0 - - - +
411C LEU* 3.6 7.4 - - + -
432C TYR* 1.3 80.1 - - - +
434C SER* 1.3 66.2 + - - +
435C PRO* 4.0 1.0 - - - +
437C TYR* 4.9 0.9 - - + -
438C ILE* 4.4 6.3 - - + -
453C GLY* 3.3 4.2 - - - -
454C ILE* 2.9 41.9 + - + +
77D GLU* 4.4 1.3 - - - +
107D PHE* 3.4 33.4 - - + -
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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