Contacts of the strand formed by residues 409 - 419 (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 LEU 409 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PRO* 5.6 3.4 - - + -
400C ALA* 4.2 5.4 - - + -
401C GLN 3.3 17.9 - - - +
402C TYR* 3.5 38.8 - - + +
407C GLY 3.6 8.5 - - - +
408C SER* 1.3 83.3 + - - +
410C THR* 1.3 59.3 + - - +
411C LEU 3.4 17.3 - - - +
412C GLY* 5.0 0.7 - - - -
432C TYR* 3.9 23.8 + - + -
434C SER* 3.7 15.1 + - - -
609C C8E 3.2 45.8 - - - +
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Residues in contact with THR 410 (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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401C GLN* 2.9 25.7 + - - +
402C TYR* 4.2 0.7 + - - -
403C ASP* 4.0 13.6 - - + +
406C LEU* 4.0 29.2 - - + +
408C SER 3.6 14.1 - - - +
409C LEU* 1.3 76.7 - - - +
411C LEU* 1.3 71.8 + - - +
432C TYR* 4.1 2.6 - - - -
433C ALA* 3.4 3.5 - - - -
434C SER* 2.8 32.6 + - - -
437C TYR* 3.6 32.1 - - + +
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Residues in contact with LEU 411 (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* 3.3 34.3 - - - +
400C ALA* 3.4 1.5 - - - -
401C GLN* 2.9 56.7 + - + +
409C LEU* 3.4 11.2 - - - +
410C THR* 1.3 82.4 + - - +
412C GLY* 1.3 57.9 + - - +
413C ASN* 5.8 3.6 - - - +
431C ARG* 5.9 0.2 - - - +
432C TYR* 3.5 7.4 - - - +
433C ALA* 3.6 28.3 - - + -
437C TYR* 3.5 22.7 - - + -
77D GLU* 3.8 9.0 - - - +
107D PHE* 3.6 14.8 - - + -
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Residues in contact with GLY 412 (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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399C GLY 3.3 11.0 - - - -
400C ALA* 4.1 3.1 - - - -
409C LEU* 5.0 1.6 - - - -
411C LEU* 1.3 77.3 - - - +
413C ASN* 1.3 67.0 + - - +
430C TYR* 5.7 0.2 - - - -
432C TYR* 2.8 35.9 + - - +
609C C8E 4.0 20.0 - - - -
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Residues in contact with ASN 413 (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* 6.2 0.4 - - - +
397C LYS* 6.1 1.2 - - - -
398C GLY* 3.2 3.6 - - - -
399C GLY* 2.9 45.9 + - - +
401C GLN* 6.2 0.2 - - - +
411C LEU* 5.6 3.8 - - - +
412C GLY* 1.3 79.9 + - - +
414C ALA* 1.3 64.3 + - - +
415C ILE* 5.8 2.6 - - - +
430C TYR* 3.2 15.0 - - - +
431C ARG* 4.0 37.0 + - - +
609C C8E 3.6 10.2 - - - -
105D THR* 5.1 4.8 + - - -
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Residues in contact with ALA 414 (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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213A LEU* 4.5 10.3 - - + -
601A C8E 3.7 28.9 - - + -
396C LEU* 5.4 3.6 - - + -
397C LYS 3.5 6.3 - - - +
398C GLY* 4.1 0.2 - - - -
413C ASN* 1.3 77.4 - - - +
415C ILE* 1.3 62.8 + - - +
429C ASN* 3.2 3.1 - - - +
430C TYR* 2.9 39.0 + - + +
609C C8E 4.5 3.1 - - - -
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Residues in contact with ILE 415 (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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396C LEU* 3.6 4.8 - - - +
397C LYS* 2.9 65.6 + - + +
413C ASN* 5.8 2.5 - - - +
414C ALA* 1.3 78.3 - - - +
416C MET* 1.3 63.0 + - - +
417C GLU* 5.2 0.2 - - + -
427C GLN* 3.5 36.8 - - + +
428C LEU 3.2 18.4 - - - +
429C ASN* 3.9 9.0 - - + +
553C GLN 5.3 0.7 - - - +
555C ALA* 3.6 24.2 - - + +
556C PHE* 3.9 2.5 - - + -
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Residues in contact with MET 416 (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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261A PHE* 3.7 33.7 - - + -
263A VAL* 4.4 12.8 - - + -
603A C8E 5.9 0.7 - - - +
605A C8E 3.9 20.4 - - - +
394C LEU* 4.0 15.7 - - + -
395C GLY 3.4 12.6 - - - +
396C LEU* 3.9 13.7 - - + -
415C ILE* 1.3 75.6 - - - +
417C GLU* 1.3 66.4 + - - +
418C TYR 5.3 0.7 - - - +
426C ILE* 4.9 5.2 - - + +
427C GLN* 3.3 4.3 - - - +
428C LEU* 2.9 73.7 + - + +
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Residues in contact with GLU 417 (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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393C GLN 3.6 2.9 - - - +
394C LEU* 4.0 4.7 - - - -
395C GLY* 2.9 34.3 + - - -
415C ILE* 5.2 0.2 - - + -
416C MET* 1.3 76.4 - - - +
418C TYR* 1.3 68.2 + - - +
419C ARG* 3.7 18.5 - - + +
425C MET* 4.1 3.7 - - + +
426C ILE 3.3 11.9 - - - +
427C GLN* 2.8 28.9 - - + +
552C TYR* 2.9 23.9 + - - -
554C SER* 3.8 3.5 + - - -
555C ALA* 2.9 30.3 + - + +
556C PHE* 3.9 16.0 - - + -
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Residues in contact with TYR 418 (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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289A TYR* 6.0 0.9 - - - -
605A C8E 3.3 70.0 - - - -
391C ASN* 5.0 3.1 - - - -
393C GLN* 3.3 41.0 - - + +
394C LEU* 3.8 19.0 - - + +
416C MET* 5.3 1.4 - - + +
417C GLU* 1.3 76.0 - - - +
419C ARG* 1.3 67.6 + - - +
420C LYS* 3.7 29.8 - - + +
424C ARG* 4.7 3.2 - - + -
425C MET* 3.3 3.1 - - - +
426C ILE* 2.9 37.4 + - + +
463C TRP* 3.9 28.7 - + - -
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Residues in contact with ARG 419 (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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392C ASP 5.1 0.2 - - - +
393C GLN* 3.1 28.5 + - - +
417C GLU* 3.7 13.2 - - + +
418C TYR* 1.3 81.4 - - - +
420C LYS* 1.3 62.1 + - - +
421C ASP 3.7 19.3 + - - +
422C ALA* 4.6 11.5 - - - +
424C ARG 3.3 14.1 + - - +
425C MET* 4.1 15.9 - - + +
552C TYR* 3.0 31.4 + - - -
554C SER* 3.4 18.9 + - - -
555C ALA 6.0 0.2 - - - -
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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