Contacts of the strand formed by residues 411 - 429 (chain C) in PDB entry 1XKH
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 VAL 411 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C GLU* 4.8 12.1 - - + +
404C HIS 3.0 25.4 - - - +
405C ASN* 3.6 19.7 - - - +
406C PHE* 4.3 1.6 - - - +
409C GLY 5.8 0.7 - - - +
410C TRP* 1.3 81.3 - - - +
412C GLY* 1.3 63.4 + - - +
413C LYS* 4.9 2.2 - - + +
460C TYR* 6.1 0.9 - - + -
461C LEU* 4.4 0.7 - - - -
462C THR* 3.1 46.1 + - + +
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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
----------------------------------------------------------
402C LEU 4.3 0.9 - - - +
403C GLU* 3.7 0.5 - - - -
404C HIS* 2.9 38.6 + - - +
406C PHE* 4.3 6.0 - - - -
411C VAL* 1.3 75.7 - - - +
413C LYS* 1.3 60.1 + - - -
414C VAL* 4.3 2.4 + - - +
460C TYR 3.1 11.2 - - - -
461C LEU* 3.3 19.6 - - - +
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Residues in contact with LYS 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLN* 3.9 23.9 - - - +
137C LEU* 5.8 2.9 - - + -
347C THR* 5.5 0.6 - - - +
401C ASN* 4.1 18.8 + - - +
402C LEU 4.0 4.7 - - - +
403C GLU* 3.1 44.3 + - + +
411C VAL* 4.4 2.4 + - + +
412C GLY* 1.3 72.8 - - - -
414C VAL* 1.3 72.1 + - - +
415C GLN* 4.2 17.0 - - + +
458C ASP 3.8 0.9 - - - +
459C ILE* 3.2 3.5 - - - +
460C TYR* 2.8 82.6 + - + +
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Residues in contact with VAL 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C ASN* 3.2 4.0 - - - +
402C LEU* 2.8 62.8 + - + +
412C GLY 5.2 1.6 - - - +
413C LYS* 1.3 76.7 - - - +
415C GLN* 1.3 63.6 + - - +
416C LEU* 4.6 15.9 - - + -
457C LEU* 4.9 1.6 - - + -
458C ASP 3.6 3.4 - - - -
459C ILE* 3.2 27.1 - - + -
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Residues in contact with GLN 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ARG* 4.9 3.3 + - - -
220C ASP* 4.2 13.5 + - - +
221C GLY* 5.7 0.7 - - - -
222C ILE* 3.8 34.3 - - + +
399C PHE* 6.2 1.6 - - - +
400C ALA 3.5 0.7 - - - +
401C ASN* 3.3 29.5 - - + +
413C LYS* 4.2 15.2 - - + +
414C VAL* 1.3 74.9 - - - +
416C LEU* 1.3 71.6 + - - +
417C ASP* 6.0 1.2 - - - +
456C SER 3.3 4.0 - - - +
457C LEU* 3.8 0.2 - - - +
458C ASP* 3.0 51.5 + - + +
460C TYR* 4.2 16.3 - - - -
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Residues in contact with LEU 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C PHE* 3.6 3.9 - - - +
400C ALA* 2.8 45.3 + - + +
414C VAL* 4.6 9.4 - - + -
415C GLN* 1.3 81.2 + - - +
417C ASP* 1.3 65.3 + - - +
456C SER 3.4 3.1 - - - -
457C LEU* 2.6 41.7 - - + -
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Residues in contact with ASP 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ILE* 4.5 28.6 - - + +
270C ARG* 5.3 4.5 + - - -
397C THR* 4.0 10.7 + - - -
398C VAL 3.6 8.1 - - - +
399C PHE* 4.3 9.6 - - + +
415C GLN* 5.5 2.0 - - - +
416C LEU* 1.3 78.4 - - - +
418C HIS* 1.3 70.0 + - - +
419C LYS* 3.8 11.1 + - - +
454C SER* 4.3 1.2 - - - +
455C ASN* 3.1 7.2 - - - +
456C SER* 2.7 53.6 + - - +
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Residues in contact with HIS 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C THR* 2.9 3.6 + - - -
398C VAL* 2.7 60.3 + - + +
417C ASP* 1.3 73.2 + - - +
419C LYS* 1.3 60.1 + - - +
420C ILE* 4.1 12.2 - - + +
453C LYS* 3.4 45.9 + - + +
454C SER 3.3 6.1 + - - -
455C ASN* 3.5 21.7 + - - +
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Residues in contact with LYS 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C TYR* 3.4 49.6 - - + +
223C PRO 5.8 0.9 - - - +
224C SER* 5.0 12.3 - - - -
270C ARG* 3.9 4.6 - - - +
351C ASP* 5.1 0.6 + - - -
395C THR* 5.1 8.9 + - - -
396C ARG 3.8 3.1 - - - +
397C THR* 3.3 41.2 + - - +
417C ASP* 3.8 11.3 + - - +
418C HIS* 1.3 72.1 - - - +
420C ILE* 1.3 71.5 + - - +
421C ASN* 3.8 26.9 - - - +
452C THR 3.9 0.5 - - - +
453C LYS* 3.4 0.9 - - - -
454C SER* 2.9 38.6 + - - +
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Residues in contact with ILE 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C TYR* 4.0 5.3 - - + +
395C THR* 3.3 23.4 - - - -
396C ARG* 3.0 51.6 + - + +
418C HIS* 4.1 11.9 - - + +
419C LYS* 1.3 88.2 - - - +
421C ASN* 1.3 64.2 + - - +
422C GLY 4.0 0.4 - - - -
451C GLU* 4.0 26.2 - - + +
452C THR 3.4 7.9 - - - +
453C LYS* 3.3 42.8 - - + +
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Residues in contact with ASN 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C TYR* 5.3 1.2 + - - -
224C SER* 5.5 3.1 - - - -
225C THR 5.6 0.9 + - - -
226C ALA* 3.8 23.3 + - + +
233C ALA* 3.5 24.7 + - + +
234C GLY* 4.8 0.8 - - - -
235C ASN* 4.7 6.9 + - - -
394C TYR 3.8 5.2 - - - -
395C THR* 3.3 22.6 - - - +
419C LYS* 3.8 26.1 - - - +
420C ILE* 1.3 77.9 - - - +
422C GLY* 1.3 61.0 + - - +
423C TYR* 4.8 1.6 - - - -
450C GLY 4.1 0.7 - - - +
451C GLU* 3.7 1.1 - - - -
452C THR* 2.6 51.0 + - + +
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Residues in contact with GLY 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ALA* 3.1 14.4 - - - +
394C TYR* 3.0 59.6 + - - -
421C ASN* 1.3 75.0 - - - +
423C TYR* 1.3 61.3 + - - -
450C GLY 3.0 10.1 - - - -
451C GLU* 3.6 3.3 - - - +
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Residues in contact with TYR 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 3.8 39.1 - - + -
232C SER 3.7 9.9 - - - +
233C ALA* 3.6 16.2 - - + -
391C TRP* 4.6 5.4 - + - +
392C GLU 3.4 7.4 - - - +
394C TYR* 3.8 4.4 - - - -
421C ASN 4.8 3.6 - - - -
422C GLY* 1.3 76.6 - - - +
424C HIS* 1.3 58.5 + - - +
425C ALA* 4.5 4.0 - - + +
448C TYR* 3.3 20.9 - - + -
449C THR* 3.0 40.7 + - - -
450C GLY* 2.4 46.0 + - - -
452C THR* 5.7 1.8 - - + -
485C TRP* 3.7 31.3 + + - -
487C GLY* 4.3 0.7 - - - -
488C LYS 3.8 6.4 + - - -
522C ILE* 4.1 4.7 - - - +
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Residues in contact with HIS 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C SER* 5.0 0.7 + - - -
392C GLU* 2.5 61.1 + - + +
394C TYR* 4.9 4.9 - - + -
423C TYR* 1.3 71.4 - - - +
425C ALA* 1.3 58.3 + - - +
426C PRO* 3.0 23.2 - - + +
447C LYS* 4.4 12.0 + - + -
448C TYR 3.9 1.1 - - - -
449C THR* 4.7 7.9 - - - +
2003C SO4 3.4 36.8 + - - -
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Residues in contact with ALA 425 (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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390C SER 3.8 2.7 - - - -
391C TRP* 3.8 38.8 - - + +
423C TYR* 4.8 2.9 - - + -
424C HIS* 1.3 74.4 - - - +
426C PRO* 1.3 58.1 - - - +
427C LEU* 3.4 12.3 + - + -
446C GLN 3.7 0.7 - - - +
447C LYS* 3.1 4.0 - - - -
448C TYR* 2.4 60.9 + - + +
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Residues in contact with PRO 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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358C LYS* 5.5 2.9 - - - +
388C TRP* 3.0 27.6 - - + +
389C SER* 3.7 5.0 - - - -
390C SER* 3.0 26.9 - - - +
424C HIS* 3.0 27.4 - - + +
425C ALA* 1.3 83.5 - - - +
427C LEU* 1.3 59.4 + - - +
446C GLN 3.4 4.9 - - - +
447C LYS* 3.7 12.6 - - + -
512C LYS* 5.1 2.7 - - - -
515C TRP* 3.9 10.8 - - + -
2003C SO4 3.5 26.9 - - - +
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Residues in contact with LEU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C SER* 4.4 5.4 - - - +
361C GLY 5.1 0.2 - - - +
362C TRP* 3.4 50.5 - - + -
388C TRP* 3.5 5.7 - - - -
389C SER* 3.2 8.5 - - - +
390C SER 3.4 24.7 - - - +
391C TRP* 3.3 46.7 - - + -
425C ALA* 4.2 10.5 - - + +
426C PRO* 1.3 74.6 - - - +
428C GLY* 1.3 59.6 + - - +
429C ALA 4.3 0.2 - - - -
444C VAL 5.0 0.4 - - - -
445C ALA* 3.5 2.6 - - - -
446C GLN 2.6 39.9 + - - +
448C TYR* 4.9 6.5 - - + -
515C TRP* 3.6 1.0 - - - -
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Residues in contact with GLY 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C SER 4.1 0.2 - - - +
385C GLY* 3.4 0.7 - - - -
386C ALA* 2.6 37.7 + - - +
388C TRP* 3.3 22.0 - - - -
389C SER* 2.5 17.1 + - - -
427C LEU* 1.3 76.1 - - - +
429C ALA* 1.3 58.8 + - - +
443C ILE* 5.2 1.8 - - - -
444C VAL 4.0 5.8 - - - -
445C ALA* 4.4 1.8 - - - -
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Residues in contact with ALA 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C TRP* 3.8 30.6 - - + +
384C ASN* 3.0 33.2 - - - +
385C GLY* 4.1 0.9 - - - -
386C ALA* 5.1 0.2 - - - -
428C GLY* 1.3 75.7 - - - +
430C ILE* 1.3 62.0 + - - +
431C MSE 3.7 3.4 + - + -
443C ILE* 3.2 10.7 - - - +
444C VAL* 2.9 36.2 + - - +
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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
------------------------------------------------------------
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