Contacts of the helix formed by residues 411 - 429 (chain C) in PDB entry 1QZW
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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400C MET* 5.4 8.7 - - + -
401C ARG* 5.1 20.4 - - + -
404C ALA* 4.0 18.1 - - + +
409C LEU 3.0 6.4 + - - -
410C GLU* 1.3 91.7 - - + +
412C GLU* 1.3 67.4 + - + +
413C GLU* 2.5 16.6 + - - +
414C VAL* 2.9 20.5 + - + +
415C ARG* 5.2 14.6 - - + +
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Residues in contact with GLU 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C GLU* 3.0 28.1 - - - +
411C VAL* 1.3 82.5 - - + +
413C GLU* 1.3 73.2 + - - +
414C VAL 2.5 3.3 + - - -
415C ARG* 3.0 6.4 + - - +
416C GLU* 2.7 47.5 + - - +
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Residues in contact with GLU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ARG* 3.9 21.1 - - - +
377C TRP* 3.9 7.7 - - + -
409C LEU* 3.2 26.6 - - + +
410C GLU* 2.4 58.2 + - - +
411C VAL 2.5 3.7 + - - +
412C GLU* 1.3 76.5 - - - +
414C VAL* 1.3 56.6 + - + +
416C GLU* 2.7 33.8 + - - +
417C LEU* 2.9 12.5 - - + +
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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
----------------------------------------------------------
395C ILE* 5.7 0.2 - - + -
400C MET* 4.5 17.7 - - + +
403C ILE* 6.1 6.3 - - + -
404C ALA* 4.4 24.2 - - + +
407C SER* 5.5 1.8 - - - +
409C LEU* 4.8 8.1 - - + +
411C VAL* 2.9 16.0 + - + +
412C GLU 2.5 4.2 + - - -
413C GLU* 1.3 72.9 - - + +
415C ARG* 1.3 72.1 + - - +
416C GLU 2.7 0.7 - - - -
417C LEU* 2.4 51.2 + - + +
418C LEU* 2.9 17.3 + - + -
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Residues in contact with ARG 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C LYS* 6.0 4.8 - - - +
400C MET* 4.6 13.4 - - + +
411C VAL* 4.5 11.0 + - + +
412C GLU* 3.0 12.2 + - - +
414C VAL* 1.3 77.1 - - - +
416C GLU* 1.3 51.8 + - + +
417C LEU 2.5 1.0 + - - -
418C LEU* 3.1 23.7 + - + +
419C GLU* 2.4 39.5 - - - +
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Residues in contact with GLU 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TRP* 3.4 9.2 - - - -
412C GLU* 2.7 47.8 + - - +
413C GLU* 2.7 16.5 - - - +
415C ARG* 1.3 75.5 - - + +
417C LEU* 1.3 59.9 + - - +
419C GLU* 3.5 9.2 - - - -
420C TRP* 4.2 12.3 + - + -
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Residues in contact with LEU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ARG 5.8 0.4 - - - +
377C TRP* 3.0 37.2 - - + +
409C LEU* 6.3 1.6 - - + -
413C GLU* 2.9 19.5 - - + +
414C VAL* 2.4 43.2 + - + +
415C ARG 2.5 9.5 + - - -
416C GLU* 1.3 71.7 - - - +
418C LEU* 1.3 76.3 + - + +
419C GLU* 2.5 10.7 + - - -
420C TRP* 2.5 33.4 + - - -
421C TYR* 2.5 48.2 - - + +
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Residues in contact with LEU 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C ILE* 3.9 35.7 - - + +
400C MET* 4.0 9.9 - - + -
414C VAL* 3.0 21.1 - - + +
415C ARG* 3.2 32.3 - - + +
417C LEU* 1.3 95.4 - - + +
419C GLU* 1.3 60.8 + - + +
421C TYR* 3.0 28.4 - - + +
422C ASN* 2.9 26.1 + - - +
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Residues in contact with GLU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C ARG 2.4 33.5 - - - +
416C GLU* 3.6 5.0 - - - -
417C LEU* 2.5 18.3 + - - -
418C LEU* 1.3 67.6 - - + -
420C TRP* 1.3 80.0 + - + +
421C TYR 2.4 17.7 + - - -
422C ASN* 3.9 9.9 - - + +
423C ASN* 2.6 35.3 + - + +
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Residues in contact with TRP 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TRP* 3.7 27.1 - + - +
416C GLU* 4.2 10.6 + - + -
417C LEU* 2.5 20.0 + - - +
419C GLU* 1.3 102.8 - - + +
421C TYR* 1.3 69.8 + - + +
423C ASN* 5.0 9.9 - - + -
424C MET* 3.6 18.6 - - - +
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Residues in contact with TYR 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LEU* 4.4 18.6 - - + +
332C VAL* 6.0 10.5 - - + -
377C TRP* 3.0 40.5 + + - -
381C LEU* 6.5 0.9 - - + -
392C PRO* 6.1 0.7 - - + -
417C LEU* 2.5 64.6 - - + +
418C LEU* 3.0 23.8 - - + +
419C GLU 2.4 1.0 + - - -
420C TRP* 1.3 95.8 - - + +
422C ASN* 1.3 57.0 + - - +
423C ASN 3.1 3.8 - - - -
424C MET* 3.7 6.4 - - - +
425C ASN* 2.7 30.9 + - - +
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Residues in contact with ASN 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LEU* 4.4 3.1 - - - +
392C PRO* 3.4 32.7 + - - +
393C ASN* 4.4 4.1 - - - +
395C ILE* 5.4 2.8 - - - +
418C LEU* 2.9 27.0 + - - +
419C GLU* 2.9 8.1 + - + +
421C TYR* 1.3 76.9 - - - +
423C ASN* 1.3 55.0 + - - +
425C ASN* 2.5 25.7 + - - +
426C ARG* 3.0 22.3 - - - -
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Residues in contact with ASN 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C GLU* 2.6 30.3 + - + +
420C TRP* 5.0 9.7 - - + -
422C ASN* 1.3 73.7 - - - +
424C MET* 1.3 70.9 + - - +
425C ASN* 2.7 1.8 - - - -
426C ARG* 2.7 39.1 + - - +
427C LEU* 2.7 47.7 + - + +
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Residues in contact with MET 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C GLN* 4.1 19.1 - - - +
355C LEU* 4.1 3.8 - - + +
356C GLY* 3.3 35.9 - - - +
357C ILE* 6.0 0.2 - - - -
419C GLU 3.8 2.0 + - - -
420C TRP* 3.6 21.8 - - - +
421C TYR* 3.7 9.4 + - - +
423C ASN* 1.3 81.5 - - - +
425C ASN* 1.3 54.3 + - + +
427C LEU* 3.0 6.7 + - - +
428C LEU* 2.4 60.3 + - + +
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Residues in contact with ASN 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LEU* 5.0 9.5 - - + +
421C TYR 2.7 11.0 + - - +
422C ASN* 2.5 49.0 - - - +
423C ASN 2.7 4.0 - - - -
424C MET* 1.3 72.3 - - + +
426C ARG* 1.3 63.4 + - - +
428C LEU* 2.4 28.0 + - + -
429C LYS* 2.3 49.3 + - + +
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Residues in contact with ARG 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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422C ASN* 3.0 19.0 - - - -
423C ASN* 2.7 42.6 + - - +
425C ASN* 1.3 78.5 - - - +
427C LEU* 1.3 64.5 + - + +
429C LYS* 2.7 34.4 - - + +
430C MET* 3.6 9.5 + - - +
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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
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360C PRO 6.0 1.8 - - - +
362C PRO* 5.3 16.8 - - + -
423C ASN* 2.7 40.7 + - + +
424C MET* 3.4 5.8 - - - +
425C ASN 2.7 4.1 + - - -
426C ARG* 1.3 81.0 - - + +
428C LEU* 1.3 55.1 + - - +
430C MET* 2.3 43.5 + - - +
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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
----------------------------------------------------------
314C GLN* 4.8 16.6 - - + +
315C LYS* 3.5 26.7 - - - +
357C ILE* 4.7 15.9 - - + -
359C LEU* 5.3 14.5 - - + +
424C MET* 2.4 63.8 + - + +
425C ASN* 2.4 16.3 + - + +
427C LEU* 1.3 65.4 - - - +
429C LYS* 1.3 77.1 + - + +
430C MET* 2.5 17.7 + - - -
431C VAL* 4.8 4.5 - - - +
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Residues in contact with LYS 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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315C LYS 4.9 4.3 - - - +
425C ASN* 2.3 30.4 + - + +
426C ARG* 2.7 51.8 - - + +
428C LEU* 1.3 78.3 - - + +
430C MET* 1.3 57.2 + - - +
431C VAL* 2.6 26.7 + - - +
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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