Contacts of the helix formed by residues 389 - 405 (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 GLY 389 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C LYS* 5.5 2.4 - - - +
387C ARG 3.4 0.2 + - - -
388C ASN* 1.3 72.7 - - - +
390C THR* 1.3 63.0 + - - +
391C ASP* 3.3 5.1 + - - +
392C LYS* 3.3 14.2 + - - +
393C ASP* 3.2 18.3 + - - +
533D ARG* 4.8 1.1 - - - -
534D SER 4.0 9.0 - - - -
535D PRO 3.4 17.8 + - - -
538D GLY* 3.6 14.3 - - - -
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Residues in contact with THR 390 (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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374C ASN* 2.6 29.8 + - - +
376C LYS* 3.3 33.4 - - + -
387C ARG* 2.6 53.1 + - - +
388C ASN 3.3 0.6 + - - -
389C GLY* 1.3 76.4 - - - +
391C ASP* 1.3 67.7 + - - +
393C ASP* 3.3 10.2 + - - +
394C ALA* 2.9 24.3 + - - +
442C LEU* 3.9 5.0 - - - +
533D ARG* 4.6 0.8 - - - +
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Residues in contact with ASP 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C ASN* 3.3 22.2 + - - +
376C LYS* 2.7 36.8 + - - +
389C GLY* 3.3 1.9 - - - +
390C THR* 1.3 85.3 - - - +
392C LYS* 1.3 58.5 + - - +
394C ALA* 3.3 2.3 + - - +
395C GLU* 2.8 30.0 + - - +
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Residues in contact with LYS 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C GLY* 3.3 13.9 + - - +
390C THR 3.2 0.4 - - - -
391C ASP* 1.3 77.3 - - + +
393C ASP* 1.3 66.5 + - - +
395C GLU* 3.1 6.6 + - - +
396C ALA* 2.9 26.3 + - - +
535D PRO 5.5 1.2 + - - -
536D GLY* 3.2 30.2 + - - +
537D ARG* 4.2 17.9 - - - +
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Residues in contact with ASP 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C ARG* 4.6 6.2 + - - -
389C GLY 3.2 10.9 + - - +
390C THR* 3.3 12.9 + - - +
392C LYS* 1.3 77.7 - - - +
394C ALA* 1.3 58.6 + - - +
396C ALA* 3.2 2.8 + - - +
397C LEU* 2.8 36.8 + - - +
442C LEU* 4.3 9.2 - - + -
484C GLN* 4.8 0.2 - - - +
533D ARG* 4.7 0.9 - - - -
537D ARG 4.2 2.8 - - - +
538D GLY* 3.2 8.8 - - - -
539D SER* 2.9 48.5 + - - +
542D VAL* 3.5 27.8 - - + +
543D GLN* 4.5 1.9 + - - +
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Residues in contact with ALA 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ILE* 4.1 9.3 - - + +
374C ASN* 3.6 30.1 - - + +
390C THR 2.9 17.5 + - - +
391C ASP* 3.6 4.7 - - - +
393C ASP* 1.3 75.7 - - - +
395C GLU* 1.3 58.3 + - - +
397C LEU* 3.9 4.0 - - - +
398C PHE* 2.9 30.8 + - - +
410C VAL* 4.6 8.9 - - + +
442C LEU* 3.9 11.6 - - + +
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Residues in contact with GLU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ASP 2.8 17.9 + - - +
392C LYS* 3.5 7.6 - - - +
394C ALA* 1.3 77.9 - - - +
396C ALA* 1.3 57.9 + - - +
398C PHE* 3.4 20.0 + - - -
399C LYS* 3.0 57.1 + - + +
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Residues in contact with ALA 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C LYS 2.9 16.2 + - - +
393C ASP* 3.7 4.7 - - - +
395C GLU* 1.3 75.0 - - - +
397C LEU* 1.3 59.3 + - - +
399C LYS* 3.9 8.6 - - - +
400C CYS* 2.9 31.0 + - - +
542D VAL* 5.1 1.1 - - + -
546D CYS* 3.4 23.4 - - + +
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Residues in contact with LEU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ILE* 3.9 12.6 - - + -
393C ASP 2.8 19.5 + - - +
394C ALA* 3.9 3.6 - - - +
396C ALA* 1.3 75.2 - - - +
398C PHE* 1.3 61.2 + - - +
400C CYS* 4.2 0.4 - - - -
401C PHE* 2.8 47.9 + - + +
440C ILE* 3.4 45.8 - - + -
442C LEU* 3.7 24.2 - - + -
542D VAL* 3.7 18.8 - - + -
545D LEU* 4.3 15.3 - - + -
546D CYS* 3.9 15.7 - - - -
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Residues in contact with PHE 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ILE* 3.7 11.4 - - + +
394C ALA 2.9 18.0 + - - +
395C GLU* 3.6 27.6 - - - +
397C LEU* 1.3 76.6 - - - +
399C LYS* 1.3 75.0 + - + +
402C ARG* 2.9 72.7 + - + +
408C VAL* 3.6 29.2 - - + +
410C VAL* 4.3 11.0 - - + -
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Residues in contact with LYS 399 (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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395C GLU* 3.0 52.1 + - + +
396C ALA* 3.9 7.0 - - - +
398C PHE* 1.3 87.0 - - + +
400C CYS* 1.3 64.9 + - - +
402C ARG* 3.1 30.4 + - - +
403C SER* 2.8 24.1 + - - -
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Residues in contact with CYS 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ALA 2.9 18.0 + - - +
397C LEU 3.5 4.0 - - - +
399C LYS* 1.3 75.1 - - - +
401C PHE* 1.3 69.2 + - + +
403C SER* 2.9 29.2 + - - -
404C LEU* 3.0 12.3 + - - +
546D CYS* 3.6 46.4 - - - -
549D LEU* 3.9 15.5 - - + -
550D GLU* 3.9 16.4 - - - -
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Residues in contact with PHE 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C CYS* 3.4 33.2 - - - -
397C LEU* 2.8 36.6 + - + +
398C PHE* 5.1 0.2 - - - -
400C CYS* 1.3 75.5 - - + +
402C ARG* 1.3 65.2 + - - +
404C LEU* 3.3 14.6 + - + +
405C GLY 3.3 0.2 + - - -
406C PHE* 3.1 51.9 + + + +
408C VAL* 3.8 7.9 - - + -
438C ALA* 4.3 4.7 - - + -
440C ILE* 3.7 20.2 - - + -
482C PHE* 3.7 38.1 - + - -
545D LEU* 4.9 1.1 - - + -
549D LEU* 3.7 26.5 - - + -
601D PHE* 5.6 2.2 - + - -
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Residues in contact with ARG 402 (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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398C PHE* 2.9 57.3 + - + +
399C LYS* 3.5 28.5 + - - +
401C PHE* 1.3 74.6 - - - +
403C SER* 1.3 58.3 - - - +
405C GLY* 2.9 21.7 + - - -
406C PHE 3.7 7.4 + - - +
408C VAL* 3.5 13.6 - - + +
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Residues in contact with SER 403 (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 LYS 2.8 13.3 + - - -
400C CYS* 2.9 17.3 - - - -
402C ARG* 1.3 79.1 - - - +
404C LEU* 1.3 61.3 + - - +
405C GLY* 3.2 1.4 + - - -
554D LYS* 3.0 27.8 + - - -
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Residues in contact with LEU 404 (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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367C LEU* 3.4 14.1 - - + +
400C CYS 3.0 16.1 + - - +
401C PHE* 3.7 18.6 - - + +
402C ARG 3.2 0.6 - - - -
403C SER* 1.3 77.4 - - - +
405C GLY* 1.3 58.1 + - - +
406C PHE* 3.6 31.0 - - + -
549D LEU* 4.5 17.0 - - + +
553D GLY* 4.0 34.5 - - - +
554D LYS* 4.0 19.0 - - + +
601D PHE* 3.6 34.8 - - + +
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Residues in contact with GLY 405 (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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366C LYS* 5.5 2.1 - - - +
367C LEU* 3.6 23.7 + - - +
368C GLY 4.5 0.5 + - - -
402C ARG 2.9 12.5 + - - -
403C SER 3.1 1.3 - - - -
404C LEU* 1.3 80.3 - - - +
406C PHE* 1.3 63.5 + - - +
407C ASP* 4.0 3.3 + - - +
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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