Contacts of the helix formed by residues 420 - 439 (chain B) in PDB entry 6R7H
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 ARG 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B GLY* 5.8 0.2 - - - -
418B GLY 4.6 0.6 - - - +
419B ALA* 1.3 78.8 - - + +
421B TYR* 1.3 73.8 + - + +
422B THR 3.2 2.2 - - - -
423B ALA* 3.4 15.8 + - - +
424B LEU* 3.8 16.2 + - + +
255E LEU* 5.7 4.6 + - - +
256E LEU* 6.2 1.2 - - - +
259E ALA* 5.3 10.5 - - - +
263E THR* 3.8 29.4 + - + +
282F GLN* 4.5 20.8 + - - +
285F ASP* 3.4 40.6 + - - +
286F VAL* 5.3 6.7 - - - +
289F MET* 5.1 17.4 - - + +
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLN* 3.7 36.3 - - + +
432A ARG* 3.3 48.5 + - + +
435A THR* 4.3 15.2 - - + +
436A PHE* 5.1 5.8 - + - -
417B GLY* 3.3 45.3 - - - +
418B GLY* 4.2 0.9 - - - -
419B ALA 3.7 1.0 - - - +
420B ARG* 1.3 85.4 - - + +
422B THR* 1.3 60.6 + - - +
423B ALA 3.2 1.3 + - - -
424B LEU* 3.5 20.7 + - + +
425B ASP* 3.5 20.4 + - - +
281F ASP* 4.7 2.3 + - - -
285F ASP* 3.8 18.2 + - - -
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Residues in contact with THR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLN* 5.7 0.9 - - - +
418B GLY* 3.4 24.6 + - - +
419B ALA* 3.4 17.0 - - - +
421B TYR* 1.3 77.4 - - - +
423B ALA* 1.3 59.7 + - - +
425B ASP* 4.2 9.9 + - - +
426B LYS* 3.9 32.2 + - - +
267E PHE* 3.8 18.1 - - + -
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Residues in contact with ALA 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ARG* 3.4 11.3 + - + +
421B TYR 3.2 0.8 - - - -
422B THR* 1.3 77.9 - - - +
424B LEU* 1.3 65.4 + - + +
425B ASP 3.3 2.0 - - - -
426B LYS* 3.5 7.4 + - - +
427B TRP* 3.2 22.5 + - - +
263E THR* 4.8 6.3 - - + +
266E VAL* 3.7 34.7 - - + +
267E PHE* 4.3 22.9 - - + -
270E SER* 5.1 0.9 + - - -
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A THR* 3.8 26.0 - - + -
436A PHE* 4.9 8.1 - - + -
439A SER* 4.5 0.8 + - - +
420B ARG* 3.9 19.1 - - + +
421B TYR* 3.5 12.8 + - + +
423B ALA* 1.3 79.2 - - + +
425B ASP* 1.3 59.7 + - - +
427B TRP* 3.5 8.6 + - + +
428B THR* 2.7 34.1 + - - -
266E VAL* 5.3 3.4 - - + -
285F ASP* 5.3 6.1 - - - +
288F LEU* 3.8 26.7 - - + -
289F MET* 4.7 27.1 - - + -
292F LEU* 4.3 17.1 - - + +
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Residues in contact with ASP 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLN* 5.0 8.0 + - - -
434A THR* 5.1 3.1 - - - +
435A THR* 3.8 24.0 + - - +
438A LYS* 3.3 34.4 + - - +
421B TYR 3.5 14.6 + - - +
422B THR* 4.4 8.8 - - - +
423B ALA 3.3 0.6 - - - -
424B LEU* 1.3 80.0 - - - +
426B LYS* 1.3 62.0 + - + +
428B THR* 3.5 3.9 + - - -
429B ASN* 3.3 22.5 + - - +
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Residues in contact with LYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B THR* 3.9 24.9 - - - +
423B ALA* 3.5 8.5 + - - +
424B LEU 3.4 0.2 - - - -
425B ASP* 1.3 77.3 - - + +
427B TRP* 1.3 64.2 - - - +
429B ASN* 4.0 5.0 - - - +
430B GLN* 3.2 30.6 + - + +
267E PHE* 5.0 18.4 - - + -
270E SER* 3.7 23.8 - - - +
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Residues in contact with TRP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B ALA 3.2 16.1 + - - +
424B LEU* 3.9 9.0 - - + +
425B ASP 3.3 0.2 - - - -
426B LYS* 1.3 76.6 - - - +
428B THR* 1.3 61.5 + - - +
430B GLN* 4.7 1.1 - - - -
431B LEU* 3.2 39.7 + - + +
266E VAL* 4.4 18.4 - - + -
269E LEU* 3.6 28.9 - - + +
270E SER* 4.5 4.9 + - - +
273E LEU* 3.6 24.3 - - + +
307E SER* 3.8 17.2 + - - -
310E THR* 3.9 17.7 - - - -
311E THR* 4.4 0.9 - - - -
289F MET* 3.6 30.1 - - + -
292F LEU* 3.5 38.8 - - + -
293F GLY* 3.8 18.8 - - - -
296F THR* 4.2 0.4 - - - -
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Residues in contact with THR 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LYS* 4.3 26.9 - - + +
439A SER* 3.2 20.1 + - - +
442A MET* 3.8 41.6 - - + +
424B LEU 2.7 23.2 + - - -
425B ASP* 3.9 5.5 - - - -
426B LYS 3.3 0.2 - - - -
427B TRP* 1.3 75.5 - - - +
429B ASN* 1.3 60.0 + - - +
431B LEU 3.5 0.7 + - - -
432B ASN* 3.0 28.1 + - - +
292F LEU* 4.4 5.1 - - - +
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Residues in contact with ASN 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ASP 3.3 14.2 + - - +
426B LYS* 4.0 5.6 - - - +
427B TRP 3.4 0.2 - - - -
428B THR* 1.3 80.0 - - - +
430B GLN* 1.3 72.5 + - - +
432B ASN* 3.5 6.8 + - - +
433B SER* 3.3 22.5 + - - -
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Residues in contact with GLN 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B LYS* 3.2 20.4 + - + +
427B TRP 4.2 0.9 - - - +
429B ASN* 1.3 90.0 - - - +
431B LEU* 1.3 61.7 + - - +
433B SER* 3.3 10.1 + - - -
434B LEU* 3.2 24.1 + - - +
270E SER* 4.5 12.6 - - - +
273E LEU* 3.8 36.0 - - + +
274E GLU* 3.4 46.1 + - + +
277E GLU* 5.0 3.5 - - - +
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Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A MET* 3.8 14.8 - - + -
446A PHE* 3.7 19.6 - - + -
427B TRP* 3.2 49.3 + - + +
429B ASN 3.4 0.2 - - - -
430B GLN* 1.3 74.4 - - - +
432B ASN* 1.3 63.0 + - - +
433B SER 3.5 0.2 - - - -
434B LEU* 3.8 22.7 - - + +
435B ASN* 3.3 16.1 + - - +
273E LEU* 4.8 5.8 - - + -
292F LEU* 3.6 26.9 - - + +
295F ILE* 3.8 19.1 - - + -
296F THR* 3.8 24.2 - - + +
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Residues in contact with ASN 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A MET* 3.5 26.9 - - + +
445A GLU* 5.9 1.4 - - - +
449A ARG* 3.9 21.7 + - - +
428B THR* 3.0 19.3 + - + +
429B ASN* 3.9 9.9 - - - +
430B GLN 3.3 0.4 - - - -
431B LEU* 1.3 78.3 - - - +
433B SER* 1.3 63.2 + - - +
434B LEU 3.5 0.2 + - - -
435B ASN* 3.6 12.0 + - - +
436B GLN* 3.7 15.8 + - - +
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Residues in contact with SER 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B ASN 3.3 11.1 + - - -
430B GLN* 3.3 20.8 + - - -
432B ASN* 1.3 78.1 + - - +
434B LEU* 1.3 62.8 + - - +
435B ASN 3.4 0.2 - - - -
436B GLN* 3.5 16.9 + - - +
437B ALA* 3.6 10.0 + - - +
243C LYS* 5.3 1.4 + - - -
277E GLU* 3.3 22.7 + - - +
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A PHE* 5.9 1.3 - - + -
430B GLN 3.2 18.6 + - - +
431B LEU* 4.0 24.2 - - + +
432B ASN 3.3 0.6 - - - -
433B SER* 1.3 76.9 + - - +
435B ASN* 1.3 64.9 + - - +
437B ALA* 3.3 3.8 + - + +
438B VAL* 3.3 25.1 + - + +
273E LEU* 4.6 16.2 - - + +
276E SER* 4.9 14.6 - - - +
277E GLU* 3.7 14.6 - - - +
280E LEU* 4.8 9.0 - - + -
300E LEU* 3.9 37.2 - - + -
296F THR* 5.5 4.0 - - + -
299F CYS* 4.3 18.8 - - + -
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Residues in contact with ASN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A PHE* 3.4 52.1 + - + -
449A ARG* 3.1 47.0 + - - +
450A ALA* 5.5 1.0 - - - +
431B LEU 3.3 8.3 + - - +
432B ASN 4.0 4.9 - - - +
433B SER 3.4 0.4 - - - -
434B LEU* 1.3 78.5 - - - +
436B GLN* 1.3 59.9 + - - +
438B VAL* 3.4 14.4 - - - +
439B VAL* 3.4 26.5 + - - +
299F CYS* 5.4 0.2 - - - -
302F MET* 4.4 11.1 - - - +
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Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A ARG* 4.4 15.7 + - - +
432B ASN* 3.7 14.2 + - - +
433B SER* 3.5 12.6 + - - +
434B LEU 3.2 0.8 - - - -
435B ASN* 1.3 78.5 - - - +
437B ALA* 1.3 59.2 + - - +
439B VAL* 3.6 8.5 - - + +
440B SER* 2.8 28.1 + - - +
240C GLN* 4.3 26.8 + - - +
241C LEU 4.5 0.2 + - - -
242C PRO* 3.8 37.4 - - + +
243C LYS* 3.6 15.3 + - - +
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B SER 3.6 4.5 + - - +
434B LEU* 3.3 8.8 + - + +
435B ASN 3.3 0.6 - - - -
436B GLN* 1.3 76.4 - - - +
438B VAL* 1.3 64.0 + - - +
439B VAL 3.2 1.7 + - - -
440B SER* 3.5 10.8 + - - -
441B LYS* 3.5 20.5 + - - +
243C LYS* 4.0 13.2 - - - +
277E GLU* 3.4 26.0 - - - +
280E LEU* 4.2 19.3 - - + -
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Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A MET* 4.7 0.9 - - - +
434B LEU* 3.3 19.0 + - + +
435B ASN* 3.4 21.8 - - - +
437B ALA* 1.3 76.1 - - - +
439B VAL* 1.3 61.7 + - + +
440B SER 3.5 0.4 + - - -
441B LYS* 4.1 8.7 + - - +
442B LEU* 5.0 0.3 + - - +
280E LEU* 3.8 14.8 - - + -
300E LEU* 4.0 6.7 - - + -
299F CYS* 3.8 27.8 - - - -
302F MET* 4.3 14.3 - - - +
303F ASN* 3.7 30.2 + - + +
306F VAL* 4.1 26.0 - - + +
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Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ARG* 4.4 22.9 - - + +
453A MET* 4.1 33.9 - - + -
435B ASN* 3.4 20.9 - - - +
436B GLN* 3.6 16.8 - - + +
438B VAL* 1.3 79.3 - - + +
440B SER* 1.3 62.6 + - - +
441B LYS 3.3 3.4 + - - -
442B LEU* 3.6 19.7 + - - +
242C PRO* 5.6 0.7 - - + -
244C TYR* 3.8 31.0 - - + +
302F MET* 5.9 1.8 - - - -
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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