Contacts of the helix formed by residues 412 - 433 (chain K) in PDB entry 1UW9
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 412 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E TRP* 3.9 6.7 - - - -
78I LEU* 3.7 24.0 - - - +
406K THR 4.3 3.4 - - - -
409K HIS* 3.2 16.9 + - - +
410K PRO 3.5 0.8 - - - -
411K TRP* 1.3 80.6 - - - +
413K ASN* 1.3 61.5 + - - -
414K ALA 3.5 2.2 - - - -
415K PRO* 3.3 3.7 - - - +
416K GLY 3.0 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 413 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E TRP* 2.8 36.1 + - + +
78I LEU* 5.0 0.4 - - - +
188K ALA* 3.1 40.2 + - - +
191K GLU* 3.6 20.1 - - + +
192K CYS* 3.5 21.1 - - - +
406K THR* 3.5 9.8 - - - +
407K LEU* 3.4 22.8 - - - +
412K GLY* 1.3 69.4 - - - -
414K ALA* 1.3 60.7 + - - +
416K GLY 3.2 0.3 + - - -
417K ALA* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191K GLU* 3.1 24.7 + - - +
194K ARG* 3.7 38.1 - - + +
195K GLY* 3.5 10.8 - - - -
413K ASN* 1.3 78.7 - - - +
415K PRO* 1.3 64.0 - - + +
417K ALA 3.3 0.9 + - - -
418K ALA* 2.9 29.6 + - - +
4P TRP* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 415 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409K HIS* 3.8 10.9 + - + -
411K TRP* 3.5 39.3 - - + +
412K GLY 3.3 13.0 - - - +
414K ALA* 1.3 94.6 - - + +
416K GLY* 1.3 55.8 + - - +
418K ALA* 3.3 2.8 + - + +
419K ALA* 2.9 30.0 + - - +
454K GLU* 3.6 23.6 - - + +
2P MET 3.9 14.1 - - - +
3P VAL* 5.4 0.2 - - - -
4P TRP* 4.7 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 416 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405K GLY 4.4 1.3 - - - +
406K THR* 3.9 13.9 - - - -
409K HIS* 3.6 29.3 - - - -
412K GLY 3.0 11.2 + - - -
413K ASN 3.2 4.0 + - - -
415K PRO* 1.3 76.5 - - - +
417K ALA* 1.3 60.3 + - - +
419K ALA* 3.3 4.0 + - - +
420K ASN* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 417 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192K CYS 3.1 28.0 - - - +
195K GLY* 3.5 13.0 - - - -
197K LEU* 3.5 25.7 - - + +
406K THR* 3.7 4.1 - - - +
413K ASN 2.8 18.4 + - - +
414K ALA 3.6 4.7 - - - +
416K GLY* 1.3 71.2 - - - +
418K ALA* 1.3 59.0 + - - +
420K ASN* 3.1 4.8 + - - +
421K ARG* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195K GLY 3.1 16.6 + - - +
414K ALA 2.9 17.9 + - - +
415K PRO 3.6 5.2 - - - +
417K ALA* 1.3 75.5 - - - +
419K ALA* 1.3 55.9 + - - +
421K ARG* 3.9 2.8 - - - +
422K VAL* 2.8 37.9 + - + +
454K GLU* 4.2 5.6 - - + -
4P TRP* 3.6 37.7 - - + -
17P TYR* 4.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384K VAL* 4.1 5.2 - - + -
409K HIS* 4.2 2.5 - - + -
415K PRO 2.9 17.8 + - - +
416K GLY 3.6 5.4 - - - +
418K ALA* 1.3 74.9 - - - +
420K ASN* 1.3 59.2 + - - +
422K VAL* 3.5 2.0 + - - +
423K ALA* 2.9 30.0 + - - +
454K GLU* 3.5 22.8 - - - +
455K LEU* 3.7 23.1 - - - +
458K ALA* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 420 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170K LEU* 3.9 3.5 - - + +
197K LEU* 4.5 9.6 - - + -
384K VAL* 3.4 25.6 - - - +
387K MET* 3.4 13.9 - - + +
402K PHE* 3.5 42.2 - - + +
405K GLY 3.1 23.4 + - - +
406K THR* 3.1 17.5 + - - -
416K GLY 3.1 10.0 + - - +
417K ALA 3.6 7.0 - - - +
419K ALA* 1.3 76.5 - - - +
421K ARG* 1.3 57.8 + - - +
423K ALA 3.4 0.3 + - - -
424K LEU* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 421 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ARG* 3.4 29.2 - - - +
170K LEU* 3.5 20.8 - - + +
196K GLY* 2.9 32.8 + - - +
198K ASP* 4.4 0.6 + - - -
234K GLU* 2.9 41.8 + - - -
417K ALA 2.8 16.5 + - - +
418K ALA 3.9 3.4 - - - +
420K ASN* 1.3 72.8 - - - +
422K VAL* 1.3 66.4 + - - +
424K LEU* 3.4 1.5 + - - +
425K GLU* 2.8 58.8 + - - +
13P GLU 3.2 16.0 + - - -
17P TYR* 3.4 38.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 422 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418K ALA* 2.8 28.0 + - + +
419K ALA 3.8 2.7 - - - +
421K ARG* 1.3 72.3 - - - +
423K ALA* 1.3 59.0 + - - +
425K GLU* 3.3 3.1 + - - +
426K ALA* 2.9 29.3 + - - +
448K ALA* 4.2 1.6 - - + -
451K TRP* 3.5 28.3 - - + -
452K SER* 3.9 22.0 - - - +
455K LEU* 3.8 21.8 - - + -
4P TRP* 5.7 3.1 - - + -
17P TYR* 3.7 33.7 - - + +
18P LEU* 4.3 1.1 - - - +
138P ARG* 5.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384K VAL* 4.2 7.4 - - + +
387K MET* 3.7 18.2 - - + -
419K ALA 2.9 19.1 + - - +
420K ASN 3.7 4.5 - - - +
422K VAL* 1.3 75.4 - - - +
424K LEU* 1.3 62.7 + - - +
426K ALA* 3.8 2.6 - - - +
427K CYS* 3.1 29.5 + - - -
445K ILE* 3.9 22.9 - - + -
455K LEU* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 424 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ARG* 4.0 14.8 - - + +
168K GLY* 3.1 38.6 - - - +
170K LEU* 3.7 26.2 - - + -
387K MET* 3.7 14.1 - - + +
391K VAL* 3.7 25.1 - - + -
400K LEU* 4.1 15.3 - - + -
420K ASN 3.0 17.6 + - - +
421K ARG* 3.8 4.5 - - - +
423K ALA* 1.3 78.0 - - - +
425K GLU* 1.3 58.0 + - - +
427K CYS* 3.3 2.6 + - - +
428K THR* 2.8 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 425 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ARG* 4.0 11.6 - - - -
421K ARG* 2.8 58.6 + - - +
422K VAL* 4.0 1.1 - - - +
424K LEU* 1.3 76.5 - - + +
426K ALA* 1.3 57.3 + - - +
428K THR* 3.6 7.1 - - - -
429K GLN* 2.8 31.5 + - - +
13P GLU 3.4 0.9 - - - +
14P THR* 3.7 3.8 - - + -
15P PHE* 3.0 34.1 + - + +
16P SER 3.8 0.2 + - - -
17P TYR* 2.8 34.6 + - - +
18P LEU* 3.7 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422K VAL 2.9 17.7 + - - +
423K ALA* 3.8 5.4 - - - +
425K GLU* 1.3 76.5 - - - +
427K CYS* 1.3 56.5 + - - +
429K GLN* 3.3 8.0 + - - +
430K ALA* 2.9 29.8 + - - +
444K VAL* 3.7 15.5 - - + +
445K ILE* 5.5 1.1 - - + -
448K ALA* 4.0 25.6 - - + -
451K TRP* 5.1 0.9 - - + -
18P LEU* 3.6 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 427 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387K MET* 3.9 3.4 - - - -
388K PRO* 3.7 42.2 - - - -
391K VAL* 4.2 18.4 - - + -
423K ALA 3.1 21.9 + - - +
424K LEU 3.7 3.6 - - - +
426K ALA* 1.3 75.5 - - - +
428K THR* 1.3 57.7 + - - +
430K ALA* 3.6 1.0 - - - +
431K ARG* 2.9 31.0 + - - +
437K LEU* 3.7 17.2 - - + +
444K VAL* 4.1 10.5 - - - -
445K ILE* 3.9 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K GLY 3.3 26.2 - - - +
167K ARG* 4.1 9.8 - - + +
168K GLY 5.0 0.2 + - - -
391K VAL* 4.8 6.0 - - - +
396K ASP* 4.3 3.4 + - - +
424K LEU* 2.8 38.5 + - - +
425K GLU* 3.6 7.0 - - - -
427K CYS* 1.3 76.3 - - - +
429K GLN* 1.3 65.1 + - - +
431K ARG* 3.4 22.6 + - - +
432K ASN* 2.9 31.6 + - - +
15P PHE* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 429 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425K GLU 2.8 17.8 + - - +
426K ALA* 3.6 6.5 - - - +
428K THR* 1.3 76.3 - - - +
430K ALA* 1.3 57.9 + - - +
432K ASN* 3.2 4.7 + - - +
433K GLU* 2.9 49.2 + - - +
15P PHE* 3.7 19.4 - - + -
18P LEU* 3.6 19.6 - - + +
21P LEU* 3.4 30.9 - - - +
25P GLN* 3.6 23.5 + - - +
29P GLN* 4.1 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426K ALA 2.9 17.5 + - - +
427K CYS 3.6 4.0 - - - +
428K THR 3.3 0.2 - - - -
429K GLN* 1.3 77.4 - - - +
431K ARG* 1.3 61.7 + - - +
433K GLU* 3.1 17.7 + - - +
434K GLY 3.3 0.3 + - - -
435K ARG* 3.0 42.1 + - + +
437K LEU* 4.3 3.1 - - + -
444K VAL* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 431 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K GLY 4.4 0.6 + - - -
391K VAL* 4.0 20.2 + - - +
392K GLU* 6.6 0.2 - - - +
395K GLY* 4.4 5.5 - - - -
396K ASP* 2.8 49.0 + - - +
427K CYS 2.9 17.2 + - - +
428K THR* 3.6 16.8 - - - +
430K ALA* 1.3 74.6 - - - +
432K ASN* 1.3 90.0 + - - +
434K GLY* 3.0 16.3 + - - -
435K ARG 3.9 13.5 + - - +
437K LEU* 3.9 18.9 - - + +
32P TYR* 3.4 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 432 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K GLY 5.0 1.9 - - - +
428K THR* 2.9 11.6 + - - +
429K GLN 3.4 7.9 - - - +
431K ARG* 1.3 111.8 + - - +
433K GLU* 1.3 59.1 + - - +
434K GLY 3.2 1.1 + - - -
15P PHE* 3.7 11.6 - - - -
28P ALA 4.2 4.3 - - - +
29P GLN* 2.9 34.8 + - - +
32P TYR* 3.2 53.5 - - + +
119P MET* 5.3 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 433 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429K GLN* 2.9 42.3 + - - +
430K ALA* 3.1 15.9 + - - +
432K ASN* 1.3 75.8 - - - +
434K GLY* 1.3 58.7 + - - +
435K ARG* 3.5 15.3 + - + +
25P GLN* 3.9 20.3 - - - +
28P ALA* 3.9 25.6 - - + +
29P GLN* 4.3 6.1 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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