Contacts of the helix formed by residues 412 - 433 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A THR 4.3 4.0 - - - -
409A HIS* 3.1 14.4 + - - +
410A PRO 3.5 0.8 + - - -
411A TRP* 1.3 80.6 - - - +
413A ASN* 1.3 61.9 + - - -
414A ALA 3.5 2.0 - - - -
415A PRO* 3.3 3.3 - - - +
416A GLY* 3.0 26.3 + - - -
70B TRP* 3.9 7.4 - - - -
77T LYS 5.5 0.2 - - - -
78T LEU* 3.7 22.7 - - - +
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Residues in contact with ASN 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA* 3.1 40.2 + - - +
191A GLU* 3.6 18.0 - - + +
192A CYS* 3.5 21.9 - - - +
406A THR* 3.5 10.6 - - - +
407A LEU* 3.4 22.0 - - - +
412A GLY* 1.3 69.3 - - - -
414A ALA* 1.3 61.5 + - - +
416A GLY 3.3 0.3 + - - -
417A ALA* 2.8 30.8 + - - +
70B TRP* 2.7 37.1 + - + +
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 3.1 24.3 + - - +
194A ARG* 3.7 37.2 - - + +
195A GLY* 3.4 13.3 - - - -
413A ASN* 1.3 77.9 - - - +
415A PRO* 1.3 66.1 - - + +
417A ALA 3.3 0.7 + - - -
418A ALA* 2.9 27.1 + - - +
4I TRP* 3.8 10.9 - - + -
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Residues in contact with PRO 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A HIS* 3.9 10.5 - - + -
411A TRP* 3.5 39.9 - - + +
412A GLY 3.3 12.1 - - - +
414A ALA* 1.3 95.4 - - + +
416A GLY* 1.3 55.7 + - - +
418A ALA* 3.3 3.4 + - + +
419A ALA* 2.9 29.6 + - - +
454A GLU* 3.6 24.2 - - + +
2I MET 3.8 14.1 - - - +
3I VAL* 5.3 0.7 - - - -
4I TRP* 4.6 11.2 - - + +
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Residues in contact with GLY 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLY 4.4 1.9 - - - +
406A THR* 3.9 14.4 - - - -
409A HIS* 3.5 29.3 - - - -
412A GLY 3.0 12.0 + - - -
413A ASN 3.6 4.3 - - - -
414A ALA 3.3 0.4 - - - -
415A PRO* 1.3 75.5 - - - +
417A ALA* 1.3 60.7 + - - +
419A ALA* 3.4 3.6 + - - +
420A ASN* 3.1 27.4 + - - +
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Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A CYS 3.1 28.3 - - - +
195A GLY* 3.4 15.0 - - - -
196A GLY* 3.9 0.4 - - - +
197A LEU* 3.5 26.4 - - + +
406A THR* 3.6 4.1 - - - +
413A ASN 2.8 17.5 + - - +
414A ALA 3.3 2.0 + - - +
416A GLY* 1.3 68.9 - - - +
418A ALA* 1.3 59.3 + - - +
420A ASN* 3.2 3.9 + - - +
421A ARG* 2.9 30.5 + - - +
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY 3.0 17.5 + - - +
414A ALA 2.9 16.0 + - - +
415A PRO 3.3 5.6 + - - +
417A ALA* 1.3 74.4 - - - +
419A ALA* 1.3 56.9 + - - +
421A ARG* 3.3 2.8 + - - +
422A VAL* 2.8 38.6 + - + +
454A GLU* 4.2 5.4 - - + -
4I TRP* 3.5 39.0 - - + -
17I TYR* 4.8 1.6 - - + -
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Residues in contact with ALA 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A VAL* 4.1 5.8 - - + -
409A HIS* 4.1 2.5 - - + -
415A PRO 2.9 16.7 + - - +
416A GLY 3.6 5.6 - - - +
417A ALA 3.2 0.2 - - - -
418A ALA* 1.3 76.5 - - - +
420A ASN* 1.3 57.7 + - - +
422A VAL* 3.7 2.2 - - - +
423A ALA* 2.9 30.7 + - - +
454A GLU* 3.6 24.0 - - - +
455A LEU* 3.8 20.0 - - - +
458A ALA* 3.8 17.3 - - + -
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Residues in contact with ASN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.9 3.8 - - + +
197A LEU* 4.5 9.4 - - + +
383A HIS* 5.0 0.2 - - - +
384A VAL* 3.4 26.5 - - - +
387A MET* 3.3 13.8 - - + +
402A PHE* 3.5 42.7 - - + +
405A GLY 3.2 12.6 + - - +
406A THR* 3.1 24.3 + - - -
416A GLY 3.1 11.5 + - - +
417A ALA 3.2 6.3 + - - +
419A ALA* 1.3 77.2 - - - +
421A ARG* 1.3 56.6 - - - +
423A ALA 3.4 0.3 + - - -
424A LEU* 2.9 25.5 + - - +
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Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 3.4 29.1 - - - +
170A LEU* 3.5 20.1 - - + +
196A GLY* 2.9 33.6 + - - +
198A ASP* 4.5 0.4 + - - -
234A GLU* 2.9 39.8 + - - -
417A ALA 2.9 17.2 + - - +
418A ALA 3.9 3.1 - - - +
420A ASN* 1.3 72.5 - - - +
422A VAL* 1.3 66.0 + - - +
424A LEU* 3.4 1.0 + - - +
425A GLU* 2.7 58.4 + - - +
13I GLU 3.2 16.8 + - - -
17I TYR* 3.4 38.8 - - + -
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ALA* 2.8 26.9 + - + +
419A ALA* 3.7 3.8 - - - +
421A ARG* 1.3 72.5 - - - +
423A ALA* 1.3 64.1 + - - +
425A GLU* 3.2 3.5 + - - +
426A ALA* 2.9 23.7 + - - +
448A ALA* 4.2 1.3 - - + -
451A TRP* 3.5 28.7 - - + -
452A SER* 3.9 22.7 - - - +
455A LEU* 3.8 22.0 - - + -
4I TRP* 5.6 3.6 - - + -
17I TYR* 3.7 33.4 - - + +
18I LEU* 4.2 0.9 - - - +
138I ARG* 5.3 1.6 - - - +
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Residues in contact with ALA 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A VAL* 4.3 7.6 - - + +
387A MET* 3.7 18.2 - - + -
419A ALA 2.9 17.2 + - - +
420A ASN 3.7 4.0 - - - +
422A VAL* 1.3 78.1 - - - +
424A LEU* 1.3 63.2 + - - +
426A ALA* 3.8 2.8 - - - +
427A CYS* 3.1 29.5 + - - -
445A ILE* 3.8 24.2 - - + -
455A LEU* 4.1 14.6 - - + -
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 4.0 15.7 - - + +
168A GLY* 3.1 38.1 - - - +
170A LEU* 3.6 26.2 - - + -
387A MET* 3.7 13.8 - - + +
391A VAL* 3.7 24.2 - - + -
400A LEU* 4.1 15.3 - - + -
420A ASN 2.9 17.4 + - - +
421A ARG* 3.8 4.5 - - - +
423A ALA* 1.3 78.6 - - - +
425A GLU* 1.3 54.6 + - - +
427A CYS* 3.3 1.6 + - - +
428A THR* 2.8 44.5 + - - +
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Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 3.9 11.0 - - + -
421A ARG* 2.7 58.2 + - - +
422A VAL* 3.9 1.1 - - - +
424A LEU* 1.3 74.6 - - + +
426A ALA* 1.3 60.2 + - - +
428A THR* 3.4 7.4 + - - -
429A GLN* 2.9 31.5 + - - +
13I GLU 3.5 0.3 - - - +
14I THR* 3.7 3.6 - - + -
15I PHE* 3.0 35.1 + - + +
17I TYR* 2.8 34.1 + - - +
18I LEU* 3.7 17.8 + - + +
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Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A VAL 2.9 17.9 + - - +
423A ALA* 3.8 5.4 - - - +
425A GLU* 1.3 75.7 - - - +
427A CYS* 1.3 57.1 + - - +
429A GLN* 3.4 8.2 + - - +
430A ALA* 2.9 29.8 + - - +
444A VAL* 3.6 15.3 - - + +
445A ILE* 5.6 1.1 - - + -
448A ALA* 3.9 25.4 - - + -
451A TRP* 5.1 0.9 - - + -
18I LEU* 3.5 14.9 - - + +
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Residues in contact with CYS 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A MET* 3.9 5.2 - - - -
388A PRO* 3.7 42.6 - - - -
391A VAL* 4.1 18.6 - - + -
423A ALA 3.1 21.2 + - - +
424A LEU 3.6 3.6 - - - +
426A ALA* 1.3 75.6 - - - +
428A THR* 1.3 57.7 + - - +
430A ALA 3.4 0.5 + - - -
431A ARG* 2.9 30.7 + - - +
437A LEU* 3.6 18.5 - - + +
444A VAL* 4.0 10.8 - - - -
445A ILE* 3.9 10.3 - - - -
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Residues in contact with THR 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY 3.3 25.6 - - - +
167A ARG* 4.2 10.1 - - + +
391A VAL* 4.7 7.3 - - - +
396A ASP* 4.3 3.5 + - - +
424A LEU* 2.8 36.7 + - - +
425A GLU* 3.6 6.7 - - - -
426A ALA 3.3 0.2 - - - -
427A CYS* 1.3 77.2 - - - +
429A GLN* 1.3 62.2 + - - +
431A ARG* 3.4 23.6 + - - +
432A ASN* 3.0 33.0 + - - +
15I PHE* 4.1 14.6 - - + -
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Residues in contact with GLN 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU 2.9 18.5 + - - +
426A ALA* 3.6 5.6 - - - +
428A THR* 1.3 75.2 - - - +
430A ALA* 1.3 65.5 + - - +
432A ASN* 3.2 4.0 + - - +
433A GLU* 2.9 43.3 + - - +
15I PHE* 3.7 14.7 - - + -
18I LEU* 3.6 23.1 - - + +
21I LEU* 3.3 32.1 - - - +
25I GLN* 3.5 21.9 + - - +
29I GLN* 4.0 10.0 + - - +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ALA 2.9 18.1 + - - +
427A CYS* 3.6 4.3 - - - +
428A THR 3.3 0.2 - - - -
429A GLN* 1.3 75.4 - - - +
431A ARG* 1.3 61.6 + - - +
433A GLU* 3.1 17.1 + - - +
434A GLY 3.4 0.2 + - - -
435A ARG* 3.0 41.2 + - + +
437A LEU* 4.4 2.9 - - + -
444A VAL* 3.6 31.9 - - + -
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Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY 4.4 0.6 + - - -
391A VAL* 4.0 20.0 + - + +
395A GLY* 4.4 5.5 - - - -
396A ASP* 2.9 49.4 + - - +
427A CYS 2.9 17.8 + - - +
428A THR* 3.6 17.3 - - - +
430A ALA* 1.3 74.3 - - - +
432A ASN* 1.3 88.3 + - - +
434A GLY* 2.9 16.3 + - - -
435A ARG 3.9 13.7 + - - +
437A LEU* 4.0 18.9 - - + +
32I TYR* 3.3 24.3 + - + +
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Residues in contact with ASN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY 5.0 2.1 - - - +
428A THR* 3.0 15.5 + - - +
429A GLN 3.4 5.6 - - - +
431A ARG* 1.3 111.4 + - - +
433A GLU* 1.3 60.1 + - - +
434A GLY* 3.4 1.0 + - - -
15I PHE* 3.7 10.6 - - - -
28I ALA 4.2 4.3 - - - +
29I GLN* 2.8 34.5 + - - +
32I TYR* 3.1 53.7 + - + +
119I MET* 5.3 4.5 - - - +
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Residues in contact with GLU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLN* 2.9 42.2 + - - +
430A ALA* 3.1 16.3 + - - +
432A ASN* 1.3 74.9 - - - +
434A GLY* 1.3 57.8 + - - +
435A ARG* 3.5 14.9 + - + +
25I GLN* 3.9 20.3 - - - +
28I ALA* 3.9 26.3 - - + +
29I GLN* 4.4 6.5 - - - +
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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