Contacts of the helix formed by residues 412 - 433 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LYS 5.4 0.2 - - - -
78C LEU* 3.8 24.0 - - - +
70O TRP* 3.9 6.5 - - - -
406V THR 4.3 3.4 - - - -
409V HIS* 3.2 16.5 + - - +
410V PRO 3.5 1.0 + - - -
411V TRP* 1.3 81.8 - - - +
413V ASN* 1.3 60.0 + - - -
414V ALA 3.5 2.0 - - - -
415V PRO* 3.3 2.7 - - - +
416V GLY 3.0 23.4 + - - -
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Residues in contact with ASN 413 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 5.1 0.2 - - - +
70O TRP* 2.7 36.8 + - - +
188V ALA* 3.1 40.4 + - - +
191V GLU* 3.6 20.3 - - + +
192V CYS* 3.5 22.1 - - - +
406V THR* 3.5 9.5 - - - +
407V LEU* 3.4 23.1 - - - +
412V GLY* 1.3 69.4 - - - -
414V ALA* 1.3 60.9 + - - +
415V PRO* 4.1 0.2 - - - +
416V GLY 3.3 0.2 + - - -
417V ALA* 2.8 30.7 + - - +
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Residues in contact with ALA 414 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191V GLU* 3.1 24.7 + - - +
194V ARG* 3.7 37.0 - - + +
195V GLY* 3.5 12.0 - - - -
413V ASN* 1.3 77.4 - - - +
415V PRO* 1.3 66.2 - - + +
417V ALA 3.3 1.2 + - - -
418V ALA* 2.9 27.1 + - - +
4W TRP* 3.8 12.3 - - + -
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Residues in contact with PRO 415 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409V HIS* 3.8 10.0 + - + -
411V TRP* 3.5 39.0 - - + +
412V GLY 3.3 12.8 - - - +
414V ALA* 1.3 94.0 - - + +
416V GLY* 1.3 55.7 + - - +
418V ALA* 3.4 2.9 + - + +
419V ALA* 2.9 30.1 + - - +
454V GLU* 3.6 24.4 - - + +
2W MET 3.7 14.6 - - - +
3W VAL* 5.3 0.7 - - - -
4W TRP* 4.6 10.7 - - + +
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Residues in contact with GLY 416 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405V GLY 4.4 1.7 - - - +
406V THR* 3.9 13.5 - - - -
409V HIS* 3.5 30.2 - - - -
412V GLY 3.0 12.0 + - - -
413V ASN 3.6 3.1 - - - -
414V ALA 3.3 0.2 - - - -
415V PRO* 1.3 75.9 - - - +
417V ALA* 1.3 60.7 + - - +
419V ALA* 3.3 4.3 + - - +
420V ASN* 3.2 27.6 + - - +
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Residues in contact with ALA 417 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192V CYS 3.0 27.6 - - - +
195V GLY* 3.5 12.8 - - - -
196V GLY* 4.7 0.3 - - - -
197V LEU* 3.5 27.0 - - + +
406V THR* 3.6 4.0 - - - +
413V ASN 2.8 17.7 + - - +
414V ALA 3.6 4.3 - - - +
416V GLY* 1.3 70.1 - - - +
418V ALA* 1.3 59.5 + - - +
420V ASN* 3.2 5.2 + - - +
421V ARG* 2.9 29.3 + - - +
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Residues in contact with ALA 418 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195V GLY 3.1 15.2 + - - +
414V ALA 2.9 17.6 + - - +
415V PRO 3.5 5.8 - - - +
417V ALA* 1.3 75.0 - - - +
419V ALA* 1.3 57.6 + - - +
421V ARG* 3.8 2.3 - - - +
422V VAL* 2.8 38.0 + - + +
454V GLU* 4.2 5.8 - - + -
4W TRP* 3.5 39.3 - - + -
17W TYR* 4.8 1.8 - - + -
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Residues in contact with ALA 419 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384V VAL* 4.1 4.9 - - + -
409V HIS* 4.2 2.5 - - + -
415V PRO 2.9 16.7 + - - +
416V GLY 3.5 6.5 - - - +
417V ALA 3.3 0.2 - - - -
418V ALA* 1.3 75.6 - - - +
420V ASN* 1.3 56.9 + - - +
422V VAL* 3.5 1.4 + - - +
423V ALA* 2.9 29.6 + - - +
454V GLU* 3.6 22.6 - - - +
455V LEU* 3.8 23.5 - - - +
458V ALA* 3.9 16.8 - - + -
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Residues in contact with ASN 420 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170V LEU* 3.9 4.3 - - + -
197V LEU* 4.5 9.1 - - + +
384V VAL* 3.4 25.0 - - - +
387V MET* 3.3 13.4 - - + +
402V PHE* 3.5 42.8 - - + +
405V GLY 3.2 13.1 + - - +
406V THR* 3.1 25.1 + - - -
416V GLY 3.2 11.0 + - - +
417V ALA* 3.2 6.5 + - - +
419V ALA* 1.3 76.0 - - - +
421V ARG* 1.3 58.2 + - - +
423V ALA 3.4 0.3 + - - -
424V LEU* 3.0 25.8 + - - +
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Residues in contact with ARG 421 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167V ARG* 3.5 28.5 - - - +
170V LEU* 3.4 20.6 - - + +
196V GLY* 2.9 32.8 + - - +
198V ASP* 4.4 1.0 + - - -
234V GLU* 2.9 41.2 + - - -
417V ALA 2.9 16.3 + - - +
418V ALA 3.8 3.4 - - - +
420V ASN* 1.3 73.6 - - - +
422V VAL* 1.3 67.1 + - - +
424V LEU* 3.4 1.1 + - - +
425V GLU* 2.7 58.8 + - - +
13W GLU 3.2 17.4 + - - -
17W TYR* 3.3 37.3 - - + -
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Residues in contact with VAL 422 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418V ALA* 2.8 24.4 + - + +
419V ALA* 3.8 4.0 - - - +
421V ARG* 1.3 75.2 - - - +
423V ALA* 1.3 64.4 + - - +
425V GLU* 3.2 3.3 + - - +
426V ALA* 2.9 22.9 + - - +
448V ALA* 4.2 1.8 - - + -
451V TRP* 3.4 31.4 - - + -
452V SER* 3.9 19.7 - - - +
454V GLU* 6.2 0.2 - - + -
455V LEU* 3.8 20.6 - - + -
4W TRP* 5.6 3.4 - - + -
17W TYR* 3.6 32.8 - - + +
18W LEU* 4.2 0.9 - - - +
138W ARG* 5.3 1.8 - - - +
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Residues in contact with ALA 423 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384V VAL* 4.3 7.2 - - + +
387V MET* 3.7 18.6 - - + -
419V ALA 2.9 18.9 + - - +
420V ASN 3.7 4.3 - - - +
422V VAL* 1.3 76.5 - - - +
424V LEU* 1.3 63.5 + - - +
426V ALA* 3.8 3.1 - - - +
427V CYS* 3.0 29.3 + - - -
445V ILE* 3.9 23.3 - - + -
455V LEU* 4.2 15.5 - - + +
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Residues in contact with LEU 424 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167V ARG* 4.0 15.9 - - + +
168V GLY* 3.1 36.8 - - - +
169V LEU 4.9 0.2 - - - +
170V LEU* 3.6 27.1 - - + -
387V MET* 3.7 13.6 - - + +
391V VAL* 3.7 24.7 - - + -
400V LEU* 4.0 15.9 - - + -
420V ASN 3.0 17.8 + - - +
421V ARG* 3.8 4.3 - - - +
423V ALA* 1.3 77.4 - - - +
425V GLU* 1.3 59.0 + - - +
427V CYS* 3.3 2.4 + - - +
428V THR* 2.8 40.5 + - - +
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Residues in contact with GLU 425 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167V ARG* 3.9 11.4 - - - +
421V ARG* 2.7 59.9 + - - +
422V VAL* 4.0 1.3 - - - +
424V LEU* 1.3 74.1 - - + +
426V ALA* 1.3 60.2 + - - +
428V THR* 3.6 7.0 - - - -
429V GLN* 2.8 31.7 + - - +
13W GLU 3.5 1.0 - - - +
14W THR* 3.7 3.6 - - + -
15W PHE* 3.0 34.3 + - + +
16W SER 3.9 0.2 + - - -
17W TYR* 2.8 33.1 + - - +
18W LEU* 3.7 19.0 + - + +
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Residues in contact with ALA 426 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422V VAL 2.9 16.9 + - - +
423V ALA* 3.8 4.7 - - - +
425V GLU* 1.3 76.2 - - - +
427V CYS* 1.3 57.1 + - - +
429V GLN* 3.4 7.7 + - - +
430V ALA* 2.9 30.8 + - - +
444V VAL* 3.6 16.0 - - + +
445V ILE* 5.5 1.1 - - + -
448V ALA* 4.0 25.8 - - + -
451V TRP* 5.1 0.9 - - + -
18W LEU* 3.5 14.2 - - + +
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Residues in contact with CYS 427 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387V MET* 3.9 3.6 - - + -
388V PRO* 3.6 43.3 - - - -
391V VAL* 4.1 17.9 - - + -
423V ALA 3.0 20.8 + - - +
424V LEU 3.6 3.4 - - - +
426V ALA* 1.3 75.0 - - - +
428V THR* 1.3 58.0 + - - +
430V ALA* 3.4 2.1 + - - +
431V ARG* 2.9 30.5 + - - +
437V LEU* 3.7 16.5 - - + +
444V VAL* 4.1 10.1 - - - -
445V ILE* 3.9 11.4 - - - -
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Residues in contact with THR 428 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166V GLY 3.3 26.9 - - - +
167V ARG* 4.2 10.0 - - + +
168V GLY 5.0 0.2 + - - -
391V VAL* 4.7 7.3 - - - +
396V ASP* 4.4 3.0 + - - +
424V LEU* 2.8 35.4 + - - +
425V GLU* 3.6 7.6 - - - -
426V ALA 3.3 0.2 - - - -
427V CYS* 1.3 74.0 - - - +
429V GLN* 1.3 59.0 + - - +
431V ARG* 3.4 23.8 + - - +
432V ASN* 3.0 37.1 + - - +
15W PHE* 4.0 15.3 - - + -
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Residues in contact with GLN 429 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425V GLU 2.8 21.2 + - - +
426V ALA* 3.7 6.6 - - - +
428V THR* 1.3 71.7 - - - +
430V ALA* 1.3 57.0 + - - +
432V ASN* 3.2 4.3 + - - +
433V GLU* 2.9 49.1 + - - +
15W PHE* 3.7 15.1 - - + -
18W LEU* 3.6 22.2 - - + +
21W LEU* 3.3 31.9 - - + +
25W GLN* 3.6 23.1 + - - +
29W GLN* 4.0 10.0 + - - +
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Residues in contact with ALA 430 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426V ALA 2.9 17.5 + - - +
427V CYS 3.6 4.7 - - - +
429V GLN* 1.3 76.0 + - - +
431V ARG* 1.3 62.4 + - - +
433V GLU* 3.1 20.1 + - - +
434V GLY 3.3 0.2 + - - -
435V ARG* 3.0 38.8 + - + +
437V LEU* 4.3 3.8 - - + -
444V VAL* 3.6 31.6 - - + -
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Residues in contact with ARG 431 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166V GLY 4.4 0.6 + - - -
391V VAL* 4.0 20.0 + - - +
395V GLY* 4.4 5.7 - - - -
396V ASP* 2.8 49.2 + - - +
427V CYS 2.9 16.9 + - - +
428V THR* 3.5 17.5 - - - +
430V ALA* 1.3 74.0 - - - +
432V ASN* 1.3 85.1 + - - +
434V GLY* 2.9 21.0 + - - -
435V ARG 3.9 13.0 + - - +
437V LEU* 3.9 19.2 - - + +
32W TYR* 3.3 23.5 + - + +
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Residues in contact with ASN 432 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166V GLY 5.0 1.9 - - - +
428V THR* 3.0 14.9 + - - +
429V GLN 3.5 4.9 - - - +
431V ARG* 1.3 112.3 + - - +
433V GLU* 1.3 60.3 + - - +
434V GLY* 3.2 0.9 + - - -
15W PHE* 3.8 10.4 - - - -
28W ALA 4.1 5.2 - - - +
29W GLN* 2.9 34.0 + - - +
32W TYR* 3.1 52.0 - - + +
119W MET* 5.3 5.2 - - - +
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Residues in contact with GLU 433 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429V GLN* 2.9 41.1 + - - +
430V ALA* 3.1 16.6 + - - +
432V ASN* 1.3 76.0 - - - +
434V GLY* 1.3 57.8 + - - +
435V ARG* 3.5 15.3 + - + +
25W GLN* 3.9 20.6 - - - +
28W ALA* 3.9 26.7 - - + +
29W GLN* 4.4 6.0 - - - +
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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