Contacts of the helix formed by residues 412 - 433 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H TRP* 4.0 5.4 - - - -
77P LYS 5.3 0.2 - - - -
78P LEU* 3.7 23.8 - - - +
406R THR 4.3 4.0 - - - -
409R HIS* 3.2 15.0 + - - +
410R PRO 3.5 0.6 - - - -
411R TRP* 1.3 78.5 - - - +
413R ASN* 1.3 61.1 + - - -
414R ALA 3.5 2.0 - - - -
415R PRO* 3.3 3.8 - - - +
416R GLY* 2.9 26.9 + - - -
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Residues in contact with ASN 413 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H TRP* 2.8 37.3 + - + +
188R ALA* 3.1 40.4 + - - +
191R GLU* 3.6 19.1 - - + +
192R CYS* 3.5 21.5 - - - +
406R THR* 3.5 10.0 - - - +
407R LEU* 3.4 22.4 - - - +
412R GLY* 1.3 69.1 - - - -
414R ALA* 1.3 56.7 + - - +
415R PRO* 4.1 0.2 - - - +
416R GLY 3.3 0.3 + - - -
417R ALA* 2.7 36.0 + - - +
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Residues in contact with ALA 414 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M TRP* 3.8 13.2 - - + -
191R GLU* 3.1 25.4 + - - +
194R ARG* 3.6 36.8 - - + +
195R GLY* 3.5 11.4 - - - -
413R ASN* 1.3 78.1 - - - +
415R PRO* 1.3 65.5 - - + +
417R ALA 3.3 0.9 + - - -
418R ALA* 2.9 27.1 + - - +
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Residues in contact with PRO 415 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M MET 3.7 14.1 - - - +
3M VAL* 5.3 0.7 - - - -
4M TRP* 4.6 11.4 - - + +
409R HIS* 3.9 10.1 - - + -
411R TRP* 3.5 39.0 - - + +
412R GLY 3.3 13.5 - - - +
414R ALA* 1.3 95.9 - - + +
416R GLY* 1.3 55.5 + - - +
418R ALA* 3.3 3.2 + - + +
419R ALA* 2.9 30.3 + - - +
454R GLU* 3.6 24.1 - - + +
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Residues in contact with GLY 416 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405R GLY 4.4 1.3 - - - +
406R THR* 3.8 14.4 - - - -
409R HIS* 3.5 30.2 - - - -
412R GLY 2.9 12.2 + - - -
413R ASN 3.3 4.0 + - - -
415R PRO* 1.3 75.9 - - - +
417R ALA* 1.3 60.8 + - - +
419R ALA* 3.4 3.5 + - - +
420R ASN* 3.2 27.2 + - - +
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Residues in contact with ALA 417 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192R CYS 3.1 28.5 - - - +
195R GLY* 3.4 15.3 - - - -
196R GLY 4.7 0.2 - - - -
197R LEU* 3.5 26.7 - - + +
406R THR* 3.7 3.9 - - - +
413R ASN 2.7 17.7 + - - +
414R ALA 3.6 1.8 - - - +
416R GLY* 1.3 68.3 - - - +
418R ALA* 1.3 61.5 + - - +
420R ASN* 3.3 3.2 + - - +
421R ARG* 2.9 30.3 + - - +
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Residues in contact with ALA 418 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M TRP* 3.6 38.1 - - + -
17M TYR* 4.8 2.2 - - + -
195R GLY 3.1 16.0 + - - +
414R ALA 2.9 16.9 + - - +
415R PRO 3.3 5.1 + - - +
417R ALA* 1.3 75.6 - - - +
419R ALA* 1.3 52.4 + - - +
421R ARG* 3.2 2.9 + - - +
422R VAL* 2.8 43.8 + - + +
454R GLU* 4.2 5.8 - - + -
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Residues in contact with ALA 419 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384R VAL* 4.1 4.7 - - + -
409R HIS* 4.2 2.0 - - + -
415R PRO 2.9 17.4 + - - +
416R GLY 3.6 5.8 - - - +
417R ALA 3.3 0.2 - - - -
418R ALA* 1.3 76.4 - - - +
420R ASN* 1.3 57.9 + - - +
422R VAL* 3.8 1.4 - - - +
423R ALA* 3.0 30.3 + - - +
454R GLU* 3.6 24.1 - - - +
455R LEU* 3.7 22.0 - - - +
458R ALA* 3.8 17.0 - - + -
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Residues in contact with ASN 420 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170R LEU* 3.9 3.7 - - + +
197R LEU* 4.5 9.9 - - + -
384R VAL* 3.4 24.7 - - - +
387R MET* 3.4 12.8 - - + +
402R PHE* 3.5 43.6 - - + +
405R GLY 3.2 13.6 + - - +
406R THR* 3.1 24.3 + - - -
416R GLY 3.2 12.3 + - - +
417R ALA 3.3 5.8 + - - +
419R ALA* 1.3 76.5 - - - +
421R ARG* 1.3 58.9 + - - +
423R ALA 3.4 0.2 + - - -
424R LEU* 3.0 26.3 + - - +
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Residues in contact with ARG 421 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M GLU 3.2 16.8 + - - -
17M TYR* 3.4 39.1 - - + -
167R ARG* 3.4 28.7 - - - +
170R LEU* 3.5 18.3 - - + +
196R GLY* 2.9 34.3 + - - +
198R ASP* 4.4 0.2 + - - -
234R GLU* 2.9 40.4 + - - -
417R ALA 2.9 17.6 + - - +
418R ALA 3.8 2.9 - - - +
420R ASN* 1.3 74.1 - - - +
422R VAL* 1.3 63.5 + - - +
424R LEU* 3.3 2.0 + - - +
425R GLU* 2.8 57.6 + - - +
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Residues in contact with VAL 422 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M TRP* 5.7 2.7 - - + -
17M TYR* 3.8 33.2 - - + +
18M LEU* 4.3 1.3 - - - +
138M ARG* 5.5 1.6 - - - +
418R ALA* 2.8 28.1 + - + +
419R ALA* 3.8 4.0 - - - +
421R ARG* 1.3 73.2 - - - +
423R ALA* 1.3 56.4 + - - +
425R GLU* 3.2 3.3 + - - +
426R ALA* 2.8 30.0 + - - +
448R ALA* 4.2 1.6 - - + -
451R TRP* 3.5 28.5 - - + -
452R SER* 3.9 22.4 - - - +
455R LEU* 3.8 21.3 - - + -
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Residues in contact with ALA 423 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384R VAL* 4.3 7.2 - - + -
387R MET* 3.7 18.6 - - + -
419R ALA 3.0 19.3 + - - +
420R ASN 3.7 4.3 - - - +
421R ARG 3.4 0.2 - - - -
422R VAL* 1.3 77.1 - - - +
424R LEU* 1.3 63.1 + - - +
426R ALA* 3.8 2.8 - - - +
427R CYS* 3.0 29.6 + - - -
445R ILE* 3.9 24.5 - - + -
455R LEU* 4.1 15.5 - - + +
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Residues in contact with LEU 424 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167R ARG* 4.0 15.9 - - + +
168R GLY* 3.1 37.2 - - - +
169R LEU 5.1 0.2 - - - +
170R LEU* 3.7 26.0 - - + -
387R MET* 3.7 14.3 - - + +
391R VAL* 3.7 24.9 - - + -
400R LEU* 4.0 16.2 - - + -
420R ASN 3.0 17.8 + - - +
421R ARG* 3.8 4.5 - - - +
423R ALA* 1.3 77.9 - - - +
425R GLU* 1.3 53.9 + - - +
427R CYS* 3.4 1.7 + - - +
428R THR* 2.7 45.3 + - - +
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Residues in contact with GLU 425 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M GLU 3.6 0.7 - - - +
14M THR* 3.7 3.9 - - + -
15M PHE* 3.0 36.8 + - + +
17M TYR* 3.0 32.7 + - - +
18M LEU* 3.8 15.9 + - + +
167R ARG* 3.9 11.5 - - + -
421R ARG* 2.8 57.3 + - - +
422R VAL* 3.9 1.3 - - - +
424R LEU* 1.3 74.2 - - + +
426R ALA* 1.3 60.7 + - - +
428R THR* 3.6 6.9 - - - -
429R GLN* 2.8 31.7 + - - +
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Residues in contact with ALA 426 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M LEU* 3.7 14.2 - - + +
422R VAL 2.8 17.4 + - - +
423R ALA* 3.8 4.9 - - - +
425R GLU* 1.3 77.8 - - - +
427R CYS* 1.3 56.5 + - - +
429R GLN* 3.4 8.1 + - - +
430R ALA* 2.9 30.1 + - - +
444R VAL* 3.6 16.2 - - + +
445R ILE* 5.5 1.1 - - + -
448R ALA* 4.0 25.1 - - + -
451R TRP* 5.1 0.9 - - + -
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Residues in contact with CYS 427 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387R MET* 3.9 5.6 - - - -
388R PRO* 3.7 42.4 - - - -
391R VAL* 4.2 18.2 - - + -
423R ALA 3.0 21.0 + - - +
424R LEU 3.7 3.6 - - - +
426R ALA* 1.3 76.2 - - - +
428R THR* 1.3 57.6 + - - +
430R ALA* 3.4 1.7 + - - +
431R ARG* 3.0 29.6 + - - +
437R LEU* 3.7 17.5 - - + +
444R VAL* 4.0 10.1 - - - -
445R ILE* 4.0 9.9 - - - -
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Residues in contact with THR 428 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M PHE* 4.1 12.6 - - + -
166R GLY 3.3 26.0 - - - +
167R ARG* 4.1 10.9 - - + +
168R GLY 5.0 0.2 + - - -
391R VAL* 4.8 7.1 - - - +
396R ASP* 4.4 2.3 + - - +
424R LEU* 2.7 37.0 + - - +
425R GLU* 3.6 7.9 - - - -
427R CYS* 1.3 73.6 - - - +
429R GLN* 1.3 61.9 + - - +
431R ARG* 3.4 22.1 + - - +
432R ASN* 2.9 39.3 + - - +
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Residues in contact with GLN 429 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 3.8 18.1 - - + -
18M LEU* 3.7 18.5 - - + +
21M LEU* 3.5 30.5 - - - +
25M GLN* 3.7 21.1 + - - +
29M GLN* 4.0 12.0 + - - +
425R GLU 2.8 17.7 + - - +
426R ALA* 3.7 6.3 - - - +
428R THR* 1.3 77.7 - - - +
430R ALA* 1.3 57.1 + - - +
432R ASN* 3.2 4.3 + - - +
433R GLU* 2.9 50.4 + - - +
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Residues in contact with ALA 430 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426R ALA 2.9 18.5 + - - +
427R CYS 3.7 4.3 - - - +
428R THR 3.3 0.2 - - - -
429R GLN* 1.3 75.6 + - - +
431R ARG* 1.3 62.8 + - - +
433R GLU* 3.0 23.0 + - - +
434R GLY 3.3 0.2 + - - -
435R ARG* 3.0 38.0 + - + +
437R LEU* 4.4 3.4 - - + -
444R VAL* 3.6 31.4 - - + -
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Residues in contact with ARG 431 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M TYR* 3.5 22.0 + - + -
166R GLY 4.4 0.6 + - - -
391R VAL* 4.0 20.6 + - + +
395R GLY* 4.4 5.1 - - - -
396R ASP* 2.8 49.0 + - - +
427R CYS 3.0 18.0 + - - +
428R THR* 3.6 16.4 - - - +
430R ALA* 1.3 73.4 - - - +
432R ASN* 1.3 94.7 + - - +
434R GLY* 3.0 15.9 + - - -
435R ARG 3.9 14.0 + - - +
437R LEU* 3.9 18.5 - - + +
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Residues in contact with ASN 432 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 3.8 10.0 - - - -
28M ALA 4.4 3.4 - - - +
29M GLN* 3.0 33.6 + - - +
32M TYR* 3.2 54.0 - - + +
119M MET* 5.5 3.6 - - - +
166R GLY 5.0 1.7 - - - +
428R THR* 2.9 21.3 + - - +
429R GLN 3.4 5.6 - - - +
431R ARG* 1.3 112.7 + - - +
433R GLU* 1.3 59.9 + - - +
434R GLY 3.5 0.9 + - - -
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Residues in contact with GLU 433 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M GLN* 4.1 17.2 - - - +
28M ALA* 4.0 27.1 - - + +
29M GLN* 4.5 6.5 - - - +
429R GLN* 2.9 42.2 + - - +
430R ALA* 3.0 15.8 + - - +
432R ASN* 1.3 76.9 - - - +
434R GLY* 1.3 57.4 + - - +
435R ARG* 3.5 14.2 + - + +
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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