Contacts of the helix formed by residues 412 - 433 (chain D) in PDB entry 1IR1
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D THR 3.9 3.5 - - - +
407D LEU* 5.6 1.1 - - - -
409D HIS* 3.3 15.0 + - - +
410D PRO 3.5 1.2 + - - -
411D TRP* 1.3 81.0 - - - +
413D ASN* 1.3 64.3 + - - -
414D ALA 3.6 1.3 - - - -
415D PRO* 3.4 3.8 - - - +
416D GLY* 3.0 25.8 + - - -
71U LYS 5.4 0.4 - - - -
72U LEU* 3.7 22.3 - - - +
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Residues in contact with ASN 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ALA* 3.2 39.4 + - - +
191D GLU* 3.6 21.6 - - + +
192D CYS* 3.4 21.7 - - - +
406D THR* 3.7 9.5 - - - +
407D LEU* 3.3 30.9 - - - +
412D GLY* 1.3 70.5 - - - -
414D ALA* 1.3 66.2 + - - +
416D GLY* 3.2 1.0 + - - -
417D ALA* 2.9 24.6 + - - +
72U LEU* 5.0 1.7 - - - +
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Residues in contact with ALA 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D GLU* 3.2 25.2 + - - +
194D ARG* 3.9 33.9 - - + +
195D GLY* 3.6 4.2 - - - -
413D ASN* 1.3 75.2 - - - +
415D PRO* 1.3 74.2 - - + +
417D ALA* 3.2 4.9 + - - +
418D VAL* 3.1 27.1 + - - +
4V TRP* 4.0 11.9 - - + +
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Residues in contact with PRO 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D HIS* 3.9 10.0 - - + -
411D TRP* 3.5 45.1 - - + +
412D GLY 3.4 12.8 - - - +
414D ALA* 1.3 97.3 - - + +
416D GLY* 1.3 60.2 + - - +
418D VAL* 3.4 5.4 + - + +
419D ALA* 3.1 23.2 + - - +
454D GLU* 3.7 17.4 - - + +
2V LYS 3.9 15.0 - - - +
3V VAL* 5.5 0.4 - - - -
4V TRP* 4.9 9.2 - - + +
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Residues in contact with GLY 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D GLY 4.5 1.7 - - - +
406D THR* 3.8 13.7 - - - -
409D HIS* 3.5 29.6 - - - -
412D GLY 3.0 11.8 + - - -
413D ASN 3.7 3.6 - - - -
414D ALA 3.2 0.2 - - - -
415D PRO* 1.3 77.1 - - - +
417D ALA* 1.3 62.7 + - - +
419D ALA* 3.5 4.5 + - - +
420D ASN* 3.1 26.6 + - - -
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Residues in contact with ALA 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D CYS 3.2 26.7 - - - +
195D GLY* 3.6 13.0 - - - -
197D LEU* 3.5 26.3 - - + +
406D THR* 3.9 3.5 - - + +
413D ASN 2.9 11.1 + - - +
414D ALA 3.2 9.2 + - - +
416D GLY* 1.3 75.8 - - - +
418D VAL* 1.3 59.0 + - - +
420D ASN* 3.2 3.5 + - - +
421D ARG* 2.9 30.3 + - - +
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Residues in contact with VAL 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D GLY* 3.3 19.1 - - - +
414D ALA 3.1 16.7 + - - +
415D PRO* 3.6 7.9 - - + +
416D GLY 3.3 0.2 - - - -
417D ALA* 1.3 77.0 - - - +
419D ALA* 1.3 57.4 + - - +
421D ARG* 3.3 2.5 + - - +
422D VAL* 2.8 52.4 + - + +
452D SER* 4.8 0.7 - - - +
454D GLU* 4.0 17.5 - - + +
4V TRP* 3.6 55.4 - - + +
17V TYR* 4.8 3.6 - - + -
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Residues in contact with ALA 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 4.3 4.3 - - + -
409D HIS* 4.2 2.2 - - + -
415D PRO 3.1 13.2 + - - +
416D GLY 3.6 9.2 - - - +
418D VAL* 1.3 76.0 - - - +
420D ASN* 1.3 57.2 + - - +
422D VAL* 4.0 1.2 - - - +
423D ALA* 3.0 30.3 + - - +
454D GLU* 3.7 20.6 - - - +
455D LEU* 3.5 26.0 - - + +
458D ALA* 3.9 16.2 - - + -
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Residues in contact with ASN 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D LEU* 4.1 4.8 - - + +
197D LEU* 4.4 11.9 - - + +
383D HIS* 5.2 0.2 - - - -
384D VAL* 3.6 18.8 + - - +
387D MET* 3.6 13.9 - - + +
402D PHE* 3.7 33.0 - - + +
405D GLY 3.4 13.7 + - - +
406D THR* 3.0 26.1 + - - -
416D GLY 3.1 15.1 + - - -
417D ALA* 3.2 8.0 + - - +
419D ALA* 1.3 76.6 - - - +
421D ARG* 1.3 64.8 + - - +
423D ALA* 3.4 0.6 + - - -
424D LEU* 3.0 24.8 + - - +
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Residues in contact with ARG 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ARG* 3.6 27.3 - - - +
170D LEU* 3.5 19.0 - - + +
195D GLY 4.5 0.2 - - - +
196D GLY* 2.9 34.0 + - - +
198D ASP* 4.6 0.8 + - - -
234D GLU* 3.0 33.1 + - - -
417D ALA 2.9 16.9 + - - +
418D VAL 3.8 3.6 - - - +
420D ASN* 1.3 76.0 - - - +
422D VAL* 1.3 63.3 + - - +
424D LEU* 3.4 1.3 + - - +
425D GLU* 2.9 50.9 + - - +
13V GLU* 3.1 32.5 + - - +
17V TYR* 3.5 38.3 - - + -
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Residues in contact with VAL 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D VAL* 2.8 39.2 + - + +
419D ALA* 4.0 3.8 - - - +
421D ARG* 1.3 70.1 - - - +
423D ALA* 1.3 60.8 + - - +
424D LEU 3.3 0.2 + - - -
425D GLU* 3.3 3.1 + - - +
426D ALA* 2.9 28.8 + - - +
448D ALA* 4.4 2.0 - - + -
451D TRP* 3.4 33.4 - - + -
452D SER* 4.1 14.1 - - - +
455D LEU* 4.1 17.7 - - + -
17V TYR* 4.0 28.7 - - + +
18V LEU* 4.1 2.1 - - - +
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Residues in contact with ALA 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 4.5 5.8 - - + -
387D MET* 3.8 17.0 - - + -
419D ALA 3.0 20.1 + - - +
420D ASN 3.8 3.4 - - - +
422D VAL* 1.3 78.8 - - - +
424D LEU* 1.3 62.4 + - - +
426D ALA* 3.4 5.7 + - - +
427D CYS* 3.1 27.9 + - - -
445D ILE* 4.0 23.0 - - + +
455D LEU* 4.0 13.9 - - + -
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Residues in contact with LEU 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ARG* 4.2 10.5 - - + +
168D PRO* 3.4 44.2 - - + +
170D LEU* 3.5 31.6 - - + -
387D MET* 3.7 13.4 - - - +
391D THR* 3.7 22.0 - - - +
400D LEU* 4.0 14.1 - - + -
420D ASN 3.0 17.7 + - - +
421D ARG* 3.7 4.7 - - - +
423D ALA* 1.3 76.7 - - - +
425D GLU* 1.3 58.8 + - - +
427D CYS* 3.0 5.7 + - - +
428D VAL* 2.9 33.9 + - + +
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Residues in contact with GLU 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ARG* 4.3 10.3 - - - -
421D ARG* 2.9 53.5 + - - +
422D VAL* 4.0 0.7 - - - +
424D LEU* 1.3 75.3 - - + +
426D ALA* 1.3 57.5 + - - +
428D VAL* 3.8 8.5 - - + +
429D GLN* 2.9 31.0 + - - +
13V GLU 3.4 1.0 - - - +
14V THR* 3.6 4.0 - - + -
15V LEU* 2.9 34.4 + - + +
17V TYR* 2.8 34.1 + - - +
18V LEU* 3.6 19.4 + - + +
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Residues in contact with ALA 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D VAL 2.9 17.7 + - - +
423D ALA* 3.6 7.2 - - - +
424D LEU 3.2 0.2 - - - -
425D GLU* 1.3 75.8 - - - +
427D CYS* 1.3 58.2 + - - +
429D GLN* 3.9 7.0 - - - +
430D ALA* 3.1 28.8 + - - +
444D ILE* 3.7 16.3 - - + +
445D ILE* 5.6 1.6 - - + -
448D ALA* 4.2 23.6 - - + -
451D TRP* 5.3 1.3 - - + -
18V LEU* 3.8 12.3 - - + +
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Residues in contact with CYS 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D MET* 3.9 8.3 - - - -
388D PRO* 3.6 42.8 - - - -
391D THR* 4.0 20.2 - - + +
423D ALA 3.1 16.8 + - - -
424D LEU 3.0 10.1 + - - +
426D ALA* 1.3 75.7 - - - +
428D VAL* 1.3 59.9 + - - +
430D ALA* 3.8 2.7 - - - +
431D ARG* 2.9 30.8 + - - +
437D LEU* 3.8 9.9 - - + +
444D ILE* 4.4 11.0 - - - -
445D ILE* 4.3 6.1 - - - -
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Residues in contact with VAL 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLY 3.7 18.2 - - - +
167D ARG* 4.0 21.8 - - + -
168D PRO* 4.1 14.4 - - + -
391D THR* 4.9 4.9 - - + -
396D ASP* 4.8 0.2 - - - +
424D LEU* 2.9 25.0 + - + +
425D GLU* 3.8 8.5 - - + +
427D CYS* 1.3 76.8 - - - +
429D GLN* 1.3 63.4 + - - +
431D ARG* 3.4 17.5 + - - +
432D ASN* 3.0 45.7 + - - +
14V THR* 4.7 5.2 - - + -
15V LEU* 4.6 11.7 - - + -
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Residues in contact with GLN 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D GLU 2.9 17.7 + - - +
426D ALA* 3.9 6.1 - - - +
428D VAL* 1.3 78.9 - - - +
430D ALA* 1.3 63.1 + - - +
432D ASN* 3.2 3.9 + - - +
433D GLU* 3.0 40.4 + - - +
15V LEU* 4.5 5.6 - - + +
18V LEU* 3.6 24.8 - - + +
19V PRO* 5.6 0.7 + - - +
21V LEU* 3.5 29.3 - - - +
25V GLN* 3.7 28.0 + - - +
29V GLN* 4.1 17.2 + - - +
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Residues in contact with ALA 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426D ALA 3.1 15.8 + - - +
427D CYS 3.8 2.9 - - - +
429D GLN* 1.3 79.4 + - - +
431D ARG* 1.3 60.8 + - - +
433D GLU* 3.3 13.0 + - - +
434D GLY 3.4 0.5 + - - -
435D ARG* 3.0 48.6 + - + +
437D LEU* 4.4 0.4 - - + -
444D ILE* 3.6 34.3 - - + -
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Residues in contact with ARG 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLY 4.2 1.6 + - - -
391D THR* 4.3 15.2 + - - +
392D GLU* 6.5 0.2 - - - +
395D GLY* 4.5 4.6 - - - -
396D ASP* 2.9 44.4 + - - +
427D CYS 2.9 18.8 + - - +
428D VAL* 3.6 21.0 - - - +
429D GLN 3.2 0.2 - - - -
430D ALA* 1.3 77.1 - - - +
432D ASN* 1.3 79.2 + - - +
434D GLY* 2.9 21.5 + - - -
435D ARG 4.0 11.7 + - - +
437D LEU* 4.0 23.1 - - + +
32V TYR* 3.5 22.9 + - + -
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Residues in contact with ASN 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLY 5.3 1.4 + - - -
428D VAL* 3.0 29.0 + - - +
429D GLN 3.2 4.5 + - - +
431D ARG* 1.3 103.2 + - - +
433D GLU* 1.3 59.3 + - - +
434D GLY 3.1 1.1 + - - -
15V LEU* 5.7 0.4 - - - +
28V ARG* 4.1 5.0 - - - +
29V GLN* 3.0 35.3 - - - +
32V TYR* 3.3 53.7 - - + +
113V VAL* 5.9 0.8 - - - +
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Residues in contact with GLU 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D GLN* 3.0 31.6 + - - +
430D ALA* 3.7 10.2 - - - +
431D ARG 3.1 0.6 - - - -
432D ASN* 1.3 76.3 - - - +
434D GLY* 1.3 59.5 + - - +
435D ARG* 3.6 14.5 + - + +
25V GLN* 3.9 34.2 + - - +
28V ARG* 3.0 61.8 + - + +
29V GLN* 4.4 6.2 - - - +
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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
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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