Contacts of the helix formed by residues 41 - 61 (chain 4) in PDB entry 1ILL
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 GLU 41 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404 THR* 1.4 73.9 - - - +
424 LYS* 1.3 94.4 + - + +
444 THR* 2.9 9.9 + - - -
454 PHE* 2.8 65.9 + - + -
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Residues in contact with LYS 42 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404 THR* 3.1 18.1 - - + +
414 GLU* 1.3 117.5 + - + +
434 GLU* 1.4 62.0 - - + +
454 PHE* 4.1 1.1 - - - -
464 CYS* 2.8 35.0 + - - +
934 LEU 2.6 23.1 + - - -
944 ALA* 2.9 29.8 - - - -
954 GLY* 5.1 1.1 - - - -
964 LEU* 3.8 25.9 - - + +
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Residues in contact with GLU 43 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354 ALA 4.9 1.0 - - - +
364 SER* 3.7 10.5 + - - -
394 THR* 2.9 32.9 + - - +
404 THR* 3.1 12.2 + - - +
424 LYS* 1.4 76.4 - - + +
444 THR* 1.4 67.7 + - - +
464 CYS* 4.2 5.4 - - - -
474 ARG* 2.8 69.6 + - - +
964 LEU* 5.7 4.3 - - + -
994 CYS* 4.8 11.0 - - - -
1004 PRO* 4.7 5.5 - - - +
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Residues in contact with THR 44 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324 ILE* 3.5 19.5 - - + +
334 PHE* 4.1 9.0 - - + -
364 SER* 3.7 9.9 + - - -
404 THR 2.8 21.5 + - - -
414 GLU* 2.9 17.6 + - - -
434 GLU* 1.4 81.6 - - - +
454 PHE* 1.3 70.8 + - + +
484 ALA* 2.8 31.0 + - + +
904 LEU* 6.2 0.4 - - + -
1154 ARG* 3.2 33.6 + - - +
1164 LEU* 5.8 4.3 - - + -
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Residues in contact with PHE 45 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414 GLU* 2.8 60.5 + - + +
444 THR* 1.3 79.5 - - + +
464 CYS* 1.4 53.7 + - - +
484 ALA* 3.9 0.7 - - - +
494 ALA* 2.8 37.4 + - - +
904 LEU* 3.7 33.8 - - + +
934 LEU* 3.5 33.7 - - + -
944 ALA* 3.7 18.8 - - - +
1164 LEU* 3.7 23.8 - - + -
1204 MET* 3.6 30.5 - - + -
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Residues in contact with CYS 46 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424 LYS 2.8 20.1 + - - +
454 PHE* 1.4 77.1 - - - +
474 ARG* 1.3 60.5 + - - +
494 ALA* 3.5 2.8 + - - +
504 THR* 2.7 34.0 + - - -
914 TRP* 6.1 0.7 - - - -
944 ALA* 3.4 10.7 - - + +
964 LEU* 3.2 20.6 - - + -
974 ASN 4.7 0.2 - - - -
984 SER* 3.4 14.4 - - - -
994 CYS* 2.0 58.1 - - - -
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Residues in contact with ARG 47 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324 ILE* 3.9 22.2 + - + +
354 ALA* 3.7 13.1 - - - +
364 SER* 2.6 39.2 + - - +
434 GLU* 2.8 66.1 + - - +
464 CYS* 1.3 71.6 - - - +
484 ALA* 1.3 56.5 + - - +
504 THR* 2.9 4.5 + - - -
514 VAL* 2.6 45.6 + - + +
994 CYS* 4.0 8.3 - - + +
1004 PRO* 2.9 52.6 + - - +
1024 LYS* 4.7 19.0 - - - +
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Residues in contact with ALA 48 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324 ILE* 3.9 26.7 - - + +
334 PHE* 5.2 4.0 - - + -
444 THR* 2.8 20.1 + - + +
454 PHE 3.9 2.5 - - - +
474 ARG* 1.3 76.7 - - - +
494 ALA* 1.3 57.0 + - - +
514 VAL* 4.4 0.4 - - - -
524 LEU* 2.8 36.9 + - - +
864 LEU* 6.3 1.8 - - + -
904 LEU* 4.1 17.0 - - + -
1124 PHE* 4.2 14.6 - - + -
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Residues in contact with ALA 49 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454 PHE 2.8 22.1 + - - +
464 CYS* 3.8 4.7 - - - +
484 ALA* 1.3 77.3 - - - +
504 THR* 1.3 57.6 + - - +
524 LEU* 4.9 0.4 - - - -
534 ARG* 2.7 55.9 + - - +
874 ASP* 3.7 28.6 - - - +
904 LEU* 4.3 7.1 - - + +
914 TRP* 4.3 5.6 - - + +
944 ALA* 5.5 0.2 - - + -
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Residues in contact with THR 50 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464 CYS 2.7 25.4 + - - -
474 ARG 3.6 1.6 - - - -
494 ALA* 1.3 73.6 - - - +
514 VAL* 1.3 58.2 + - - +
534 ARG* 3.5 12.6 + - - +
544 GLN* 2.8 46.2 + - - +
984 SER* 3.3 20.0 + - - -
994 CYS 2.9 41.2 + - - +
1014 VAL* 4.7 9.4 - - + +
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Residues in contact with VAL 51 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294 VAL* 4.6 7.0 - - + -
304 THR* 3.9 29.2 - - - +
324 ILE* 3.6 28.0 - - + -
474 ARG* 2.6 28.7 + - + +
484 ALA* 3.8 2.0 - - - +
504 THR* 1.3 71.0 - - - +
524 LEU* 1.3 68.8 + - + +
534 ARG 3.1 0.9 - - - -
544 GLN* 2.8 24.6 + - - +
554 PHE* 2.8 14.0 + - - +
1014 VAL* 3.8 31.9 - - + -
1024 LYS 4.7 2.0 - - - +
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Residues in contact with LEU 52 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294 VAL* 4.5 5.8 - - + -
484 ALA* 2.8 20.9 + - + +
494 ALA* 4.2 2.5 - - - +
514 VAL* 1.3 78.5 - - + +
534 ARG* 1.3 54.9 - - - +
554 PHE* 3.1 4.3 + - + +
564 TYR* 2.7 44.4 + - + +
834 LEU* 3.9 26.0 - - + +
864 LEU* 4.1 20.2 - - + -
874 ASP* 5.4 4.9 - - + +
1094 LEU* 3.5 31.2 - - + -
1124 PHE* 3.3 44.2 - - + -
1134 LEU* 5.3 1.8 - - + -
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Residues in contact with ARG 53 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494 ALA* 2.7 41.2 + - - +
504 THR* 3.5 19.1 + - - +
524 LEU* 1.3 72.6 - - - +
544 GLN* 1.4 67.9 + - - +
564 TYR* 3.7 11.8 - - + +
574 SER* 2.7 43.5 + - - +
874 ASP* 2.6 38.9 + - - +
914 TRP* 3.2 39.4 - - - -
984 SER* 2.8 29.1 + - - -
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Residues in contact with GLN 54 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504 THR* 2.8 36.0 + - - +
514 VAL* 2.8 13.7 + - - +
534 ARG* 1.4 83.1 - - - +
554 PHE* 1.3 56.8 + - - +
574 SER* 3.3 2.9 + - - -
584 HIS* 2.8 37.6 + - - +
1014 VAL* 3.8 36.5 - - + +
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Residues in contact with PHE 55 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244 CYS* 3.4 30.7 - - + -
274 LEU* 3.6 33.9 - - + -
294 VAL* 3.6 28.5 - - + -
514 VAL 2.8 13.2 + - - +
524 LEU* 3.7 7.0 - - + +
544 GLN* 1.3 73.2 - - - +
564 TYR* 1.4 65.0 + - - +
584 HIS* 4.9 0.7 - - - -
594 HIS* 2.8 59.6 + + + +
764 HIS* 5.6 3.1 - + - -
794 LEU* 5.5 2.0 - - + -
804 ILE* 6.0 1.1 - - + -
834 LEU* 4.6 7.2 - - + -
1094 LEU* 3.5 32.5 - - + -
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Residues in contact with TYR 56 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524 LEU 2.7 30.2 + - - +
534 ARG* 3.7 6.1 - - + +
554 PHE* 1.4 78.3 - - - +
574 SER* 1.3 73.3 + - - +
594 HIS 5.2 0.2 - - - -
604 GLU* 2.7 42.3 + - + +
804 ILE* 3.3 38.4 - - + -
834 LEU* 3.7 35.4 - - + -
844 LYS* 3.8 24.1 + - + +
874 ASP* 2.9 41.7 + - + -
884 ARG* 5.2 2.1 - - - +
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Residues in contact with SER 57 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534 ARG* 2.7 34.5 + - - +
544 GLN* 4.1 2.9 - - - -
564 TYR* 1.3 96.9 - - - +
584 HIS* 1.4 50.3 + - - +
604 GLU* 3.6 7.3 - - - +
614 LYS* 2.4 31.5 + - - +
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Residues in contact with HIS 58 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544 GLN 2.8 19.3 + - - +
554 PHE* 3.9 1.8 - - - +
574 SER* 1.4 72.6 - - - +
594 HIS* 1.4 101.1 + + + +
604 GLU 3.0 7.0 + - - -
614 LYS* 2.6 29.0 + - - +
624 ASP* 4.5 5.8 + - + -
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Residues in contact with HIS 59 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244 CYS* 5.3 6.7 - - + -
274 LEU* 4.4 17.2 - - + +
554 PHE* 2.8 59.8 + + + +
564 TYR 3.7 0.4 - - - -
584 HIS* 1.4 102.8 + + + +
604 GLU* 1.4 54.1 + - - +
614 LYS 3.0 5.4 - - - -
624 ASP* 2.8 54.7 + - + +
644 ARG* 5.4 1.8 - - - -
664 LEU* 3.8 9.9 - - - +
764 HIS* 5.4 2.2 - - + -
804 ILE* 4.6 3.9 - - - +
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Residues in contact with GLU 60 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564 TYR* 2.7 38.6 + - + +
574 SER* 3.6 14.8 - - - +
584 HIS 3.0 0.4 + - - -
594 HIS* 1.4 70.6 - - - +
614 LYS* 1.4 68.5 + - + +
624 ASP 3.6 0.2 - - - -
664 LEU* 3.5 16.4 - - - +
774 LYS* 2.5 47.1 + - - +
804 ILE* 3.0 40.0 - - + +
61R ASP* 3.9 4.6 - - - +
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Residues in contact with LYS 61 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574 SER 2.4 32.5 + - - +
584 HIS* 2.6 24.3 + - - +
594 HIS 3.0 0.6 - - - -
604 GLU* 1.4 88.6 - - + +
624 ASP* 1.4 53.3 + - - +
634 THR* 2.7 30.4 + - - +
664 LEU* 3.4 8.9 - - - +
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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