Contacts of the helix formed by residues 34 - 52 (chain 3) in PDB entry 5IY6
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 LEU 34 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282 PRO* 3.9 10.6 - - + +
173 ALA* 5.7 1.8 - - - +
213 TRP* 3.1 61.6 + - + +
333 THR* 1.3 71.7 + - - +
353 SER* 1.3 69.0 + - - +
373 CYS* 2.9 26.4 - - - -
383 ILE* 3.0 26.5 + - + +
1153 ILE* 4.0 21.3 - - + -
1193 MET* 5.1 14.4 - - + -
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Residues in contact with SER 35 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333 THR* 3.0 19.3 + - - +
343 LEU* 1.3 85.2 - - - +
363 LYS* 1.3 69.3 + - - +
383 ILE* 3.3 6.6 + - - +
393 ASP* 3.1 20.3 + - - +
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Residues in contact with LYS 36 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312 LEU* 4.2 2.0 - - + -
612 PHE* 3.3 29.2 + - - -
622 LEU* 3.7 33.1 + - + +
333 THR* 2.8 28.1 - - + +
353 SER* 1.3 79.9 + - - +
373 CYS* 1.3 65.6 + - - +
393 ASP* 3.0 22.7 + - + +
403 ALA* 3.0 25.2 + - + +
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Residues in contact with CYS 37 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153 VAL* 6.6 0.2 - - - -
213 TRP* 3.3 46.4 - - + -
243 LYS* 5.8 0.7 - - - +
333 THR 2.8 8.8 + - - +
343 LEU* 2.9 32.5 + - - +
363 LYS* 1.3 76.4 - - - +
383 ILE* 1.3 68.1 + - - +
403 ALA* 3.4 6.3 + - - +
413 VAL* 2.9 29.1 + - - +
1643 ILE* 6.1 2.0 - - + +
1963 LEU* 5.5 0.7 - - + -
2233 LEU* 5.2 13.9 - - + +
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Residues in contact with ILE 38 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182 LEU* 5.7 0.2 - - + -
153 VAL* 5.8 11.2 - - + -
343 LEU* 3.0 30.2 + - + +
353 SER* 3.5 9.0 - - - +
373 CYS* 1.3 86.9 - - - +
393 ASP* 1.3 65.5 + - - +
413 VAL* 2.7 30.2 - - + +
423 MET* 2.9 7.6 + - + +
703 LEU* 6.0 0.4 - - + -
1113 ILE* 3.4 31.2 - - + -
1123 VAL* 5.0 10.5 - - + -
1153 ILE* 4.1 25.1 - - + -
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Residues in contact with ASP 39 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182 LEU* 1.7 87.6 - - - +
1222 LEU* 4.1 18.3 - - - +
353 SER 3.1 9.7 + - - +
363 LYS* 3.0 30.2 + - + +
383 ILE* 1.3 76.9 - - - +
403 ALA* 1.3 62.7 + - - +
423 MET 3.2 0.2 + - - -
433 VAL* 3.1 10.4 + - - +
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Residues in contact with ALA 40 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363 LYS* 3.0 15.4 + - + +
373 CYS* 3.7 9.6 - - - +
393 ASP* 1.3 73.6 - - - +
413 VAL* 1.3 65.1 + - - +
433 VAL* 3.1 11.1 + - - +
443 LEU* 3.0 18.4 + - - +
2233 LEU* 4.4 16.6 - - + -
2243 LEU* 3.6 33.6 - - + +
2273 LEU* 4.9 0.9 - - - -
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Residues in contact with VAL 41 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 ILE* 4.1 28.6 - - + +
153 VAL* 5.2 2.9 - - + -
373 CYS* 2.9 12.4 + - - +
383 ILE* 2.7 44.4 - - + +
403 ALA* 1.3 76.7 - - - +
423 MET* 1.3 60.8 + - + +
443 LEU* 3.3 2.9 + - + +
453 GLY* 2.9 25.3 + - - -
593 VAL* 6.1 2.2 - - + -
1113 ILE* 4.8 3.4 - - + -
1643 ILE* 4.5 17.9 - - + -
2233 LEU* 5.8 0.2 - - + -
2273 LEU* 4.3 20.8 - - + +
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Residues in contact with MET 42 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ASN* 2.5 61.6 - - + +
1182 LEU* 3.0 26.7 - - + -
383 ILE* 2.9 7.1 + - + +
403 ALA 3.1 0.2 - - - -
413 VAL* 1.3 81.4 - - - +
433 VAL* 1.3 62.9 + - - +
453 GLY* 3.3 2.3 + - - -
463 ASN* 2.9 23.0 + - - +
1043 LEU* 3.6 11.8 - - + +
1073 ALA* 4.4 5.2 - - - +
1083 ASN* 3.1 13.7 - - + +
1113 ILE* 2.9 40.8 - - + -
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Residues in contact with VAL 43 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002 LEU* 4.8 14.1 - - + +
1012 LEU 6.0 1.8 - - - +
1172 ASN 6.1 0.2 - - - +
1182 LEU* 2.9 33.4 - - + -
1192 ARG* 4.7 15.9 - - + +
1222 LEU* 5.1 4.0 - - + -
393 ASP* 3.1 10.5 + - - +
403 ALA* 3.1 9.7 + - - +
423 MET* 1.3 74.6 - - - +
443 LEU* 1.3 64.1 + - - +
463 ASN* 3.2 6.8 + - - +
473 SER* 3.0 22.9 + - - -
2243 LEU* 4.3 22.0 - - + -
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Residues in contact with LEU 44 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 LEU* 6.1 2.2 - - + -
133 ILE* 5.1 12.1 - - + -
403 ALA 3.0 11.9 + - - +
413 VAL* 3.5 8.7 - - + +
433 VAL* 1.3 77.2 - - - +
453 GLY* 1.3 66.8 + - - +
473 SER* 2.6 30.2 + - - +
483 HIS* 2.9 17.6 + - + -
1623 LEU* 6.1 3.8 - - + -
2243 LEU* 4.3 9.1 - - + +
2273 LEU* 3.7 30.7 - - + +
2283 LEU* 3.7 40.6 - - + +
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Residues in contact with GLY 45 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413 VAL 2.9 15.1 + - - -
423 MET* 3.7 3.1 - - - -
433 VAL 3.2 0.2 - - - -
443 LEU* 1.3 82.3 - - - +
463 ASN* 1.3 63.2 + - - +
483 HIS* 3.0 3.3 + - - -
493 LEU* 2.8 30.8 + - - +
573 LEU* 3.9 24.9 - - - -
1043 LEU* 5.0 3.1 - - - -
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Residues in contact with ASN 46 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172 ASN 3.1 12.7 - - - +
1192 ARG* 5.0 13.6 - - + +
1202 ILE* 5.0 5.3 - - - +
423 MET 2.9 13.9 + - - +
433 VAL* 3.2 9.4 + - + +
453 GLY* 1.3 75.5 - - - +
473 SER* 1.3 63.7 + - - +
493 LEU* 3.4 5.4 + - - +
503 PHE* 3.0 28.1 + - - +
1013 TYR* 4.9 3.3 - - - +
1043 LEU* 2.9 43.9 - - + +
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Residues in contact with SER 47 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433 VAL* 3.0 13.4 + - - -
443 LEU* 2.6 32.3 + - - +
463 ASN* 1.3 77.4 - - - +
483 HIS* 1.3 66.3 + - - +
503 PHE* 3.1 7.9 + - - +
513 MET* 3.0 22.7 + - - +
2283 LEU* 5.6 7.2 - - - +
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Residues in contact with HIS 48 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 ASN* 4.7 6.2 - - + +
113 LEU* 2.8 46.9 - - + +
443 LEU* 2.9 17.1 + - + +
453 GLY* 3.0 10.7 + - - +
473 SER* 1.3 85.8 + - - +
493 LEU* 1.3 69.8 + - + +
513 MET* 3.3 17.3 + - + +
553 ASN* 2.9 61.8 + - + +
563 LYS 4.1 10.1 + - - -
573 LEU* 5.3 2.9 - - + +
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Residues in contact with LEU 49 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453 GLY 2.8 35.4 + - - +
463 ASN* 3.9 4.9 - - - +
483 HIS* 1.3 82.5 - - + +
503 PHE* 1.3 58.0 + - - +
523 ASN 2.8 23.7 - - - +
553 ASN* 3.1 35.0 - - - +
563 LYS* 3.9 9.0 - - - -
573 LEU* 4.0 27.4 - - + +
1003 LYS* 3.6 9.0 - - - +
1013 TYR* 2.9 52.2 - - + +
1043 LEU* 6.0 5.2 - - + -
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Residues in contact with PHE 50 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463 ASN* 3.0 23.8 + - - +
473 SER* 3.1 8.5 + - - +
493 LEU* 1.3 74.7 - - - +
513 MET* 1.3 69.2 + - - +
523 ASN* 3.3 1.7 + - - -
1013 TYR* 4.1 20.9 - + - +
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Residues in contact with MET 51 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 ASN* 5.7 2.5 - - - +
473 SER 3.0 11.7 + - - +
483 HIS* 3.5 19.5 - - + +
493 LEU 3.2 0.8 - - - -
503 PHE* 1.3 80.3 - - - +
523 ASN* 1.3 94.0 + - - +
553 ASN* 3.4 15.7 - - - +
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Residues in contact with ASN 52 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53 GLU* 4.2 33.1 + - + +
93 ASN* 5.1 4.4 - - - +
493 LEU 2.8 18.7 + - - +
503 PHE 3.2 2.0 - - - -
513 MET* 1.3 126.9 - - - +
533 ARG* 1.3 64.5 + - - +
543 SER* 3.2 4.7 - - - +
553 ASN* 3.3 29.2 + - - +
1013 TYR* 3.9 2.6 - - - -
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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