Contacts of the helix formed by residues 549 - 564 (chain A) in PDB entry 1SIW
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 HIS 549 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A TRP* 3.1 3.3 - - + +
548A TYR* 1.3 89.2 - + + +
550A LEU* 1.3 64.1 + - - +
551A ASP 3.0 4.4 + - - -
552A MET* 3.0 17.0 + - + +
553A ASN* 3.4 16.5 + - - +
628A LEU* 4.5 6.5 - - + +
1056A GLU* 4.2 0.4 + - - -
1062A ARG* 3.5 56.2 - - + +
1063A PRO* 3.4 23.7 + - - +
1064A PRO* 5.0 1.1 - - + -
1065A ILE* 3.7 24.5 - - + +
1193A LYS* 2.8 35.1 + - - +
1219A ASP* 5.0 0.6 + - - -
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Residues in contact with LEU 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A CYS* 4.3 7.2 - - - -
223A LEU 3.8 2.9 - - - +
225A PRO* 3.5 18.8 - - + -
544A LEU 3.7 17.9 - - - +
545A ASN* 3.0 52.3 - - - +
547A TRP 3.1 18.6 + - - +
548A TYR 3.6 10.5 - - - +
549A HIS* 1.3 76.0 - - - +
551A ASP* 1.3 79.1 + - - +
553A ASN* 3.4 2.6 + - - +
554A TYR* 3.0 29.9 + - - +
1196A HIS* 3.9 13.7 - - + -
1214A VAL* 4.2 9.0 - - + -
1216A SER* 4.9 1.1 - - - -
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Residues in contact with ASP 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PRO* 3.4 13.6 - - - +
226A ALA* 3.9 10.5 + - - +
229A GLN* 2.6 42.3 + - - +
549A HIS 3.0 1.7 + - - -
550A LEU* 1.3 82.4 - - - +
552A MET* 1.3 58.7 + - - +
554A TYR 3.9 0.2 - - - -
555A ARG* 2.9 37.9 + - - +
1056A GLU* 4.0 20.8 - - - +
1193A LYS* 4.9 5.5 + - - +
1195A THR* 5.1 0.3 + - - -
1196A HIS* 2.7 31.5 + - - -
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Residues in contact with MET 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 4.0 15.0 - - + +
549A HIS* 3.0 14.2 + - + +
551A ASP* 1.3 79.5 - - + +
553A ASN* 1.3 67.0 + - - +
555A ARG* 3.9 10.2 - - - +
556A GLY* 2.9 21.7 + - - -
1056A GLU* 3.7 32.8 - - - +
1058A LEU 4.2 1.6 - - - +
1059A LEU* 3.0 23.6 - - + +
1060A VAL* 2.8 52.3 - - + +
1062A ARG* 3.8 23.1 - - + +
1193A LYS* 5.3 0.2 - - - +
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Residues in contact with ASN 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLY* 4.7 8.0 + - - +
302A ASP* 3.8 8.0 + - - +
303A ALA* 3.0 33.3 + - - +
306A ALA* 5.0 0.5 - - - +
544A LEU* 3.3 49.5 + - + +
547A TRP* 4.1 17.6 - - - +
549A HIS* 3.4 13.2 + - - +
550A LEU* 3.4 5.7 + - - +
552A MET* 1.3 79.0 - - - +
554A TYR* 1.3 64.6 + - - +
556A GLY* 3.3 1.4 + - - -
557A LEU* 3.3 29.0 + - - +
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Residues in contact with TYR 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PRO* 3.8 9.0 - - + -
226A ALA* 3.7 18.4 - - + -
540A VAL* 3.4 24.6 - - + +
541A GLY 3.4 10.4 + - - -
544A LEU* 3.9 5.6 - - + -
545A ASN* 3.2 44.7 - - + +
550A LEU 3.0 19.5 + - - +
553A ASN* 1.3 80.6 - - + +
555A ARG* 1.3 60.5 + - - +
557A LEU* 3.1 7.7 + - + +
558A ILE* 2.7 35.7 + - + +
574A TRP* 3.3 37.2 - + - -
576A HIS* 2.7 37.3 + - - -
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Residues in contact with ARG 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 4.0 13.5 - - + -
229A GLN* 4.0 14.4 + - - +
230A THR* 4.6 12.5 + - - +
551A ASP* 2.9 30.1 + - - +
552A MET* 4.1 12.0 - - - +
554A TYR* 1.3 75.7 - - - +
556A GLY* 1.3 57.0 + - - +
558A ILE* 4.1 7.9 - - - -
559A ASN* 2.9 41.4 + - - +
1043A GLN 5.2 2.2 + - - -
1044A LEU* 2.9 29.3 + - - +
1046A GLN* 4.0 17.6 - - - +
1051A MET* 4.1 7.1 - - - +
1056A GLU* 2.8 30.9 + - - +
1057A SER 3.2 15.6 + - - -
1058A LEU* 3.7 8.7 - - - +
1059A LEU* 3.8 22.2 - - + +
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Residues in contact with GLY 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ALA 5.3 2.5 - - - -
306A ALA* 3.7 21.9 - - - +
481A TYR* 4.9 1.0 + - - -
552A MET 2.9 15.5 + - - -
553A ASN* 3.7 2.5 - - - -
554A TYR 3.1 0.2 - - - -
555A ARG* 1.3 79.9 - - - +
557A LEU* 1.3 60.1 + - - +
559A ASN* 3.9 2.6 - - - +
560A MET* 3.5 23.9 + - - +
1059A LEU* 3.5 19.2 - - - +
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Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TRP* 3.8 40.4 - - + -
302A ASP* 5.4 1.6 - - + +
306A ALA* 3.9 11.4 - - + -
538A ILE* 3.6 30.9 - - + +
540A VAL* 3.9 18.6 - - + -
544A LEU* 3.7 24.5 - - + -
553A ASN* 3.3 13.0 - - - +
554A TYR* 3.1 10.4 + - - +
556A GLY* 1.3 74.8 - - - +
558A ILE* 1.3 66.3 + - + +
560A MET* 3.3 11.3 + - - +
561A LEU* 3.2 27.2 + - + +
574A TRP* 5.3 4.3 - - + -
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Residues in contact with ILE 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ALA* 4.2 16.6 - - + +
230A THR* 3.9 22.4 - - + +
231A TRP* 3.7 42.8 - - + -
554A TYR 2.7 30.1 + - - +
555A ARG* 3.8 7.4 - - - +
557A LEU* 1.3 72.6 - - - +
559A ASN* 1.3 60.5 + - - +
561A LEU* 3.2 10.4 + - + +
562A ILE* 2.9 48.1 + - + +
574A TRP* 3.9 20.2 - - + +
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Residues in contact with ASN 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A THR* 6.1 0.6 - - - +
477A THR* 5.9 0.3 - - - +
481A TYR* 3.2 19.1 + - - +
555A ARG* 2.9 25.2 + - - +
556A GLY 3.9 3.1 - - - +
558A ILE* 1.3 81.4 - - - +
560A MET* 1.3 57.0 + - - +
562A ILE* 3.1 6.7 + - - +
563A PHE* 2.7 55.8 + - + -
1044A LEU* 4.3 23.4 - - - +
1059A LEU* 3.1 32.9 - - - +
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Residues in contact with MET 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ILE* 6.0 1.1 - - + -
252A TRP* 4.0 23.3 - - + -
306A ALA* 4.0 17.9 - - - +
309A MET* 3.7 35.4 - - + -
310A GLY* 4.2 10.8 - - - +
313A MET* 3.5 33.9 - - + -
481A TYR* 6.1 0.2 - - - +
525A PHE* 4.7 10.1 - - + -
538A ILE* 4.4 12.6 - - + -
556A GLY 3.5 16.1 + - - +
557A LEU* 3.3 11.8 + - - +
559A ASN* 1.3 79.2 - - + +
561A LEU* 1.3 63.1 + - - +
563A PHE* 3.4 6.5 + - - +
564A CYS* 3.2 29.0 + - - -
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A PHE* 3.8 17.3 - - + -
536A SER 3.7 19.5 - - - +
538A ILE* 4.2 20.0 - - + +
557A LEU* 3.2 18.1 + - + +
558A ILE* 3.4 8.5 - - - +
559A ASN 3.1 0.4 - - - -
560A MET* 1.3 79.7 - - - +
562A ILE* 1.3 60.5 + - - +
564A CYS* 3.3 2.8 + - - -
565A GLY 3.1 3.5 + - - -
566A CYS* 2.9 36.1 + - + +
567A VAL* 4.1 13.7 - - + -
573A GLY 3.4 37.7 - - - +
574A TRP* 3.5 19.5 - - + +
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Residues in contact with ILE 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A THR* 4.1 6.5 - - + -
329A TYR* 3.6 17.0 - - + -
330A VAL* 3.9 6.7 - - + +
334A THR* 3.4 31.2 - - + -
558A ILE* 2.9 40.9 + - + +
559A ASN* 3.7 9.2 - - - +
561A LEU* 1.3 71.0 - - - +
563A PHE* 1.3 63.9 + - + +
564A CYS 2.9 4.7 - - - -
565A GLY* 2.8 20.8 + - - +
567A VAL* 4.3 5.6 - - + -
1042A GLN* 3.4 38.8 - - + +
1044A LEU* 4.2 17.3 - - + -
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Residues in contact with PHE 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLY* 4.4 9.2 - - - -
313A MET* 5.1 6.5 - - + -
314A LEU* 3.6 36.8 - - + -
318A HIS* 2.8 34.3 + + + +
326A PHE* 3.4 14.0 - - - +
330A VAL* 4.4 6.0 - - + +
336A MET* 3.6 26.5 - - + -
477A THR* 3.9 22.2 - - + -
481A TYR* 3.7 21.8 - + - -
559A ASN* 2.7 42.5 + - + +
560A MET* 3.7 8.5 - - - +
562A ILE* 1.3 78.0 - - + +
564A CYS* 1.3 61.3 + - - +
1044A LEU* 3.9 13.9 - - + -
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Residues in contact with CYS 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A MET* 3.7 25.1 - - - -
325A TYR* 3.7 3.8 - - - -
326A PHE* 3.2 30.4 - - + -
525A PHE* 4.2 7.9 - - + -
526A ALA* 3.9 24.7 - - - -
529A ALA* 3.6 18.7 - - + +
534A GLY* 4.1 0.2 - - - -
560A MET 3.2 19.3 + - - +
562A ILE 2.9 1.4 - - - -
563A PHE* 1.3 81.2 - - - +
565A GLY* 1.3 63.6 + - - +
566A CYS* 3.3 15.4 + - - -
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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