Contacts of the helix formed by residues 301 - 318 (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 THR 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A PRO* 4.1 1.4 - - - +
298A LYS* 2.5 47.9 + - + +
299A GLN 3.8 1.6 - - - +
300A GLY* 1.3 81.1 - - - +
302A ASP* 1.3 64.2 + - - +
303A ALA 3.3 2.2 - - - -
304A ALA* 3.1 21.3 + - - +
442A PHE* 3.8 12.3 - - + -
510A ILE* 3.7 17.5 - - + +
511A THR* 3.3 23.4 - - - +
1061A TYR* 3.8 22.2 - - - +
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Residues in contact with ASP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TRP* 2.9 37.5 + - + +
280A VAL* 3.9 2.8 - - - +
282A PRO* 5.7 5.0 - - - +
297A PRO* 3.6 22.4 - - - +
298A LYS 4.3 2.4 - - - +
299A GLN* 4.7 1.9 - - - -
300A GLY* 3.5 20.5 + - - -
301A THR* 1.3 74.5 + - - +
303A ALA* 1.3 67.7 + - - +
305A MET* 3.0 20.3 + - - +
306A ALA* 3.2 10.0 + - - +
511A THR* 5.2 0.2 - - - -
543A GLY 4.9 3.3 - - - +
544A LEU* 3.9 22.9 - - + +
547A TRP* 5.4 0.7 + - - -
553A ASN* 3.8 9.7 + - + +
557A LEU* 5.9 0.9 - - + -
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLY 5.8 0.4 - - - +
301A THR 3.3 1.0 + - - -
302A ASP* 1.3 73.6 - - - +
304A ALA* 1.3 61.8 + - - +
306A ALA* 3.4 7.5 + - - +
307A LEU* 3.0 31.5 + - + +
552A MET* 4.0 18.2 - - + +
553A ASN* 3.0 39.5 + - - +
556A GLY* 5.3 0.5 - - - -
1060A VAL 5.1 0.7 - - - +
1061A TYR* 4.1 19.7 - - + -
1062A ARG 5.2 2.0 - - - +
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Residues in contact with ALA 304 (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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301A THR 3.1 14.0 + - - +
302A ASP 3.0 0.4 - - - -
303A ALA* 1.3 79.8 - - - +
305A MET* 1.3 62.8 + - - +
307A LEU* 3.3 6.3 + - - +
308A ALA 3.2 16.6 + - - -
506A TRP* 3.5 36.0 - - + -
507A ALA* 3.8 5.7 - - + +
510A ILE* 3.9 9.4 - - + -
511A THR* 3.5 13.5 - - + -
1061A TYR* 3.7 13.7 - - + -
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Residues in contact with MET 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TRP* 3.6 29.2 - - + -
280A VAL* 3.6 35.4 - - + -
295A LEU* 4.0 13.9 - - + -
297A PRO* 4.5 4.7 - - + -
302A ASP* 3.0 11.9 + - - +
304A ALA* 1.3 78.1 - - - +
306A ALA* 1.3 61.5 + - - +
308A ALA* 3.4 3.5 + - - +
309A MET* 3.0 41.4 + - + +
507A ALA* 4.4 7.4 - - - -
511A THR* 3.8 13.7 - - + +
513A VAL* 3.7 34.1 - - + -
518A ILE* 4.2 19.9 - - + +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TRP* 4.0 10.0 - - + -
302A ASP 3.2 7.0 + - - +
303A ALA* 3.6 9.6 - - - +
304A ALA 3.2 0.2 - - - -
305A MET* 1.3 76.9 - - - +
307A LEU* 1.3 59.6 + - - +
309A MET* 3.2 2.5 + - - +
310A GLY* 2.9 27.0 + - - -
481A TYR* 4.9 0.9 + - - -
556A GLY* 3.7 33.8 - - - +
557A LEU* 3.9 18.2 - - + -
560A MET* 4.0 11.7 - - - +
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Residues in contact with LEU 307 (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* 3.0 21.0 + - + +
304A ALA* 3.6 8.3 - - - +
306A ALA* 1.3 78.1 - - + +
308A ALA* 1.3 56.4 + - - +
311A HIS* 2.9 23.6 + - - +
480A ASN* 5.1 0.9 - - - +
481A TYR* 3.2 30.1 - - + -
502A TYR* 3.8 42.7 - - + +
1059A LEU* 3.5 41.5 - - + +
1060A VAL 4.0 3.4 - - - -
1061A TYR* 3.6 34.1 - - + +
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Residues in contact with ALA 308 (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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304A ALA 3.2 3.0 + - - +
305A MET 3.8 5.2 - - - +
306A ALA 3.3 0.2 - - - -
307A LEU* 1.3 75.9 - - - +
309A MET* 1.3 65.4 + - - +
311A HIS* 3.1 3.8 - - - +
312A VAL* 3.1 26.2 + - - +
502A TYR 3.4 12.9 + - - +
503A THR 3.7 11.9 - - - +
504A PRO* 3.8 12.0 - - + +
507A ALA* 3.6 31.0 - - + -
518A ILE* 3.9 8.3 - - + -
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Residues in contact with MET 309 (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* 5.9 2.9 - - + -
252A TRP* 3.8 25.1 - - + -
295A LEU* 6.3 1.1 - - + -
305A MET* 3.0 27.0 + - + +
306A ALA 3.6 4.0 - - - +
308A ALA* 1.3 72.8 - - - +
310A GLY* 1.3 68.6 + - - +
312A VAL 3.2 1.9 + - - -
313A MET* 3.0 28.4 + - + +
518A ILE* 3.8 21.1 - - + +
521A ILE* 3.7 21.5 - - + +
522A ALA* 3.5 40.8 - - + +
525A PHE* 5.4 1.6 - - + -
560A MET* 3.7 30.1 - - + -
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Residues in contact with GLY 310 (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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306A ALA 2.9 16.2 + - - -
307A LEU 3.7 2.2 - - - -
309A MET* 1.3 75.1 - - - +
311A HIS* 1.3 63.0 + - - +
313A MET* 3.2 8.3 + - - +
314A LEU* 2.9 29.4 + - - +
481A TYR* 3.9 15.5 - - - -
560A MET* 4.2 12.9 - - - +
563A PHE* 4.6 8.3 - - - -
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Residues in contact with HIS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU 2.9 9.2 + - - +
308A ALA 3.1 10.3 - - - +
310A GLY* 1.3 76.3 - - - +
312A VAL* 1.3 63.7 + - - +
314A LEU* 3.8 2.1 - - - +
315A ARG* 3.1 25.3 + - - +
481A TYR* 3.0 27.8 + - + -
482A GLY 3.5 25.1 - - - -
483A LEU* 3.5 26.5 - - + +
493A ALA* 4.5 5.5 - - + +
495A SER 5.7 0.2 - - - -
496A TYR* 3.9 29.4 - + - -
502A TYR 3.4 18.4 + - - +
503A THR* 4.2 16.1 - - + +
504A PRO* 4.0 11.2 - - + -
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Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA 3.1 14.4 + - - +
309A MET* 3.7 5.8 - - - +
311A HIS* 1.3 76.7 - - - +
313A MET* 1.3 56.9 + - - +
315A ARG 3.6 0.2 + - - -
316A GLU* 3.0 54.2 + - - +
317A PHE* 4.6 0.8 - - + -
496A TYR* 3.6 21.8 - - + +
504A PRO* 3.7 22.9 - - + -
518A ILE* 5.1 0.9 - - + +
519A ILE* 4.3 22.4 - - + +
522A ALA* 4.1 16.4 - - + -
523A ARG* 4.7 6.3 - - + +
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A MET 3.0 12.9 + - - +
310A GLY* 3.5 7.0 - - - +
312A VAL* 1.3 74.6 - - - +
314A LEU* 1.3 59.5 + - - +
317A PHE* 2.8 44.4 + - + +
318A HIS* 3.7 3.7 + - + -
522A ALA* 3.4 37.7 - - + +
525A PHE* 3.5 27.6 - - + -
526A ALA* 4.1 9.6 - - + +
560A MET* 3.5 42.4 - - + +
563A PHE* 5.1 9.2 - - + -
564A CYS* 3.7 21.1 - - - -
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Residues in contact with LEU 314 (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 2.9 16.3 + - - +
311A HIS 3.8 2.9 - - - +
313A MET* 1.3 75.3 - - - +
315A ARG* 1.3 65.0 + - - +
318A HIS* 3.0 42.4 + - + +
319A LEU* 3.0 16.0 + - + +
336A MET* 5.0 3.8 - - + -
474A TYR* 6.0 0.7 - - + -
477A THR* 4.6 4.9 - - + -
478A LEU* 4.4 17.7 - - + -
481A TYR* 3.7 34.8 - - + -
483A LEU* 4.3 11.4 - - + -
563A PHE* 3.6 48.9 - - + -
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Residues in contact with ARG 315 (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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311A HIS* 3.1 18.4 + - - +
314A LEU* 1.3 77.9 - - - +
316A GLU* 1.3 60.5 + - + +
319A LEU* 3.5 22.3 - - - +
320A ASP* 2.9 67.4 + - - +
483A LEU* 3.4 29.0 - - + +
484A GLU* 2.8 46.1 + - - +
493A ALA 5.3 1.0 + - - -
496A TYR* 3.3 33.1 - - + +
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Residues in contact with GLU 316 (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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312A VAL* 3.0 21.3 + - - +
315A ARG* 1.3 82.0 - - + +
317A PHE* 1.3 74.3 + - + +
318A HIS 3.7 0.2 - - - -
320A ASP* 4.3 10.2 - - + +
321A ASN* 3.6 26.6 + - - +
496A TYR* 2.5 27.9 + - - +
523A ARG* 2.8 51.3 + - - +
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Residues in contact with PHE 317 (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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312A VAL* 5.0 1.1 - - + -
313A MET* 2.8 25.0 + - + +
316A GLU* 1.3 97.3 - - + +
318A HIS* 1.3 65.5 + - + +
321A ASN 3.8 8.7 - - - -
323A SER* 2.8 36.0 + - - +
326A PHE* 3.7 32.3 - + + +
327A THR* 5.0 0.2 + - - -
523A ARG* 3.9 18.8 - - + -
526A ALA* 3.4 25.6 - - + -
527A ASP* 3.7 31.4 - - + -
530A ASP* 4.8 9.2 - - + -
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Residues in contact with HIS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A MET* 4.0 9.9 - - + -
314A LEU* 3.0 35.4 + - + +
317A PHE* 1.3 81.9 + - + +
319A LEU* 1.3 75.6 + - + +
322A PRO* 4.0 15.4 - - - +
323A SER 4.9 0.2 - - - +
326A PHE* 3.7 25.4 - + + +
327A THR* 4.7 8.8 + - - -
330A VAL* 4.0 27.5 - - + +
336A MET* 6.0 1.1 - - + +
417A LEU* 6.1 0.4 - - - +
474A TYR* 4.1 21.4 + + - +
478A LEU* 6.0 0.2 - - + -
563A PHE* 2.8 37.3 + + + +
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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