Contacts of the helix formed by residues 362 - 378 (chain A) in PDB entry 3SMP
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 ASP 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A THR* 3.5 0.2 - - - -
361A LEU* 1.3 74.5 - - - +
363A GLU* 1.3 70.2 + - - +
364A LEU* 3.4 5.0 + - - +
365A ASP* 2.9 40.8 + - - +
366A CYS* 3.1 22.9 + - - -
1001A ACO 4.1 15.8 + - - -
485B ARG* 2.9 38.6 + - - -
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Residues in contact with GLU 363 (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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242A ASP* 5.7 0.4 - - - +
339A THR* 3.2 20.2 - - + +
340A GLY* 3.8 18.3 - - - +
341A GLY* 3.8 16.9 + - - +
361A LEU 4.3 2.4 - - - +
362A ASP* 1.3 81.9 - - - +
364A LEU* 1.3 58.8 + - - +
366A CYS* 3.3 2.8 + - - +
367A LEU* 2.9 30.9 + - - +
583A GLY* 5.2 1.4 - - - -
1001A ACO 3.9 35.9 + - - +
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Residues in contact with LEU 364 (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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362A ASP* 3.4 10.3 + - - +
363A GLU* 1.3 77.9 - - - +
365A ASP* 1.3 63.9 + - - +
367A LEU* 3.2 23.8 + - + +
368A ILE* 3.0 39.5 + - + +
412A LEU* 5.5 0.2 - - + -
414A ASN* 4.4 12.8 - - - +
422A LEU* 3.8 22.0 - - + -
430A TYR* 4.0 20.9 - - + -
485B ARG* 3.9 11.9 - - - +
486B PHE* 3.4 38.6 - - + -
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Residues in contact with ASP 365 (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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362A ASP* 2.9 35.4 + - + +
363A GLU 3.4 0.2 - - - -
364A LEU* 1.3 72.6 - - - +
366A CYS* 1.3 62.3 + - - +
368A ILE* 4.0 1.3 - - - +
369A GLN* 3.0 35.4 + - + +
430A TYR* 2.0 36.6 + - - -
485B ARG* 2.8 14.7 + - - -
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Residues in contact with CYS 366 (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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339A THR* 3.9 15.7 - - + -
361A LEU* 3.5 29.8 - - - -
362A ASP 3.1 19.5 + - - +
363A GLU 3.6 3.1 - - - +
365A ASP* 1.3 78.8 - - - +
367A LEU* 1.3 66.5 + - - +
369A GLN* 4.8 0.4 - - - -
370A GLY 3.0 19.4 + - - -
582A PHE 3.3 9.5 - - - +
583A GLY* 3.5 14.8 - - - +
586A GLY* 3.4 11.3 - - - -
587A ALA* 3.7 17.9 - - - -
590A GLU* 5.8 1.6 - - - -
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLU 2.9 18.6 + - - +
364A LEU* 3.2 17.2 + - + +
366A CYS* 1.3 76.3 - - - +
368A ILE* 1.3 58.0 + - + +
371A LEU* 3.0 42.7 + - + +
412A LEU* 4.3 15.7 - - + -
414A ASN* 4.0 26.7 - - - +
545A VAL* 4.5 12.1 - - + -
582A PHE* 3.7 25.9 - - + +
583A GLY* 4.1 11.3 - - - +
3002A CL 3.9 14.1 - - + -
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Residues in contact with ILE 368 (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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364A LEU* 3.0 30.8 + - + +
365A ASP 4.0 2.9 - - - +
367A LEU* 1.3 72.8 - - + +
369A GLN* 1.3 73.4 + - - +
371A LEU* 3.8 4.8 - - + +
372A LEU* 2.9 50.2 + - + +
412A LEU* 3.7 31.0 - - + -
422A LEU* 5.5 1.6 - - + -
424A VAL* 4.1 20.4 - - + -
427A LYS 4.7 0.7 - - - +
430A TYR* 4.1 41.3 - - + -
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Residues in contact with GLN 369 (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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365A ASP* 3.0 25.6 + - + +
366A CYS* 4.1 2.2 - - - +
368A ILE* 1.3 82.2 - - - +
370A GLY* 1.3 57.8 + - - +
372A LEU* 3.8 3.0 - - - +
373A TYR* 2.8 30.7 + - - +
427A LYS* 2.5 56.4 + - - +
428A ASP* 4.8 4.3 + - - +
430A TYR* 5.0 4.4 - - - -
586A GLY* 4.5 7.0 - - - +
589A LEU* 3.5 16.2 - - + +
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Residues in contact with GLY 370 (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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366A CYS 3.0 10.1 + - - -
369A GLN* 1.3 74.4 - - - +
371A LEU* 1.3 56.4 + - - +
373A TYR* 3.2 1.7 + - - +
374A VAL* 2.8 39.8 + - - +
582A PHE* 3.6 27.1 - - - -
585A VAL* 3.7 10.5 - - - -
586A GLY* 3.7 10.4 - - - -
589A LEU* 4.3 0.2 - - - -
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Residues in contact with LEU 371 (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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367A LEU* 3.0 31.5 + - + +
368A ILE* 3.8 4.5 - - + +
370A GLY* 1.3 75.2 - - - +
372A LEU* 1.3 77.8 + - + +
374A VAL* 3.3 2.3 + - - +
375A ASP* 2.9 34.8 + - + +
384A GLU* 5.4 0.9 - - - +
410A MET* 4.1 21.1 - - + -
412A LEU* 3.7 33.9 - - + -
545A VAL* 4.4 3.1 - - + -
576A LEU* 3.5 33.2 - - + +
582A PHE* 3.4 20.1 - - + -
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Residues in contact with LEU 372 (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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368A ILE* 2.9 35.9 + - + +
369A GLN* 4.0 3.6 - - - +
371A LEU* 1.3 92.1 - - + +
373A TYR* 1.3 63.6 + - - +
375A ASP* 3.4 5.7 + - + +
376A SER* 3.0 24.1 + - - -
408A TYR* 3.5 39.0 + - + +
410A MET* 4.4 13.2 - - + -
424A VAL* 4.0 12.6 - - + -
427A LYS* 3.4 37.9 - - + -
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Residues in contact with TYR 373 (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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298A LEU* 3.8 20.0 - - + +
299A THR 3.9 16.0 + - - -
300A MET* 3.1 35.8 - - + +
307A LEU* 4.6 7.4 - - + -
369A GLN 2.8 20.6 + - - +
370A GLY 3.2 2.4 + - - +
372A LEU* 1.3 77.1 - - - +
374A VAL* 1.3 67.0 + - + +
376A SER* 2.7 27.2 + - - -
377A VAL* 3.2 35.6 + - + +
585A VAL* 4.0 16.4 - - + -
589A LEU* 3.6 25.4 - - + -
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Residues in contact with VAL 374 (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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295A LEU* 4.4 19.7 - - + -
307A LEU* 5.4 0.7 - - + -
309A PHE* 5.1 2.9 - - + -
370A GLY 2.8 23.5 + - - +
373A TYR* 1.3 75.0 - - + +
375A ASP* 1.3 63.7 + - - +
377A VAL* 3.2 8.0 + - - +
378A GLY* 2.9 24.1 + - - +
384A GLU* 3.3 33.5 - - + +
578A HIS* 3.9 14.4 - - + +
582A PHE* 4.0 19.7 - - + -
585A VAL* 4.1 23.8 - - + -
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Residues in contact with ASP 375 (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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371A LEU* 2.9 22.5 + - + +
372A LEU* 3.9 8.2 - - + +
374A VAL* 1.3 77.6 - - - +
376A SER* 1.3 60.3 + - - +
377A VAL 3.5 0.2 + - - -
378A GLY* 3.5 9.4 + - - -
384A GLU* 4.0 25.5 + - + +
385A CYS* 4.7 2.9 - - - +
407A PRO* 4.4 20.1 - - - +
576A LEU* 5.9 2.2 - - + -
2385A ARS 3.9 24.1 - - - -
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Residues in contact with SER 376 (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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372A LEU 3.0 14.3 + - - -
373A TYR* 2.7 28.3 + - - -
375A ASP* 1.3 78.8 - - - +
377A VAL* 1.3 66.7 + - - +
408A TYR* 6.1 0.4 - - - -
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Residues in contact with VAL 377 (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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295A LEU* 4.0 11.0 - - + -
298A LEU* 3.5 33.6 - - + +
299A THR 5.6 2.7 - - - +
373A TYR* 3.4 39.9 - - + +
374A VAL* 3.5 13.7 - - - +
376A SER* 1.3 86.9 + - - +
378A GLY* 1.3 68.4 + - - +
380A ASN 5.2 1.2 + - - -
381A GLY 5.4 1.9 + - - -
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Residues in contact with GLY 378 (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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295A LEU* 3.8 14.2 - - - +
298A LEU* 5.4 0.7 - - - +
374A VAL* 2.9 17.2 + - - +
375A ASP 3.5 7.0 + - - -
376A SER 3.5 2.6 - - - -
377A VAL* 1.3 88.4 - - - +
379A PHE* 1.3 59.3 + - - -
380A ASN 3.7 3.0 + - - -
381A GLY* 5.4 1.8 - - - -
382A LYS 3.7 7.9 - - - -
383A PRO* 5.3 0.7 - - - -
384A GLU* 4.6 9.6 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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