Contacts of the helix formed by residues 373 - 383 (chain B) in PDB entry 3SWD
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 SER 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B HIS* 5.8 2.3 - - - +
366B MET 4.7 0.2 + - - -
367B ALA* 3.4 26.6 - - - -
368B THR* 2.9 26.0 + - - -
369B ASP* 3.1 24.1 + - - +
372B ALA* 1.3 71.2 - - - +
374B ALA* 1.3 64.7 + - - +
375B SER 2.9 2.9 - - - -
376B LEU* 2.9 30.6 + - - +
377B VAL 3.8 2.1 + - - -
395B ILE* 3.9 13.1 - - - +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B THR* 4.4 10.3 - - + -
309B GLN* 5.2 1.6 - - - +
369B ASP 4.8 0.2 + - - -
370B LEU 5.6 0.2 + - - -
371B ARG 3.2 15.0 + - - +
372B ALA 3.2 1.0 + - - -
373B SER* 1.3 76.6 - - - +
375B SER* 1.3 62.0 + - - +
377B VAL* 3.1 15.7 + - - +
378B LEU* 3.1 24.3 + - - +
395B ILE* 4.4 7.4 - - + +
399B TYR* 3.6 29.8 - - + +
402B ILE* 4.3 13.5 - - + -
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Residues in contact with SER 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA* 3.5 33.7 + - - +
309B GLN* 4.1 12.8 - - - +
312B LEU* 3.3 16.9 - - - +
334B HIS* 4.0 13.2 - - - +
338B LEU* 4.5 5.0 - - - +
372B ALA 2.8 20.0 + - - -
373B SER 2.9 1.6 - - - -
374B ALA* 1.3 80.5 - - - +
376B LEU* 1.3 59.3 + - - +
378B LEU* 3.3 6.9 + - - -
379B ALA* 2.9 26.9 + - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B HIS* 4.3 9.9 - - + +
337B GLU* 3.7 28.0 - - + -
338B LEU* 4.0 22.2 - - + +
341B MET* 4.8 1.7 - - - +
365B VAL* 4.1 23.1 - - + -
366B MET 3.5 34.1 - - - +
367B ALA* 4.0 9.2 - - - +
373B SER* 2.9 20.6 + - - +
375B SER* 1.3 78.0 - - - +
377B VAL* 1.3 60.1 + - - +
379B ALA* 3.4 5.8 + - - +
380B GLY* 3.0 23.9 + - - -
387B THR* 4.7 3.3 - - - +
389B VAL* 4.0 15.5 - - + +
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.2 17.0 - - + -
6B VAL* 4.6 5.8 - - + +
373B SER 4.1 1.1 - - - +
374B ALA* 3.1 11.4 + - - +
376B LEU* 1.3 74.7 - - - +
378B LEU* 1.3 67.5 + - + +
380B GLY* 3.1 11.2 + - - -
381B CYS* 3.2 14.8 + - - -
389B VAL* 4.4 12.6 - - + -
395B ILE* 3.5 33.7 - - + -
402B ILE* 5.2 5.6 - - + -
406B LEU* 3.6 27.4 - - + -
413B ILE* 3.9 20.2 - - + -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 5.4 2.0 - - + +
237B THR* 3.6 42.0 - - + +
238B PHE* 6.2 0.9 - - + -
240B VAL* 4.1 13.9 - - + -
241B ALA* 4.0 25.1 - - + +
244B ILE* 4.1 8.7 - - + +
309B GLN* 4.8 8.1 - - + -
312B LEU* 3.6 17.7 - - + -
374B ALA* 3.1 19.6 + - + +
375B SER* 3.7 3.4 - - - +
376B LEU 3.3 0.2 - - - -
377B VAL* 1.3 76.0 - - + +
379B ALA* 1.3 65.4 + - - +
381B CYS* 3.1 18.8 + - - +
382B ILE* 3.5 12.0 + - - +
402B ILE* 5.0 3.8 - - + -
406B LEU* 4.6 23.6 - - + -
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 3.6 15.8 - - + +
338B LEU* 3.7 22.9 - - + -
341B MET* 3.6 19.5 - - + -
360B LEU* 4.1 4.4 - - + +
375B SER 2.9 17.3 + - - +
376B LEU 3.5 6.3 - - - +
377B VAL 3.2 0.2 - - - -
378B LEU* 1.3 74.6 - - - +
380B GLY* 1.3 59.7 + - - +
382B ILE* 3.1 9.9 + - - +
383B ALA* 2.8 30.0 + - - +
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Residues in contact with GLY 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.3 24.1 - - - +
8B GLY* 4.1 11.6 + - - -
341B MET* 3.9 0.8 - - - +
376B LEU 3.0 13.0 + - - -
377B VAL 3.1 5.9 + - - -
379B ALA* 1.3 77.6 - - - +
381B CYS* 1.3 60.3 + - - +
382B ILE 3.4 0.5 + - - -
383B ALA* 3.5 8.5 + - - +
385B GLY 5.0 0.7 - - - +
387B THR* 3.8 27.6 + - - -
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Residues in contact with CYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.9 14.4 - - - -
7B GLN 5.0 0.9 - - - -
8B GLY* 3.9 1.6 - - - -
9B PRO* 3.7 2.4 - - - +
10B THR* 2.9 32.4 + - - +
12B LEU* 4.2 28.7 - - + -
377B VAL* 3.4 17.7 - - - -
378B LEU* 3.1 11.0 + - - +
380B GLY* 1.3 77.6 - - - +
382B ILE* 1.3 59.5 + - + +
406B LEU* 4.4 16.2 - - - -
411B ALA* 4.1 22.9 - - + -
412B ASN 6.1 0.7 - - - +
413B ILE* 5.6 1.8 - - - -
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Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 3.7 16.8 - - + +
10B THR 4.1 4.5 - - - +
12B LEU* 5.5 1.1 - - + -
241B ALA 5.2 0.2 - - - +
244B ILE* 3.6 42.6 - - + +
245B SER* 3.6 34.8 - - - -
312B LEU* 4.8 3.6 - - + -
316B VAL* 4.0 25.4 - - + -
359B LYS* 5.1 6.1 - - - +
360B LEU* 4.7 12.2 + - + +
378B LEU 3.5 7.4 + - - +
379B ALA* 3.5 11.4 - - - +
381B CYS* 1.3 81.5 - - + +
383B ALA* 1.3 67.6 + - - +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 3.1 28.1 + - - -
9B PRO* 3.2 1.4 - - - -
341B MET* 3.6 22.7 - - + -
360B LEU* 3.6 24.0 - - + -
362B GLY* 3.9 9.4 - - - +
379B ALA 2.8 16.7 + - - +
380B GLY 3.5 6.9 + - - +
382B ILE* 1.3 81.0 - - - +
384B GLU* 1.3 60.7 + - - +
385B GLY 3.5 1.1 + - - +
387B THR* 4.2 3.1 - - - +
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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
------------------------------------------------------------
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