Contacts of the helix formed by residues 373 - 383 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334H HIS* 5.8 2.3 - - - +
367H ALA* 3.3 26.9 - - - -
368H THR* 2.9 25.9 + - - -
369H ASP* 3.1 23.9 + - - +
372H ALA* 1.3 71.4 - - - +
374H ALA* 1.3 61.5 + - - +
375H SER 2.9 5.6 - - - -
376H LEU* 3.0 28.8 + - - +
377H VAL 3.7 1.9 + - - -
395H ILE* 3.9 15.2 - - - +
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Residues in contact with ALA 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H THR* 4.3 13.9 - - + -
309H GLN* 5.2 2.0 - - + +
371H ARG 3.2 14.8 + - - +
372H ALA 3.1 1.0 + - - -
373H SER* 1.3 76.9 - - - +
375H SER* 1.3 63.0 + - - +
377H VAL* 3.1 15.4 + - - +
378H LEU* 3.0 24.4 + - - +
395H ILE* 4.5 6.4 - - - +
399H TYR* 3.6 31.8 - - + +
402H ILE* 4.4 8.7 - - + -
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Residues in contact with SER 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H ALA* 3.5 32.9 + - - +
309H GLN* 4.2 12.4 - - - +
312H LEU* 3.4 18.3 - - - +
334H HIS* 4.0 12.3 - - - +
338H LEU* 4.6 4.7 - - - +
372H ALA 2.8 19.7 + - - -
373H SER 2.9 1.2 - - - -
374H ALA* 1.3 81.0 - - - +
376H LEU* 1.3 59.9 + - - +
378H LEU* 3.2 6.0 + - - +
379H ALA* 2.8 26.7 + - - +
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Residues in contact with LEU 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H HIS* 4.2 8.5 - - + +
337H GLU* 3.6 31.0 - - + -
338H LEU* 3.9 22.9 - - + -
341H MET* 4.9 2.2 - - - +
365H VAL* 4.1 21.1 - - + -
366H MET 3.4 34.5 - - - +
367H ALA* 4.0 9.4 - - - +
373H SER* 3.0 20.5 + - - +
375H SER* 1.3 80.7 + - - +
377H VAL* 1.3 61.6 + - - +
379H ALA* 3.4 6.4 + - - +
380H GLY* 3.1 18.9 + - - -
387H THR* 4.7 2.8 - - - +
389H VAL* 4.0 15.6 - - + +
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Residues in contact with VAL 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H PHE* 4.3 16.2 - - + -
6H VAL* 4.7 5.9 - - + +
373H SER 4.0 1.1 - - - +
374H ALA* 3.1 12.7 + - - +
376H LEU* 1.3 74.8 - - - +
378H LEU* 1.3 65.6 + - + +
380H GLY* 3.2 10.8 + - - -
381H CYS* 3.3 15.2 + - - -
389H VAL* 4.4 13.5 - - + -
395H ILE* 3.5 33.4 - - + -
402H ILE* 5.2 5.8 - - + -
406H LEU* 3.6 26.9 - - + -
413H ILE* 3.9 21.5 - - + -
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Residues in contact with LEU 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 5.4 1.7 - - + +
237H THR* 3.5 42.4 - - + +
238H PHE* 6.1 0.7 - - + -
240H VAL* 4.2 14.4 - - + -
241H ALA* 4.0 24.2 - - + +
244H ILE* 4.1 8.6 - - + +
309H GLN* 4.8 7.6 - - + -
312H LEU* 3.7 17.9 - - + -
374H ALA* 3.0 19.2 + - + +
375H SER* 3.7 2.7 - - - +
377H VAL* 1.3 75.1 - - + +
379H ALA* 1.3 66.4 + - - +
381H CYS* 3.1 21.9 + - - +
382H ILE* 3.5 9.7 + - - +
402H ILE* 5.0 3.1 - - + -
406H LEU* 4.5 24.9 - - + -
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Residues in contact with ALA 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H LEU* 3.6 14.7 - - + +
338H LEU* 3.7 23.1 - - + -
341H MET* 3.6 18.6 - - + -
360H LEU* 4.1 4.7 - - + +
375H SER 2.8 16.3 + - - +
376H LEU 3.5 5.8 - - - +
377H VAL 3.2 0.2 - - - -
378H LEU* 1.3 77.6 - - - +
380H GLY* 1.3 59.0 + - - +
382H ILE* 3.2 8.8 + - - +
383H ALA* 2.8 31.5 + - - +
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Residues in contact with GLY 380 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H VAL* 3.3 19.9 - - - +
8H GLY* 4.1 11.4 + - - -
341H MET* 3.9 0.8 - - - +
376H LEU 3.1 14.0 + - - -
377H VAL 3.2 4.6 + - - -
379H ALA* 1.3 77.3 - - - +
381H CYS* 1.3 59.9 + - - +
382H ILE 3.4 0.3 + - - -
383H ALA* 3.5 8.4 + - - +
385H GLY 5.1 0.9 - - - +
387H THR* 3.7 31.0 + - - -
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Residues in contact with CYS 381 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H VAL* 3.9 15.9 - - - -
7H GLN 5.0 0.9 - - - -
8H GLY* 3.9 1.8 - - - -
9H PRO* 3.6 2.4 - - - +
10H THR* 2.9 32.7 + - + +
12H LEU* 4.2 27.4 - - + -
377H VAL* 3.3 18.4 - - - -
378H LEU* 3.1 11.7 + - - +
380H GLY* 1.3 77.8 - - - +
382H ILE* 1.3 59.7 + - + +
406H LEU* 4.5 15.3 - - - -
411H ALA* 4.1 22.2 - - + -
412H ASN 6.1 0.2 - - - +
413H ILE* 5.6 1.6 - - - -
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Residues in contact with ILE 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PRO* 3.6 16.2 - - + +
10H THR 4.1 3.4 - - - +
12H LEU* 5.5 1.3 - - + -
241H ALA 5.3 0.2 - - - +
244H ILE* 3.6 41.3 - - + +
245H SER* 3.6 35.0 - - - -
312H LEU* 4.8 3.6 - - + -
316H VAL* 4.1 26.0 - - + -
359H LYS* 5.1 6.4 - - - +
360H LEU* 4.7 12.0 + - + +
378H LEU 3.5 7.4 + - - +
379H ALA* 3.6 10.1 - - - +
381H CYS* 1.3 81.1 - - + +
383H ALA* 1.3 69.4 + - - +
384H GLU 3.8 0.3 + - - -
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Residues in contact with ALA 383 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLY* 3.1 28.6 - - - -
9H PRO* 3.2 0.8 - - - -
341H MET* 3.5 23.8 - - + -
360H LEU* 3.6 18.2 - - + -
362H GLY* 3.9 14.1 - - - +
379H ALA 2.8 16.5 + - - +
380H GLY 3.5 6.5 + - - +
382H ILE* 1.3 79.7 - - - +
384H GLU* 1.3 61.3 + - - +
385H GLY 3.5 1.7 + - - +
387H THR* 4.2 3.4 - - - +
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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
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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