Contacts of the helix formed by residues 389 - 401 (chain G) in PDB entry 3SRF
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 PHE 389 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19G ALA 3.8 3.1 - - - -
20G ALA* 3.7 24.9 - - - -
22G ALA 4.2 0.2 - - - -
23G ASP 3.5 42.2 - - - -
24G THR 3.7 18.6 - - - -
25G PHE* 3.7 20.0 - + + -
28G HIS* 3.2 33.3 + + + +
387G ALA 3.8 0.2 + - - -
388G MET* 1.3 71.6 - - - +
390G HIS* 1.3 64.8 + - - +
391G ARG* 3.1 17.2 + - + -
392G LYS* 3.3 42.5 + - + +
393G LEU* 3.0 26.4 + - + +
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Residues in contact with HIS 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ALA* 6.0 2.1 - - + +
385G GLU* 3.0 26.3 + - + -
386G ALA* 4.7 6.0 - - - -
388G MET* 3.2 29.1 + - + +
389G PHE* 1.3 73.2 - - - +
391G ARG* 1.3 58.5 + - - +
393G LEU* 3.7 9.9 - - - +
394G PHE* 2.8 31.9 + - - +
420G TYR* 3.6 20.0 + - + +
444G ARG* 3.9 18.4 + - + +
445G PRO 4.2 4.5 - - - -
446G ARG* 3.4 62.7 - - + +
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Residues in contact with ARG 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C VAL* 6.1 6.5 - - + -
399C ARG* 3.9 22.8 - - - +
20G ALA* 3.1 29.2 + - + +
21G MET* 3.5 7.9 - - - +
22G ALA 3.4 4.6 - - - +
23G ASP* 3.0 48.4 + - - +
389G PHE* 3.3 13.7 - - + -
390G HIS* 1.3 79.0 - - - +
392G LYS* 1.3 66.4 + - - +
394G PHE* 3.6 6.5 + - + +
395G GLU* 3.3 44.8 + - + +
417G GLU* 6.1 1.8 - - - +
420G TYR* 5.3 8.3 - - + -
446G ARG* 5.8 1.5 - - - +
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Residues in contact with LYS 392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ASP 5.1 4.7 - - - +
25G PHE* 3.2 34.4 - - + +
389G PHE* 3.3 37.7 + - + +
391G ARG* 1.3 81.5 - - - +
393G LEU* 1.3 66.2 + - - +
395G GLU* 3.5 11.0 + - - +
396G GLU* 3.1 43.6 + - + +
25H PHE* 4.2 22.4 - - - -
392H LYS* 3.0 36.1 - - - +
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Residues in contact with LEU 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G ASN* 5.1 8.5 - - - +
352G LEU 5.9 0.7 - - - +
353G ASP 5.6 3.4 - - - +
388G MET* 3.8 33.0 - - + -
389G PHE 3.0 19.5 + - - +
390G HIS* 3.7 11.2 - - - +
392G LYS* 1.3 77.3 - - - +
394G PHE* 1.3 65.6 + - - +
396G GLU* 3.2 13.4 + - - +
397G LEU* 2.9 37.7 + - + +
444G ARG* 4.0 30.3 - - + +
25H PHE* 6.1 4.3 - - + -
26H LEU* 4.9 14.4 - - + -
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Residues in contact with PHE 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C GLU* 3.7 14.6 - - - -
390G HIS 2.8 22.4 + - - +
391G ARG* 3.7 5.6 - - + +
393G LEU* 1.3 72.6 - - - +
395G GLU* 1.3 63.7 + - + +
397G LEU* 3.0 12.0 + - - +
398G VAL* 2.8 56.6 + - + +
413G MET* 3.4 33.2 - - - -
416G VAL* 3.9 13.5 - - + -
417G GLU* 3.4 32.5 - - + -
420G TYR* 3.6 24.7 - + + +
443G TYR* 3.5 26.0 - + + -
444G ARG* 6.1 0.7 - - - -
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Residues in contact with GLU 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395C GLU* 3.1 46.1 - - + +
398C VAL* 6.0 2.1 - - - +
391G ARG* 3.3 37.8 + - + +
392G LYS* 3.8 10.4 - - - +
394G PHE* 1.3 88.5 - - + +
396G GLU* 1.3 53.6 + - + +
398G VAL* 3.3 10.2 + - - +
399G ARG* 2.7 36.1 + - - +
417G GLU* 5.6 2.9 - - - +
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Residues in contact with GLU 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392G LYS* 3.1 36.8 + - + +
393G LEU* 3.5 11.2 - - - +
395G GLU* 1.3 74.3 - - + +
397G LEU* 1.3 61.9 + - - +
399G ARG* 3.8 6.5 - - - +
400G ALA* 3.0 29.1 + - - +
24H THR* 3.3 28.8 + - + +
25H PHE* 2.7 36.3 + - - +
26H LEU* 2.9 31.6 + - + +
392H LYS* 4.7 1.4 + - - -
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Residues in contact with LEU 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317G ASN* 3.4 43.7 - - + +
318G ARG* 4.1 3.9 - - - +
393G LEU* 2.9 32.9 + - + +
394G PHE* 3.4 7.0 - - - +
396G GLU* 1.3 73.4 - - - +
398G VAL* 1.3 65.3 + - - +
400G ALA* 3.6 1.7 + - - +
401G SER* 3.1 27.0 + - - -
442G ARG* 3.5 23.0 + - - +
443G TYR* 4.1 20.8 - - + -
444G ARG* 4.0 21.5 - - + -
26H LEU* 4.1 17.0 - - + -
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Residues in contact with VAL 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C ARG* 6.0 6.3 - - + -
417C GLU* 4.3 9.2 - - - +
421C LYS* 5.3 0.9 + - - +
394G PHE* 2.8 51.1 + - + +
395G GLU* 3.4 11.4 - - - +
397G LEU* 1.3 76.8 - - - +
399G ARG* 1.3 63.9 + - - +
401G SER* 3.7 2.2 + - - -
402G SER* 3.1 24.9 + - - -
413G MET* 3.7 36.6 - - + +
443G TYR* 4.3 7.4 - - + -
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Residues in contact with ARG 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C MET* 2.6 35.9 + - - +
22C ALA 4.3 0.8 + - - -
23C ASP* 3.1 37.2 + - - +
391C ARG* 4.1 30.7 - - - +
395G GLU 2.7 20.0 + - - +
396G GLU* 3.8 8.1 - - - +
398G VAL* 1.3 76.3 - - - +
400G ALA* 1.3 61.1 + - - +
402G SER* 3.0 32.1 + - - -
23H ASP* 4.8 5.7 + - - -
24H THR* 5.1 11.1 + - + +
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Residues in contact with ALA 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318G ARG* 3.7 36.2 - - + +
396G GLU 3.0 18.6 + - - +
397G LEU* 4.1 3.4 - - - +
398G VAL 3.4 0.2 - - - -
399G ARG* 1.3 77.1 - - - +
401G SER* 1.3 57.9 + - - +
402G SER 3.4 0.2 - - - -
403G HIS* 3.5 18.2 + - - -
24H THR* 6.2 1.1 - - + -
26H LEU* 4.0 9.4 - - + -
27H GLU* 5.5 6.3 - - + +
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Residues in contact with SER 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C LYS* 2.4 30.2 + - - -
318G ARG 4.6 4.5 - - - -
397G LEU 3.1 16.5 + - - -
398G VAL* 3.7 2.7 + - - -
399G ARG 3.3 0.4 - - - -
400G ALA* 1.3 76.6 - - - +
402G SER* 1.3 55.6 + - - +
403G HIS* 3.2 12.1 - - - -
404G SER* 3.2 9.2 + - - -
409G GLU* 4.1 4.3 - - - -
413G MET* 5.5 0.3 - - - -
442G ARG* 3.7 23.0 + - - -
443G TYR* 3.0 24.7 + - - -
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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