Contacts of the helix formed by residues 384 - 396 (chain G) in PDB entry 4D1Q
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 384 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B THR* 3.9 25.6 - - + -
501B THR* 5.8 1.8 - - + -
504B PHE* 3.3 34.4 - + + -
505B PHE* 4.3 11.2 - + - -
373G GLU* 4.4 12.6 - - + +
374G LEU* 5.2 6.1 - - + +
379G SER* 5.6 2.5 - - - -
380G PRO* 3.8 24.7 - - + -
381G SER* 2.7 19.0 + - - +
383G CYS* 1.3 77.8 - - - +
385G VAL* 1.3 51.3 + - - -
387G PRO* 3.1 16.8 - - + +
388G SER* 2.3 30.7 + - - -
433G PHE* 6.1 0.9 - + - -
436G TYR* 3.8 38.6 - + - -
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Residues in contact with VAL 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266G SER* 3.7 17.9 - - - +
374G LEU* 4.1 17.7 - - + -
381G SER 3.9 0.4 + - - -
382G LEU* 3.2 24.9 - - + +
383G CYS 2.9 3.8 + - - -
384G PHE* 1.3 74.4 - - - +
386G VAL* 1.3 66.7 + - + +
388G SER* 2.9 30.2 + - - -
389G ILE* 3.2 9.9 + - + +
421G TRP* 4.2 8.6 - - + +
425G LEU* 3.9 17.0 - - + -
429G HIS* 3.3 35.9 - - + -
566G ALA* 4.2 3.6 - - + -
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Residues in contact with VAL 386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383G CYS 4.3 0.9 - - - +
385G VAL* 1.3 82.2 - - + +
387G PRO* 1.3 64.9 - - + +
389G ILE* 3.2 18.1 + - + +
390G LEU* 3.1 33.4 + - + +
425G LEU* 5.4 1.6 - - + -
429G HIS* 3.0 35.0 - - + +
430G TYR* 4.3 25.1 - - + -
433G PHE* 3.8 22.7 - - + -
442G MET* 4.3 11.0 - - + -
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Residues in contact with PRO 387 (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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504B PHE* 4.2 20.1 - - + +
505B PHE* 3.7 25.6 - - + -
383G CYS 3.4 9.2 - - - +
384G PHE* 3.1 40.8 - - + +
386G VAL* 1.3 93.6 - - + +
388G SER* 1.3 49.9 + - - +
390G LEU* 3.2 17.8 + - + +
391G LYS* 2.7 29.8 + - - +
433G PHE* 3.8 16.6 - - + -
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Residues in contact with SER 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B PHE* 3.6 16.8 - - - -
370G ILE* 3.7 25.0 - - - +
374G LEU* 4.2 6.6 - - - +
384G PHE 2.3 30.1 + - - -
385G VAL* 2.9 10.5 + - - -
387G PRO* 1.3 71.5 - - - +
389G ILE* 1.3 54.9 + - - +
390G LEU 3.0 1.1 - - - -
391G LYS* 2.6 28.9 + - - +
392G VAL* 2.7 23.0 + - - +
421G TRP* 4.0 7.6 - - - -
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Residues in contact with ILE 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G VAL* 3.4 16.6 - - + +
386G VAL* 3.3 14.6 - - + +
388G SER* 1.3 75.3 - - - +
390G LEU* 1.3 62.3 + - + +
392G VAL* 3.2 4.7 - - - +
393G LYS* 3.1 39.2 + - + +
417G VAL* 3.6 21.5 - - + -
421G TRP* 3.9 38.6 - - + +
422G GLU* 3.7 20.9 - - + +
425G LEU* 3.3 34.8 - - + -
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Residues in contact with LEU 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386G VAL* 3.1 27.8 + - + +
387G PRO* 3.3 16.2 - - + +
388G SER 3.0 0.4 - - - -
389G ILE* 1.3 87.5 - - + +
391G LYS* 1.3 62.3 + - - +
393G LYS* 3.6 14.8 + - + +
394G GLU* 3.2 23.6 + - - +
433G PHE* 4.8 15.3 - - + -
441G HIS* 5.0 13.5 - - + +
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Residues in contact with LYS 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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502B SER 5.5 0.2 + - - -
503B PHE* 3.3 72.2 + - + +
504B PHE* 4.8 5.4 - - + +
506B PRO* 4.9 6.6 - - + +
370G ILE* 3.8 12.3 - - + -
387G PRO 2.7 13.5 + - - +
388G SER* 2.6 19.7 + - - +
390G LEU* 1.3 73.6 - - - +
392G VAL* 1.3 55.2 - - - +
394G GLU* 3.0 31.2 + - - +
395G ILE* 3.0 44.9 + - + +
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Residues in contact with VAL 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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270G LEU* 5.0 0.9 - - + -
367G PHE* 4.4 20.6 - - + -
370G ILE* 4.0 15.5 - - + -
388G SER 2.7 13.4 + - - +
389G ILE* 3.2 10.1 - - - +
391G LYS* 1.3 73.7 - - - +
393G LYS* 1.3 58.8 + - + +
394G GLU 2.7 4.3 + - - -
395G ILE* 2.6 31.5 + - - +
396G CYS* 3.1 17.0 + - + -
413G ILE* 4.1 15.0 - - + -
414G ILE* 5.3 1.1 - - + -
417G VAL* 3.6 28.9 - - + -
421G TRP* 4.0 21.8 - - + -
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Residues in contact with LYS 393 (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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389G ILE* 3.1 24.8 + - + +
390G LEU* 4.0 15.4 - - + +
392G VAL* 1.3 85.0 - - + +
394G GLU* 1.3 58.4 + - - +
395G ILE 3.5 0.2 - - - -
396G CYS 3.8 1.7 - - - -
397G SER* 3.5 19.6 + - - -
398G PRO* 5.4 0.3 - - - +
414G ILE* 4.7 25.4 - - + +
417G VAL* 4.4 10.1 - - + -
418G ARG* 4.6 10.7 - - - +
422G GLU* 2.7 36.0 + - - -
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Residues in contact with GLU 394 (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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506B PRO* 4.9 13.4 - - - +
390G LEU 3.2 16.4 + - - +
391G LYS* 3.0 40.5 + - - +
392G VAL 2.7 6.1 + - - -
393G LYS* 1.3 73.4 - - - +
395G ILE* 1.3 62.4 + - - +
397G SER* 3.5 17.3 - - - -
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Residues in contact with ILE 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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503B PHE* 5.6 0.2 - - + -
362G ASN 4.4 5.6 - - - +
363G ILE* 4.1 36.5 - - + +
366G GLY* 4.1 28.7 - - - +
367G PHE* 5.1 3.8 - - + +
370G ILE* 5.5 2.0 - - + -
391G LYS* 3.0 38.8 - - + +
392G VAL* 2.6 14.1 + - - +
394G GLU* 1.3 73.9 - - + +
396G CYS* 1.3 60.5 + - - +
397G SER* 3.2 8.3 + - - +
410G LYS* 3.6 19.9 + - - -
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Residues in contact with CYS 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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363G ILE* 4.6 10.5 - - - -
367G PHE* 4.7 3.8 - - - -
392G VAL* 3.1 17.5 + - - +
393G LYS 3.8 2.0 - - - +
395G ILE* 1.3 78.2 - - - +
397G SER* 1.3 61.1 + - - +
398G PRO* 3.2 3.6 - - - +
410G LYS* 3.6 28.6 - - + +
413G ILE* 3.5 41.3 - - - -
414G ILE* 2.8 46.1 - - + +
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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
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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