Contacts of the helix formed by residues 376 - 386 (chain G) in PDB entry 1R4N
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 376 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373G GLU* 4.7 6.1 - - - -
374G SER 4.2 1.0 + - - -
375G ILE* 1.3 79.8 - - - +
377G GLU* 1.3 65.7 + - - +
378G LYS* 4.0 13.2 - - - +
379G GLU* 2.9 48.1 + - - +
380G LEU* 3.1 10.4 + - - +
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Residues in contact with GLU 377 (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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373G GLU* 5.1 2.8 + - - -
375G ILE 3.9 1.2 + - - -
376G SER* 1.3 72.6 - - - +
378G LYS* 1.3 58.5 + - + +
380G LEU* 3.1 13.0 + - + +
381G LYS* 2.8 62.4 + - + +
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Residues in contact with LYS 378 (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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376G SER* 3.1 11.9 - - - +
377G GLU* 1.3 80.6 - - + +
379G GLU* 1.3 65.1 + - + +
381G LYS* 3.4 4.4 + - - +
382G LEU* 3.1 24.9 + - - +
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Residues in contact with GLU 379 (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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172G ILE* 4.9 7.5 - - + +
303G SER* 3.5 24.0 + - - -
307G LEU* 4.7 10.7 - - + +
374G SER 4.8 3.5 - - - +
375G ILE* 4.2 13.5 - - + -
376G SER* 2.9 37.1 + - - +
378G LYS* 1.3 78.4 - - + +
380G LEU* 1.3 57.2 - - - +
382G LEU* 3.5 6.9 - - - +
383G LEU* 2.9 31.7 + - - +
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Residues in contact with LEU 380 (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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307G LEU* 4.6 3.6 - - + -
354G ALA* 3.8 13.9 - - + +
355G ALA* 5.0 2.0 - - - -
357G VAL* 4.2 9.6 - - + -
358G GLY* 3.4 37.0 - - - +
361G VAL* 4.3 11.9 - - + -
375G ILE* 4.8 4.9 - - + +
376G SER 3.1 8.3 + - - +
377G GLU* 3.1 15.7 + - + +
378G LYS 3.1 0.4 - - - -
379G GLU* 1.3 75.8 - - - +
381G LYS* 1.3 64.9 + - + +
382G LEU 2.8 10.1 + - - -
383G LEU* 3.0 13.8 + - + +
384G CYS* 3.0 37.5 + - - -
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Residues in contact with LYS 381 (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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351G LYS* 4.3 32.9 - - - +
354G ALA* 4.9 15.9 - - + -
377G GLU* 2.8 50.2 + - + +
378G LYS* 4.2 4.3 - - - +
380G LEU* 1.3 76.6 - - + +
382G LEU* 1.3 57.3 + - - +
384G CYS* 4.2 6.6 - - - +
385G SER* 3.3 23.2 + - - -
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Residues in contact with LEU 382 (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 HIS* 5.7 4.0 - - + +
172G ILE* 4.3 14.1 - - + -
173G GLU* 4.3 27.8 - - + +
378G LYS 3.1 16.0 + - - +
379G GLU* 3.5 7.2 - - - +
380G LEU 2.9 0.8 - - - -
381G LYS* 1.3 76.4 - - - +
383G LEU* 1.3 67.8 + - - +
384G CYS 3.0 1.3 - - - -
385G SER* 3.0 7.7 + - - -
386G ASN* 3.0 51.0 + - - +
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Residues in contact with LEU 383 (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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172G ILE* 3.6 24.8 - - + +
304G PHE* 5.7 1.3 - - + -
307G LEU* 3.0 56.8 - - + +
308G ALA 5.3 0.2 - - - +
311G LEU* 3.8 28.5 - - + -
357G VAL* 4.9 1.8 - - + -
379G GLU 2.9 17.3 + - - +
380G LEU* 3.4 14.1 - - + +
382G LEU* 1.3 76.0 - - - +
384G CYS* 1.3 59.1 + - - +
386G ASN 3.4 1.9 - - - -
387G SER* 2.9 23.4 + - - -
390G LEU* 4.1 21.8 - - + -
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Residues in contact with CYS 384 (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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311G LEU* 4.9 2.0 - - - -
324G PRO* 4.6 15.4 - - + +
325G VAL 5.8 3.5 - - - +
326G ARG* 5.5 2.1 - - - -
350G ALA 5.7 0.9 - - - +
354G ALA* 4.1 21.3 - - + -
357G VAL* 4.0 36.3 - - - -
380G LEU* 3.0 28.5 + - - +
381G LYS* 4.3 5.8 - - - +
383G LEU* 1.3 75.1 - - - +
385G SER* 1.3 59.8 + - - +
387G SER* 2.6 37.8 + - - -
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Residues in contact with SER 385 (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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325G VAL 5.9 0.2 - - - -
326G ARG* 3.8 47.6 + - - +
328G THR* 5.9 3.5 - - - +
381G LYS 3.3 14.6 + - - -
382G LEU* 3.0 12.1 + - - -
384G CYS* 1.3 79.0 - - - +
386G ASN* 1.3 64.2 + - - +
387G SER* 3.4 2.9 + - - -
388G ALA 4.9 0.2 + - - -
389G PHE* 4.4 4.0 - - - -
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Residues in contact with ASN 386 (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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172G ILE* 3.4 25.5 - - + +
173G GLU* 3.9 19.9 - - - +
174G SER 4.3 3.3 + - - -
175G HIS 5.0 2.4 + - - -
176G PRO* 5.4 1.0 - - - +
382G LEU* 3.0 49.2 + - - +
383G LEU 3.4 3.4 - - - -
385G SER* 1.3 79.8 - - - +
387G SER* 1.3 66.3 + - - +
388G ALA 3.2 2.7 - - - -
389G PHE* 2.8 34.7 + - + -
390G LEU* 3.3 10.0 + - - +
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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