Contacts of the helix formed by residues 385 - 394 (chain B) in PDB entry 4XZC
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 ARG 385 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ALA 5.7 0.2 + - - -
305B ILE* 3.3 34.7 - - - +
314B TRP* 4.0 11.1 - - + -
373B LYS 4.1 8.9 + - - -
374B LEU* 5.4 3.8 + - - +
376B MET* 3.5 38.3 + - - +
377B HIS 3.3 19.9 + - - -
378B PRO* 3.5 10.9 + - - +
380B VAL 3.4 19.2 + - - -
381B LEU* 3.9 9.2 - - + -
382B THR* 2.9 29.0 + - - +
384B GLY* 1.3 74.2 - - - +
386B MET* 1.3 55.9 + - - +
387B SER* 2.9 8.7 - - - -
388B GLU* 2.8 33.5 + - + +
389B MET 3.7 1.0 + - - -
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Residues in contact with MET 386 (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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328B LEU* 5.8 2.7 - - + -
331B PHE* 4.9 4.0 - - + -
332B LEU* 4.3 20.8 - - + +
335B MET* 4.0 11.1 - - - +
345B MET* 3.7 30.5 - - + -
349B LEU* 4.4 10.3 - - + -
356B TRP* 5.9 1.1 - - + -
360B ILE* 3.6 34.3 - - + -
364B PHE* 3.8 11.7 - - + -
381B LEU* 3.8 12.7 - - - +
382B THR 3.3 8.3 + - - +
383B ALA 3.3 18.6 - - - +
385B ARG* 1.3 76.1 - - - +
387B SER* 1.3 49.8 + - - +
388B GLU 3.0 0.2 - - - -
389B MET* 2.9 19.7 + - + +
390B GLY* 2.6 33.6 + - - -
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B MET* 4.9 4.9 - - - +
384B GLY 2.2 29.6 + - - -
385B ARG* 3.7 2.6 - - - -
386B MET* 1.3 74.1 - - - +
388B GLU* 1.3 59.1 + - - +
390B GLY* 3.9 4.2 - - - +
391B ALA* 3.1 24.9 + - - +
410B HIS* 4.1 8.6 - - - +
411B SER* 4.7 21.9 + - - -
412B LYS* 4.8 4.2 + - - +
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Residues in contact with GLU 388 (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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305B ILE* 4.1 26.7 - - + +
307B SER* 2.5 39.6 + - - +
311B SER* 3.7 4.0 - - - +
314B TRP* 4.0 17.7 - - + -
385B ARG* 2.8 24.6 + - + +
387B SER* 1.3 78.7 + - - +
389B MET* 1.3 65.3 + - - +
391B ALA* 3.2 5.5 + - - +
392B CYS* 3.1 28.8 + - - -
412B LYS* 3.0 35.9 + - - +
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Residues in contact with MET 389 (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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311B SER* 3.3 18.4 - - - +
314B TRP* 3.6 41.7 - - + -
315B ALA* 4.7 5.4 - - + +
328B LEU* 3.7 40.4 - - + -
332B LEU* 3.4 13.8 - - + +
360B ILE* 4.3 10.3 - - + -
381B LEU* 4.5 0.7 - - - -
386B MET* 2.9 34.4 + - + +
388B GLU* 1.3 77.5 - - - +
390B GLY* 1.3 53.2 + - - +
392B CYS* 3.0 2.8 + - - +
393B PHE* 2.7 45.2 + - + +
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Residues in contact with GLY 390 (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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332B LEU* 3.7 15.3 - - - +
335B MET* 3.9 2.2 - - - -
386B MET 2.6 18.1 + - - -
387B SER 4.1 0.7 - - - -
389B MET* 1.3 72.2 - - - +
391B ALA* 1.3 58.9 + - - +
394B GLY* 2.9 23.6 + - - -
410B HIS* 3.2 38.1 - - - -
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Residues in contact with ALA 391 (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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80B CYS* 3.4 18.9 - - - -
387B SER 3.1 19.9 + - - +
388B GLU* 3.2 6.0 + - - +
390B GLY* 1.3 75.1 - - - +
392B CYS* 1.3 57.3 + - - +
395B VAL* 3.7 5.7 - - - +
410B HIS* 3.5 18.1 - - + -
412B LYS* 3.7 20.4 - - + +
413B SER* 4.7 6.1 + - - +
466B HIS* 3.3 29.1 + - + -
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Residues in contact with CYS 392 (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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80B CYS* 4.1 15.6 - - - +
83B ALA* 4.8 1.0 - - - +
84B CYS* 3.4 15.2 - - - -
307B SER* 3.6 24.0 - - - -
308B ILE* 3.6 11.0 - - + -
311B SER* 3.5 16.6 - - - +
388B GLU 3.1 14.5 + - - +
389B MET 3.0 6.5 + - - +
391B ALA* 1.3 79.5 - - - +
393B PHE* 1.3 75.0 + - + +
394B GLY 3.8 0.2 - - - -
395B VAL 5.1 1.2 + - - -
396B VAL 5.8 0.2 + - - -
466B HIS* 3.8 10.1 - - - -
467B PHE* 3.7 22.8 - - + -
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Residues in contact with PHE 393 (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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83B ALA 4.0 4.9 - - - -
84B CYS* 3.6 20.6 - - - -
308B ILE* 3.8 19.5 - - + -
311B SER* 3.7 37.5 - - - -
312B TYR* 3.9 35.2 - + - -
315B ALA* 4.3 3.6 - - + -
325B PHE* 3.8 17.0 - + + -
328B LEU* 3.7 23.8 - - + -
329B SER* 2.9 32.8 + - - -
332B LEU* 3.5 13.0 - - + -
389B MET* 2.7 25.9 + - + -
392B CYS* 1.3 80.0 - - + +
394B GLY* 1.3 56.0 + - - +
395B VAL 3.5 4.5 + - - -
396B VAL 4.3 2.7 - - - +
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Residues in contact with GLY 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER 3.7 1.8 - - - -
332B LEU* 3.6 8.2 - - - +
333B PHE* 3.3 31.0 - - - -
390B GLY 2.9 16.0 + - - -
393B PHE* 1.3 77.0 - - - +
395B VAL* 1.3 57.5 + - - +
397B PRO 5.6 0.2 - - - -
408B SER* 3.2 15.8 + - - -
410B HIS* 3.0 17.5 + - - -
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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