Contacts of the helix formed by residues 385 - 394 (chain X) in PDB entry 3FEW
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 ASP 385 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383X SER 3.5 4.7 + - - +
384X ILE* 1.3 74.3 - - - +
386X ALA* 1.3 65.9 + - - +
387X GLN* 3.1 14.7 + - - +
388X ASP* 2.8 53.4 + - + +
389X MET* 3.1 22.2 + - - +
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Residues in contact with ALA 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384X ILE* 3.6 6.8 + - - -
385X ASP* 1.3 73.4 - - - +
387X GLN* 1.3 57.0 + - - +
389X MET* 3.4 1.0 + - - -
390X ALA* 3.0 30.5 + - - +
406X VAL* 3.9 15.4 - - + +
409X VAL* 3.8 24.3 - - + +
410X GLU* 4.1 21.3 - - + -
413X ARG* 4.8 8.2 - - - +
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Residues in contact with GLN 387 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385X ASP* 3.1 11.9 + - - +
386X ALA* 1.3 79.2 - - - +
388X ASP* 1.3 63.5 + - - +
390X ALA* 3.5 1.1 + - - +
391X ASN* 3.2 57.6 + - - +
406X VAL* 3.5 38.4 - - + +
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Residues in contact with ASP 388 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385X ASP* 2.8 41.7 + - + +
387X GLN* 1.3 75.4 - - - +
389X MET* 1.3 62.5 + - - +
391X ASN* 3.4 9.6 + - - +
392X LYS* 3.3 24.5 + - - +
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Residues in contact with MET 389 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381X TRP* 4.2 12.3 - - + -
384X ILE* 3.9 35.7 - - + -
385X ASP 3.1 13.3 + - - +
386X ALA 3.9 4.0 - - - +
387X GLN 3.3 0.2 - - - -
388X ASP* 1.3 80.8 - - - +
390X ALA* 1.3 62.1 + - - +
392X LYS* 3.1 10.4 + - + +
393X LEU* 3.0 24.8 + - + +
409X VAL* 3.9 24.7 - - + -
452X THR* 3.9 22.0 - - + +
455X ALA* 4.1 17.2 - - + +
456X TYR 4.1 21.5 - - - +
459X SER* 5.8 0.7 - - - +
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Residues in contact with ALA 390 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386X ALA 3.0 17.7 + - - +
387X GLN 3.8 4.7 - - - +
389X MET* 1.3 77.0 - - - +
391X ASN* 1.3 59.3 + - - +
393X LEU* 3.1 10.7 + - - +
394X GLY* 2.9 25.3 + - - -
400X PHE 4.3 3.8 - - - +
405X VAL* 3.9 24.5 - - + +
406X VAL* 4.0 22.7 - - + -
409X VAL* 4.3 10.2 - - + +
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Residues in contact with ASN 391 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387X GLN* 3.2 39.1 + - - +
388X ASP* 3.7 8.9 + - - +
389X MET 3.3 0.4 - - - -
390X ALA* 1.3 77.9 - - - +
392X LYS* 1.3 62.1 + - + +
394X GLY* 3.3 9.6 + - - +
395X ASN* 3.2 18.9 + - - +
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Residues in contact with LYS 392 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388X ASP 3.3 12.0 + - - +
389X MET* 3.1 13.8 + - + +
391X ASN* 1.3 75.7 - - + +
393X LEU* 1.3 66.5 + - + +
395X ASN* 3.1 32.4 + - - +
396X ILE* 4.1 5.4 + - - +
455X ALA* 6.1 7.0 - - + -
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Residues in contact with LEU 393 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389X MET* 3.0 18.3 + - + +
390X ALA* 3.1 8.7 + - - +
392X LYS* 1.3 70.3 - - + +
394X GLY* 1.3 58.8 + - - +
395X ASN 3.0 4.5 - - - -
396X ILE* 2.8 33.9 + - + +
400X PHE* 3.2 35.9 - - + +
405X VAL* 5.0 6.5 - - + -
409X VAL* 3.9 19.5 - - + -
448X VAL* 4.7 8.7 - - + +
451X ALA* 3.6 38.1 - - + +
452X THR* 3.4 25.6 - - + +
455X ALA* 4.7 9.0 - - + -
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Residues in contact with GLY 394 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390X ALA 2.9 12.7 + - - -
391X ASN* 3.5 8.7 - - - -
392X LYS 3.2 0.6 - - - -
393X LEU* 1.3 75.4 - - - +
395X ASN* 1.3 61.5 + - - +
396X ILE 3.4 0.3 + - - -
397X SER 3.6 13.8 + - - +
400X PHE 3.6 17.1 + - - -
401X LYS* 3.6 29.1 + - - +
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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