Contacts of the strand formed by residues 379 - 390 (chain L) in PDB entry 1DZG
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 GLY 379 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223L GLY 3.6 12.3 - - - -
224L LEU* 4.7 1.1 - - - +
225L TRP* 3.4 21.9 + - - -
374L GLU 4.2 0.2 - - - +
375L VAL* 3.6 1.2 - - - -
376L ASN* 2.8 44.4 + - - +
378L GLU* 1.3 78.3 - - - +
380L SER* 1.3 59.1 + - - -
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Residues in contact with SER 380 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221L PHE* 3.9 4.7 - - - -
222L LYS* 3.4 5.1 - - - +
223L GLY 3.0 30.9 + - - +
225L TRP* 4.5 1.8 - - - -
274L PHE* 3.6 28.5 - - - -
281L MET* 3.3 21.4 - - - +
373L LEU* 3.7 12.0 - - - +
374L GLU 3.1 14.8 + - - -
375L VAL* 3.8 3.9 - - - +
379L GLY* 1.3 76.0 - - - -
381L GLU* 1.3 59.8 + - - +
382L ALA 4.3 0.2 - - - -
412L ILE* 4.2 3.6 - - - +
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Residues in contact with GLU 381 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L GLU* 4.7 1.4 - - - +
197L ARG* 2.7 55.4 + - - +
220L TYR* 2.7 32.9 + - + +
221L PHE 3.6 9.9 - - - +
222L LYS* 3.4 17.9 + - - +
372L PHE* 3.7 10.1 - - + +
373L LEU* 3.5 1.4 - - - -
374L GLU* 2.7 46.9 + - + +
380L SER* 1.3 77.4 + - - +
382L ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 382 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L PHE* 4.1 1.1 - - + -
220L TYR* 3.8 1.4 - - - -
221L PHE* 2.8 36.3 + - + +
372L PHE* 3.1 9.2 - - - +
373L LEU* 4.1 7.2 - - + -
381L GLU* 1.3 76.3 - - - +
383L ALA* 1.3 63.5 + - - +
412L ILE* 4.0 15.9 - - + -
422L PHE* 3.5 39.5 - - + -
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Residues in contact with ALA 383 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194L THR* 4.3 4.7 - - - -
197L ARG* 4.3 13.0 - - + -
198L ILE* 3.4 19.3 - - + +
219L ILE 3.4 9.6 - - - +
220L TYR* 3.7 22.9 - - + -
371L ALA* 3.3 2.4 - - - +
372L PHE* 2.9 32.7 + - + -
382L ALA* 1.3 77.2 - - - +
384L ALA* 1.3 63.1 - - - +
422L PHE* 3.6 5.7 - - - -
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Residues in contact with ALA 384 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L SER* 3.5 32.3 - - - -
82L SER* 4.4 4.5 + - - -
194L THR* 4.2 3.1 - - - +
198L ILE* 3.9 5.9 - - - +
218L THR* 3.5 3.1 - - - -
219L ILE* 2.9 34.3 + - + +
369L HIS* 3.8 11.2 - - + +
370L LYS 3.1 12.3 - - - +
371L ALA* 4.2 4.0 - - + -
383L ALA* 1.3 76.0 - - - +
385L SER* 1.3 63.8 + - - +
422L PHE* 4.0 4.5 - - + -
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Residues in contact with SER 385 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L SER* 4.1 0.9 - - - -
190L VAL* 3.2 41.7 - - - +
198L ILE* 3.7 6.1 - - - -
201L VAL* 3.6 15.8 - - - +
216L VAL* 3.9 1.9 - - - +
217L ASN 2.7 19.2 + - - -
218L THR* 3.4 2.9 + - - -
368L PHE 3.5 1.9 - - - +
369L HIS* 3.3 4.3 - - - -
370L LYS 2.9 32.1 + - - +
384L ALA* 1.3 76.8 - - - +
386L THR* 1.3 62.6 + - - +
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Residues in contact with THR 386 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L SER* 2.7 25.0 + - - -
83L ILE* 3.2 12.8 + - - -
86L ALA* 3.9 24.8 - - + +
87L PHE* 4.4 4.9 - - + -
215L LEU 3.8 0.3 - - - +
216L VAL* 3.3 3.1 - - - +
217L ASN* 2.8 35.5 + - - +
331L LEU* 3.7 26.0 - - + -
368L PHE 3.3 9.2 - - - +
369L HIS* 2.7 19.5 + - - +
385L SER* 1.3 73.4 - - - +
387L ALA* 1.3 66.1 + - - +
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Residues in contact with ALA 387 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L VAL* 4.4 9.6 - - + -
202L ILE* 4.2 22.9 - - + -
214L VAL* 4.3 5.4 - - + -
215L LEU 3.1 5.4 - - - +
216L VAL* 3.9 19.7 - - + -
367L ALA* 3.3 5.2 - - - -
368L PHE* 3.0 38.4 + - + +
386L THR* 1.3 77.6 - - - +
388L VAL* 1.3 63.0 + - - +
389L VAL* 3.8 1.3 + - + +
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Residues in contact with VAL 388 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L ALA* 4.3 13.7 - - + +
87L PHE* 4.0 33.9 - - + -
90L THR* 3.4 28.3 - - + +
214L VAL* 3.3 5.8 - - - +
215L LEU* 2.8 46.9 + - + +
364L VAL* 3.5 35.4 - - + -
367L ALA* 4.2 5.8 - - + -
387L ALA* 1.3 73.9 - - - +
389L VAL* 1.3 62.5 + - - +
390L ILE* 4.1 0.4 - - + -
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Residues in contact with VAL 389 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ILE* 5.6 1.8 - - + -
206L ALA 4.5 9.0 - - - +
207L ILE* 3.8 14.8 - - + -
211L THR* 3.6 28.3 - - + +
213L LEU 3.8 0.4 - - - -
214L VAL* 3.6 21.1 - - + -
364L VAL* 3.4 3.5 - - - +
365L SER* 2.6 51.8 + - - +
366L ASP* 3.1 34.2 + - + +
368L PHE* 4.1 18.6 - - + -
387L ALA* 3.8 1.7 + - + +
388L VAL* 1.3 73.7 - - - +
390L ILE* 1.3 61.5 + - - +
393L ARG 5.0 0.2 - - - +
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Residues in contact with ILE 390 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L THR* 6.2 1.8 - - + -
211L THR* 3.4 4.8 - - - +
212L VAL* 3.0 22.1 + - + -
213L LEU* 2.8 53.2 + - + +
215L LEU* 3.9 15.9 - - + -
351L LEU* 4.6 7.2 - - + -
354L ILE* 3.8 20.2 - - + -
362L LEU* 3.9 23.6 - - + -
363L TYR 3.3 28.3 - - - +
364L VAL* 4.3 11.7 - - + +
388L VAL* 5.0 0.2 - - + -
389L VAL* 1.3 70.2 - - - +
391L ALA* 1.3 69.9 + - + +
392L GLY 3.5 0.7 - - - -
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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