Contacts of the strand formed by residues 312 - 318 (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 GLU 312 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259L ARG* 4.2 4.5 - - - -
260L TYR* 2.9 34.3 + - - +
261L ARG* 4.0 22.4 - - - +
309L ASP 5.2 3.8 - - - +
310L GLU 3.9 3.3 + - - +
311L LEU* 1.3 83.6 - - - +
313L GLU* 1.3 72.0 + - - +
314L MET* 4.5 8.5 - - + +
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Residues in contact with GLU 313 (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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257L LYS* 3.4 43.8 + - - +
258L PHE 3.3 17.0 - - - +
259L ARG* 4.4 9.9 - - + +
312L GLU* 1.3 80.6 + - - +
314L MET* 1.3 78.3 + - - +
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Residues in contact with MET 314 (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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232I GLU* 4.9 3.8 - - - +
385I SER 5.1 5.2 - - - +
387I ALA* 4.4 14.6 - - + +
256L GLY 3.0 5.5 - - - +
257L LYS* 3.2 6.0 - - - -
258L PHE 3.0 31.2 + - - +
260L TYR* 4.4 30.7 - - + +
261L ARG* 5.7 5.6 - - - +
312L GLU* 4.5 14.6 - - + +
313L GLU* 1.3 92.7 - - - +
315L MET* 1.3 76.3 + - - +
316L LEU* 3.5 4.7 + - + +
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Residues in contact with MET 315 (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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385I SER 4.1 6.5 + - - +
386I THR* 3.4 19.4 - - - +
387I ALA 3.2 16.1 + - - -
255L GLU* 3.5 38.8 - - + +
256L GLY* 3.5 24.5 - - - +
257L LYS* 4.5 19.5 - - + +
314L MET* 1.3 78.3 - - - +
316L LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 316 (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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386I THR* 3.6 4.0 - - - +
387I ALA* 3.1 18.6 - - + +
389I VAL* 3.6 18.2 - - + -
254L GLN 3.8 0.5 - - - +
255L GLU* 3.2 5.5 - - - +
256L GLY 3.1 30.4 + - - +
258L PHE* 3.4 40.6 - - + -
260L TYR* 3.4 51.1 - - + -
270L LEU* 4.5 3.1 - - + -
314L MET* 4.4 6.1 - - + +
315L MET* 1.3 77.9 - - - +
317L VAL* 1.3 65.4 + - - +
318L VAL* 3.6 11.7 + - + +
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Residues in contact with VAL 317 (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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228I LYS* 4.8 10.8 - - + -
386I THR* 3.9 8.7 - - + -
387I ALA 2.9 6.3 + - - -
388I VAL* 3.5 21.1 - - + -
389I VAL* 2.6 36.0 + - - +
253L TYR* 3.4 32.8 - - + +
254L GLN 3.4 2.9 - - - -
255L GLU* 3.7 29.2 - - + +
316L LEU* 1.3 72.7 - - - +
318L VAL* 1.3 57.7 + - - +
319L HIS* 3.5 22.4 - - + +
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Residues in contact with VAL 318 (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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389I VAL* 3.5 3.6 - - + +
229L PHE* 4.2 16.3 - - + -
253L TYR* 3.2 7.6 + - - -
254L GLN* 2.8 42.1 + - + +
258L PHE* 3.9 21.1 - - + -
270L LEU* 3.8 28.7 - - + -
272L LEU* 4.4 7.6 - - + -
283L LEU* 5.7 0.4 - - + -
316L LEU* 3.6 28.0 - - + -
317L VAL* 1.3 72.5 - - - +
319L HIS* 1.3 66.2 + - - +
320L MET* 4.1 14.0 + - + -
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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