Contacts of the strand formed by residues 267 - 273 (chain I) 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 THR 267 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262I ARG* 3.6 1.8 - - - -
263I VAL* 2.7 51.7 + - + +
264I ALA 3.6 15.7 + - - -
265I GLU 3.9 4.5 + - - -
266I GLY* 1.3 76.1 - - - +
268I GLN* 1.3 62.8 + - - +
269I VAL* 5.0 0.2 - - + -
284I ILE* 3.6 31.4 - - + -
285I LEU 3.5 11.7 - - - +
286I PRO* 3.4 18.9 - - + +
290I LYS* 4.6 4.3 - - - -
295I VAL* 4.3 10.4 - - + +
307I TRP* 4.4 8.5 - - + -
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Residues in contact with GLN 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260I TYR* 2.6 37.0 + - + +
261I ARG 3.7 4.9 - - - -
262I ARG* 4.0 15.8 - - + +
266I GLY 4.2 6.1 - - - +
267I THR* 1.3 76.2 - - - +
269I VAL* 1.3 60.7 + - - +
270I LEU 4.2 0.2 - - - -
283I LEU 3.6 1.7 - - - +
284I ILE* 3.7 1.0 - - - -
285I LEU* 2.8 66.0 + - - +
400I VAL* 4.7 1.4 - - - +
401I THR 3.0 24.6 + - - +
402I PHE* 3.8 20.9 - - + -
403I LYS 4.9 0.5 + - - -
406I ARG* 4.9 4.0 + - - -
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Residues in contact with VAL 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I TYR* 3.4 4.7 - - - -
261I ARG* 3.0 35.7 + - + +
263I VAL* 4.4 10.1 - - + -
268I GLN* 1.3 75.2 - - - +
270I LEU* 1.3 61.1 + - - +
282I VAL* 3.6 26.9 - - + -
283I LEU 3.3 3.6 - - - +
284I ILE* 3.8 13.7 - - + -
307I TRP* 3.8 41.7 - - + +
308I LEU* 5.0 4.3 - - + -
311I LEU* 3.4 26.4 - - + +
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Residues in contact with LEU 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258I PHE* 3.5 31.2 - - + -
259I ARG 3.7 4.9 - - - +
260I TYR* 4.7 2.7 - - + +
269I VAL* 1.3 74.4 - - - +
271I GLU* 1.3 67.7 + - - +
272I LEU* 3.7 23.3 - - + -
281I MET 3.8 1.2 - - - +
282I VAL* 3.4 6.5 - - - +
283I LEU* 2.9 38.5 + - + +
316I LEU* 4.3 12.1 - - + -
318I VAL* 3.6 23.8 - - + -
402I PHE* 3.6 50.8 - - + -
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Residues in contact with GLU 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258I PHE* 3.7 18.7 - - - +
259I ARG* 3.1 47.9 + - + +
269I VAL 4.3 0.2 + - - -
270I LEU* 1.3 73.7 - - - +
272I LEU* 1.3 61.1 + - - +
273I PRO* 3.2 16.0 - - + +
280I THR* 2.8 42.4 + - + +
281I MET 3.8 3.1 - - - +
282I VAL* 4.0 8.7 - - + +
311I LEU* 3.9 19.4 - - + +
413I ARG* 3.3 24.0 + - - -
415I VAL* 4.7 2.5 - - - +
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Residues in contact with LEU 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I TRP* 3.4 26.1 - - + -
229I PHE* 4.5 11.0 - - + -
258I PHE* 3.5 35.0 - - + -
270I LEU* 3.7 29.8 - - + +
271I GLU* 1.3 70.7 - - - +
273I PRO* 1.3 68.3 - - - +
274I PHE* 4.0 0.5 + - - -
280I THR* 4.4 0.2 - - - -
281I MET* 2.9 36.1 + - + +
283I LEU* 4.4 9.0 - - + -
318I VAL* 4.7 3.1 - - + -
320I MET* 3.5 41.5 - - + -
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Residues in contact with PRO 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I TRP* 3.8 4.7 - - - -
226I LYS* 2.8 35.9 + - + +
227I SER* 4.4 2.1 + - - -
258I PHE* 4.4 14.4 - - + -
259I ARG 5.9 0.4 - - - +
271I GLU* 3.2 16.4 - - + +
272I LEU* 1.3 87.1 - - - +
274I PHE* 1.3 63.3 + - - +
277I ASP* 4.0 24.0 - - - +
280I THR* 3.6 26.0 - - + -
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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