Contacts of the strand formed by residues 267 - 273 (chain H) in PDB entry 3DHW
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 PRO 267 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265H CYS* 4.1 9.6 - - - +
266H VAL* 1.3 85.8 - - + +
268H MET* 1.3 56.5 + - - +
269H LEU* 4.8 5.0 - - + +
315H GLU* 3.2 3.5 - - - -
316H MET* 2.7 67.7 + - + +
317H HIS* 5.1 1.8 - - - -
318H GLY 5.9 2.5 - - - +
320H GLN* 5.1 11.7 - - + +
323H THR* 5.4 7.6 - - + +
339H VAL* 5.1 5.2 - - + -
342H TYR* 3.9 25.1 - - + -
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Residues in contact with MET 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H ILE* 3.3 25.6 - - + -
253H TYR* 3.6 8.5 - - + -
257H LEU* 4.0 21.5 - - + -
266H VAL 3.5 1.0 + - - -
267H PRO* 1.3 72.4 - - - +
269H LEU* 1.3 64.9 + - - +
297H ILE* 3.5 30.7 - - + -
314H THR 3.9 8.3 - - - +
315H GLU* 3.6 12.1 - - + +
339H VAL* 2.7 31.2 - - - +
340H LEU* 2.9 25.7 + - + -
341H GLY 2.8 19.3 + - - +
343H VAL* 3.5 25.6 - - + -
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Residues in contact with LEU 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H PRO* 4.8 7.6 - - + +
268H MET* 1.3 80.6 - - - +
270H ARG* 1.3 59.1 + - - +
271H LEU* 3.7 28.7 - - + -
313H LEU* 3.7 3.1 - - - +
314H THR* 2.6 44.0 + - + +
316H MET* 4.0 32.1 - - + -
327H ILE* 4.7 10.1 - - + -
330H LEU* 5.7 0.7 - - + -
337H VAL* 4.1 13.9 - - + -
338H GLU 3.5 6.7 - - - +
339H VAL* 3.2 34.8 - - + -
340H LEU* 3.3 16.2 - - - +
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Residues in contact with ARG 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242H GLN* 3.5 22.6 + - - -
245H LEU* 4.7 3.4 + - - +
246H HIS* 4.2 30.1 + - - +
249H ILE* 6.0 2.0 - - - +
269H LEU* 1.3 71.2 - - - +
271H LEU* 1.3 66.4 + - - +
272H GLU* 3.5 22.3 + - + +
311H ILE* 4.8 2.8 - - + +
313H LEU* 3.3 26.8 - - + +
336H LYS 4.1 0.7 - - - +
338H GLU* 2.9 53.7 + - + +
340H LEU* 3.6 32.2 - - + +
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Residues in contact with LEU 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269H LEU* 3.7 28.7 - - + -
270H ARG* 1.3 72.6 - - - +
272H GLU* 1.3 60.8 + - - +
273H PHE* 3.9 24.4 - - + -
283H LEU* 5.2 5.6 - - + -
311H ILE* 3.9 7.1 - - - +
312H MET* 3.1 46.6 + - - +
314H THR* 3.4 29.2 - - + +
316H MET* 6.1 0.9 - - + -
330H LEU* 4.5 15.7 - - + -
335H VAL* 4.9 3.8 - - + -
336H LYS 3.6 13.2 - - - +
337H VAL* 4.3 15.0 - - + -
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Residues in contact with GLU 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242H GLN* 5.6 2.5 - - - +
270H ARG* 3.5 25.5 + - + +
271H LEU* 1.3 73.6 - - - +
273H PHE* 1.3 65.8 + - - +
311H ILE* 4.8 13.0 - - + -
335H VAL* 4.6 0.6 - - - +
336H LYS* 2.9 59.2 + - + +
338H GLU* 4.8 7.4 - - + +
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Residues in contact with PHE 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271H LEU* 3.9 27.4 - - + -
272H GLU* 1.3 78.1 - - - +
274H THR* 1.3 69.7 + - - +
276H GLN* 2.9 33.2 - - - +
280H ALA* 5.9 0.2 - - + -
282H LEU* 3.5 19.5 - - + -
283H LEU* 5.8 1.8 - - + -
301H MET* 5.7 8.7 - - + -
308H LYS 5.1 0.2 - - - +
309H PHE* 4.8 19.2 - - - -
310H GLY* 2.8 40.3 + - - +
311H ILE* 4.8 2.1 - - - +
312H MET* 3.5 43.5 - - + -
334H HIS 5.1 2.0 - - - -
335H VAL* 4.1 21.1 - - + -
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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