Contacts of the strand formed by residues 306 - 313 (chain N) in PDB entry 3H1I
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 SER 306 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280N TYR 3.1 15.9 - - - -
281N ASP* 3.9 11.0 - - - +
304N CYS* 3.1 8.5 - - - +
305N HIS* 1.3 86.0 - - - +
307N PHE* 1.3 59.7 + - - +
323N HIS* 5.5 0.7 - - - -
324N PHE* 3.1 3.9 - - - +
325N VAL* 2.7 52.1 + - - +
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Residues in contact with PHE 307 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277N ILE* 3.4 18.4 - - + -
278N GLY 3.3 22.9 - - - -
279N ARG* 3.4 6.7 - - - +
280N TYR* 3.0 53.6 + - + +
292N SER* 4.1 0.7 - - - -
294N LEU* 3.4 47.1 - - + -
295N ALA* 3.7 15.7 - - - -
298N ALA* 4.2 2.0 - - + -
304N CYS* 3.9 14.4 - - - -
306N SER* 1.3 75.3 - - - +
308N GLN* 1.3 71.7 + - - +
309N THR* 5.3 0.2 - - + -
322N PHE* 5.9 4.0 - - + -
323N HIS 3.2 8.5 - - - +
324N PHE* 3.3 20.4 - - + -
334N MET* 4.8 2.7 - - + -
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Residues in contact with GLN 308 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146N THR* 4.1 10.6 - - - +
150N PHE* 4.4 10.5 - - + -
279N ARG* 3.8 20.9 - - + +
307N PHE* 1.3 83.2 - - - +
309N THR* 1.3 70.3 + - - +
310N PHE* 4.1 5.0 - - + +
322N PHE* 3.3 6.6 - - - +
323N HIS* 2.7 68.6 + - + +
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Residues in contact with THR 309 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274N ASN* 3.1 44.2 + - - +
277N ILE* 3.7 30.5 - - + -
278N GLY* 3.1 22.9 + - - +
279N ARG* 4.5 6.2 - - - +
307N PHE* 4.9 0.4 - - + -
308N GLN* 1.3 83.5 + - - +
310N PHE* 1.3 65.7 + - - +
321N GLY 4.0 7.9 - - - +
322N PHE* 5.0 4.7 - - + -
342N TRP* 6.2 0.7 - - - +
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Residues in contact with PHE 310 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N PHE* 3.9 31.6 - + + -
153N LEU* 4.2 14.4 - - + -
254N ALA* 5.4 1.6 - - + -
255N LEU 4.1 1.8 - - - -
256N ALA* 4.0 10.3 - - + -
274N ASN* 3.3 9.8 + - - +
308N GLN* 4.1 7.6 - - + +
309N THR* 1.3 80.0 - - - +
311N ASN* 1.3 57.5 + - - +
312N THR* 3.6 19.1 - - - +
319N LEU* 3.2 26.9 - - + +
320N PHE* 3.7 0.5 - - - -
321N GLY* 3.1 35.2 + - - +
322N PHE* 2.8 42.0 - - - -
323N HIS* 4.1 2.9 - - + -
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Residues in contact with ASN 311 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259N GLY* 5.0 0.5 - - - -
260N PRO* 4.8 5.4 - - - +
267N ASN* 3.1 24.5 + - - +
270N LEU* 3.7 22.1 - - + +
271N HIS* 3.5 36.9 + - + +
274N ASN* 3.4 12.6 + - - +
310N PHE* 1.3 72.7 - - - +
312N THR* 1.3 67.8 + - - +
313N SER* 3.0 12.3 + - - -
318N GLY* 5.4 0.3 - - - -
319N LEU 4.0 3.5 + - - -
320N PHE* 3.9 27.6 + - + +
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Residues in contact with THR 312 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N PHE* 5.1 4.7 - - - -
154N HIS* 4.8 7.1 - - + +
310N PHE* 3.6 17.7 - - - +
311N ASN* 1.3 72.0 - - - +
313N SER* 1.3 62.3 + - - +
314N TYR* 3.6 31.6 - - + +
318N GLY* 3.3 2.8 - - - -
319N LEU* 2.7 48.9 + - - -
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Residues in contact with SER 313 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260N PRO* 5.8 0.3 - - - +
261N GLY* 4.8 1.9 + - - -
262N TRP* 3.5 53.7 + - - -
267N ASN* 3.0 26.5 + - - -
271N HIS* 5.1 3.1 - - - -
311N ASN* 3.0 13.7 + - - -
312N THR* 1.3 76.2 - - - +
314N TYR* 1.3 77.4 + - - +
317N THR 4.4 3.1 - - - -
318N GLY* 4.4 1.3 - - - -
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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