Contacts of the helix formed by residues 300 - 311 (chain B) in PDB entry 5I4V
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 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU* 4.2 23.6 - - + +
298B GLU 3.9 4.9 - - - +
299B MET* 1.3 86.5 - - - +
301B VAL* 1.3 64.0 + - - +
302B ASP* 4.3 8.7 - - + +
303B ARG* 3.3 33.1 + - + +
304B ILE* 3.4 13.3 + - - +
358B PRO* 3.9 18.6 - - + -
359B HIS* 5.4 0.7 - - + -
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 5.6 0.8 - - - +
299B MET 3.3 4.0 + - - -
300B PRO* 1.3 68.9 - - - +
302B ASP* 1.3 72.3 + - - +
304B ILE* 3.4 9.1 + - + +
305B LEU* 3.0 22.0 + - + +
436B THR* 3.5 23.1 - - + +
440B CYS* 3.9 25.4 - - - -
470B SER* 3.8 30.7 - - - +
474B TYR* 3.8 23.1 - - + -
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO* 4.2 6.3 - - + +
301B VAL* 1.3 86.8 - - - +
303B ARG* 1.3 60.3 + - + +
305B LEU* 3.0 15.2 + - - +
306B GLU* 2.9 37.7 + - + +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B PRO* 3.3 27.0 + - + +
302B ASP* 1.3 80.3 - - + +
304B ILE* 1.3 62.1 + - - +
306B GLU* 3.4 20.0 + - - +
307B ALA* 3.2 20.4 + - - +
355B LYS 4.8 3.0 + - - -
356B ARG* 3.7 29.9 + - - +
357B ILE 4.5 1.0 + - - -
358B PRO* 3.8 41.8 - - + +
359B HIS* 4.8 4.6 + - - +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B MET* 4.0 26.9 - - + +
300B PRO 3.4 14.3 + - - +
301B VAL* 3.4 11.4 + - + +
302B ASP 3.2 0.4 - - - -
303B ARG* 1.3 74.5 - - - +
305B LEU* 1.3 65.2 + - - +
307B ALA* 3.1 16.8 + - - +
308B GLU* 3.3 12.6 + - - +
357B ILE* 4.3 14.1 - - + -
358B PRO* 4.2 15.0 - - + -
436B THR* 4.4 3.6 - - - +
439B GLY* 3.4 36.3 - - - +
440B CYS* 3.6 23.6 - - - +
443B ALA* 4.6 11.0 - - + -
467B VAL* 4.9 2.5 - - + -
470B SER* 5.7 0.9 - - - -
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B VAL* 3.0 13.0 + - + +
302B ASP* 3.0 17.0 + - - +
304B ILE* 1.3 77.6 - - - +
306B GLU* 1.3 63.0 + - + +
308B GLU* 3.3 5.1 + - + +
309B LEU* 3.2 43.7 + - + +
435B LYS* 3.6 29.8 - - + -
436B THR* 3.5 30.3 - - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ASP* 2.9 19.2 + - - +
303B ARG* 3.5 29.2 + - - +
304B ILE 3.2 0.4 - - - -
305B LEU* 1.3 76.3 - - + +
307B ALA* 1.3 53.9 + - - +
309B LEU* 3.3 9.4 + - + +
310B ALA* 2.7 38.2 + - + +
356B ARG* 5.2 3.4 - - + +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ARG 3.2 7.8 + - - +
304B ILE 3.1 11.1 + - - +
306B GLU* 1.3 80.4 - - - +
308B GLU* 1.3 60.3 + - - +
310B ALA* 3.6 2.8 + - - +
311B VAL* 3.5 17.8 + - - +
353B TRP* 3.5 32.3 - - + +
356B ARG* 3.6 36.2 - - + +
357B ILE* 4.2 8.7 - - + -
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ILE 3.3 8.7 + - - +
305B LEU* 3.3 8.3 + - - +
307B ALA* 1.3 76.5 - - - +
309B LEU* 1.3 62.2 + - - +
311B VAL* 3.0 25.2 + - - +
312B GLU 3.8 7.8 - - - +
353B TRP* 2.6 16.1 + - - +
383B SER* 5.4 1.4 - - - -
435B LYS* 4.0 31.3 - - + +
438B LEU* 3.3 24.3 - - - +
439B GLY* 3.7 26.2 - - - -
442B ARG* 2.5 38.1 + - - -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B LEU* 3.2 40.3 + - + +
306B GLU* 3.8 7.4 - - + +
308B GLU* 1.3 72.0 - - - +
310B ALA* 1.3 58.1 + - - +
311B VAL 3.0 4.5 - - - -
312B GLU* 2.8 29.8 + - - +
435B LYS* 4.3 24.5 - - + -
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLU 2.7 23.2 + - - +
307B ALA 3.8 2.9 - - - +
309B LEU* 1.3 71.7 - - - +
311B VAL* 1.3 59.1 + - + +
312B GLU* 3.3 5.9 + - - +
356B ARG* 3.6 42.9 + - - +
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 3.5 13.2 - - - +
308B GLU* 3.0 24.4 - - - +
309B LEU 3.0 1.6 + - - -
310B ALA* 1.3 82.1 - - + +
312B GLU* 1.3 68.9 + - - +
349B THR* 3.4 43.0 - - + +
352B GLU* 5.0 6.1 - - + -
353B TRP* 4.2 21.3 - - + +
356B ARG* 5.6 1.6 - - - +
442B ARG* 5.5 2.9 - - - +
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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