Contacts of the helix formed by residues 306 - 310 (chain B) in PDB entry 4R7P
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 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LYS 5.2 0.7 - - - +
292B GLY* 4.0 1.7 - - - -
293B GLY* 2.9 31.3 + - - +
304B LEU* 4.0 21.0 + - - +
305B VAL* 1.3 76.5 - - - +
307B ILE* 1.3 68.7 + - + +
308B ALA* 3.2 7.9 - - + +
309B GLN* 3.2 35.6 + - - +
310B VAL* 3.5 13.2 - - - +
318B PHE* 4.2 2.9 - - - -
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL 4.6 4.0 - - - +
291B LYS* 3.4 52.7 - - + +
292B GLY 4.5 3.4 - - - +
306B GLU* 1.3 78.8 - - + +
308B ALA* 1.3 64.2 + - - +
310B VAL* 3.0 23.7 + - - +
315B VAL* 4.1 24.3 - - + +
318B PHE* 3.6 25.4 - - + -
319B LYS* 4.8 7.6 - - + -
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Residues in contact with ALA 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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306B GLU* 3.2 5.6 - - + +
307B ILE* 1.3 79.4 - - - +
309B GLN* 1.3 68.4 + - - +
310B VAL 3.7 3.6 + - - +
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 4.1 20.9 + - - -
73B VAL* 2.9 28.6 - - + +
304B LEU 4.1 5.7 - - - +
305B VAL* 4.0 13.0 - - + +
306B GLU* 3.2 38.9 + - - +
307B ILE 3.1 1.2 - - - -
308B ALA* 1.3 84.7 - - - +
310B VAL* 1.3 61.9 + - - +
311B PRO* 3.7 0.7 - - - +
351B GLU* 4.0 38.3 - - + +
352B ILE 5.6 3.0 + - - -
353B ILE* 5.7 7.1 - - - +
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 4.4 2.0 - - + -
305B VAL* 3.9 7.0 - - + -
306B GLU 3.5 18.2 - - - +
307B ILE* 3.0 15.4 + - - +
308B ALA 4.4 2.9 - - - +
309B GLN* 1.3 79.4 - - - +
311B PRO* 1.3 82.7 - - + +
312B LYS* 3.8 0.3 + - - -
314B HIS* 3.5 37.2 - - + +
315B VAL* 3.9 9.0 - - + +
318B PHE* 3.6 34.3 - - + -
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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
------------------------------------------------------------
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