Contacts of the helix formed by residues 311 - 319 (chain B) in PDB entry 3RIE
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 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B LEU* 3.9 33.0 - - + -
234B TRP* 5.1 0.2 - - + -
258B ASN* 5.9 1.1 - - + +
309B LYS 4.5 1.8 - - - +
310B LEU* 1.3 91.2 - - + +
312B ALA* 1.3 66.5 + - - +
313B PHE* 3.6 25.6 - - + -
314B LEU* 2.9 15.5 + - + +
315B LEU 3.2 8.1 + - - -
260C SER* 5.7 2.7 - - - -
297C LYS 4.0 0.7 - - - +
298C TYR* 3.6 42.4 - - + +
303C ASN* 3.7 6.9 - - - +
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Residues in contact with ALA 312 (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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310B LEU 3.4 1.7 + - - -
311B PRO* 1.3 71.1 - - - +
313B PHE* 1.3 62.8 + - - +
315B LEU* 3.4 10.2 + - + +
316B LYS* 3.1 23.4 + - - +
296C LEU* 4.2 11.2 - - + +
297C LYS* 3.4 11.7 + - - -
298C TYR 3.0 18.6 + - - +
299C TYR 4.0 11.7 - - - +
300C ASN* 4.2 13.9 - - + +
303C ASN* 3.8 0.2 - - - +
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Residues in contact with PHE 313 (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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233B LEU* 3.6 39.5 - - + -
234B TRP* 4.4 5.6 - + - -
237B VAL* 4.1 13.5 - - + -
311B PRO* 3.1 20.2 + - + -
312B ALA* 1.3 73.5 - - - +
314B LEU* 1.3 72.3 + - + +
316B LYS* 3.5 7.2 + - - +
317B GLU* 3.1 28.3 + - + +
100C PHE* 3.8 20.6 - + - -
296C LEU 5.7 0.2 - - - -
297C LYS* 2.8 43.7 + - + +
601C GOL 3.9 39.0 - - - +
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Residues in contact with LEU 314 (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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233B LEU* 3.8 26.2 - - + -
237B VAL* 3.8 36.8 - - + -
240B ILE* 4.5 8.3 - - + -
256B TYR* 4.0 14.6 - - + -
310B LEU* 3.5 32.3 - - + -
311B PRO* 2.9 13.1 + - + +
313B PHE* 1.3 92.5 - - + +
315B LEU* 1.3 66.6 + - - +
317B GLU* 3.0 3.8 + - - +
318B ILE* 2.9 38.7 + - + +
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Residues in contact with LEU 315 (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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310B LEU* 4.3 20.7 - - + +
311B PRO 3.2 6.3 + - - +
312B ALA* 3.5 9.9 - - - +
314B LEU* 1.3 78.1 - - - +
316B LYS* 1.3 60.5 + - - +
318B ILE* 4.0 9.6 - - + +
319B GLU* 3.2 24.6 + - - +
300C ASN* 3.7 26.9 - - - +
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Residues in contact with LYS 316 (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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312B ALA 3.1 13.3 + - - +
313B PHE* 3.8 8.1 - - - +
315B LEU* 1.3 80.7 - - - +
317B GLU* 1.3 61.9 + - + +
319B GLU* 3.4 22.4 - - - +
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Residues in contact with GLU 317 (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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237B VAL* 3.8 28.9 - - + -
241B LYS* 3.2 49.9 + - + -
313B PHE* 3.1 22.2 + - + +
314B LEU* 3.0 9.4 + - - +
316B LYS* 1.3 77.6 - - + +
318B ILE* 1.3 60.8 + - + +
319B GLU* 3.8 8.8 - - - +
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Residues in contact with ILE 318 (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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240B ILE* 4.4 4.3 - - + -
241B LYS* 4.2 16.6 - - + -
244B ILE* 3.9 37.6 - - + +
248B LYS* 5.5 4.0 + - - -
256B TYR* 4.5 6.7 - - + -
310B LEU* 4.0 26.5 - - + -
314B LEU* 2.9 37.2 + - + +
315B LEU* 4.0 10.5 - - + +
317B GLU* 1.3 78.6 - - + +
319B GLU* 1.2 75.1 + - - +
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Residues in contact with GLU 319 (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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241B LYS* 4.9 7.4 + - - -
248B LYS* 6.0 3.1 - - - -
315B LEU* 3.2 15.8 + - - +
316B LYS* 3.4 18.5 - - - +
317B GLU 3.8 12.7 - - - +
318B ILE* 1.2 93.8 - - - +
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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