Contacts of the helix formed by residues 311 - 320 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B SER* 5.9 2.0 - - - -
298B TYR* 3.6 39.9 - - + +
303B ASN* 3.4 10.5 - - - +
233C LEU* 4.0 35.2 - - + -
258C ASN* 5.7 2.2 - - + +
309C LYS 4.6 1.1 - - - +
310C LEU* 1.4 89.9 - - + +
312C ALA* 1.3 66.9 + - - +
313C PHE* 3.9 19.1 - - + -
314C LEU* 2.9 18.5 + - + +
315C LEU* 3.1 9.7 + - - +
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Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU* 3.7 22.2 - - + +
297B LYS* 3.7 4.7 - - - -
298B TYR 3.0 19.2 + - - +
299B TYR 4.0 9.9 - - - +
300B ASN* 4.2 13.9 - - + +
303B ASN* 4.0 0.4 - - - +
310C LEU 3.5 1.4 + - - -
311C PRO* 1.3 70.2 - - - +
313C PHE* 1.3 63.7 + - - +
314C LEU 3.2 0.7 + - - -
315C LEU* 3.2 8.1 + - - +
316C LYS* 3.2 20.1 + - - +
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Residues in contact with PHE 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 3.8 23.8 - + - -
296B LEU 5.6 0.2 - - - -
297B LYS* 2.8 41.3 + - + +
602B GOL 3.8 42.2 - - - +
233C LEU* 3.6 43.3 - - + -
234C TRP* 4.2 8.5 - + - -
237C VAL* 4.3 10.5 - - + -
311C PRO* 3.1 17.2 + - + -
312C ALA* 1.3 75.4 - - - +
314C LEU* 1.3 74.8 - - + +
316C LYS* 3.3 12.3 + - + +
317C GLU* 3.1 32.3 + - + +
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 3.8 30.3 - - + -
237C VAL* 4.1 25.6 - - + -
240C ILE* 4.5 13.7 - - + -
241C LYS* 6.4 0.2 - - + -
256C TYR* 4.0 15.7 - - + -
310C LEU* 3.6 28.5 - - + -
311C PRO* 2.9 13.7 + - + +
313C PHE* 1.3 94.0 - - + +
315C LEU* 1.3 68.7 + - - +
317C GLU* 3.1 7.7 + - + +
318C ILE* 2.9 38.8 + - + +
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Residues in contact with LEU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASN* 3.6 26.7 - - - +
308C PHE 5.6 1.8 - - - +
310C LEU* 3.8 34.1 - - + +
311C PRO 3.1 10.2 + - - +
312C ALA* 3.2 9.2 + - - +
314C LEU* 1.3 80.0 - - - +
316C LYS* 1.3 60.0 + - - +
318C ILE* 3.2 11.5 + - + +
319C GLU* 3.1 28.1 + - + +
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Residues in contact with LYS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ALA 5.9 0.6 + - - -
295B ASP* 5.5 10.7 - - - +
312C ALA 3.2 11.8 + - - +
313C PHE* 3.7 13.5 - - + +
314C LEU 3.1 0.6 - - - -
315C LEU* 1.3 75.9 - - - +
317C GLU* 1.4 63.5 + - + +
319C GLU* 3.4 17.1 + - - +
320C ASN* 3.5 21.8 + - - +
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Residues in contact with GLU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C VAL* 3.8 32.7 - - + +
241C LYS* 3.4 38.5 + - + +
313C PHE* 3.1 20.1 + - + +
314C LEU* 3.1 13.0 + - + +
316C LYS* 1.4 78.9 - - + +
318C ILE* 1.4 58.4 + - - +
320C ASN* 2.9 31.6 + - - +
321C ILE* 3.8 0.5 + - - +
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Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C ILE* 5.0 2.2 - - + -
241C LYS* 5.6 1.3 - - + -
244C ILE* 3.8 33.4 - - + -
248C LYS* 5.1 6.7 + - + +
256C TYR* 4.5 6.1 - - + -
310C LEU* 4.0 19.1 - - + -
314C LEU* 2.9 44.7 + - + +
315C LEU* 3.8 11.4 - - + +
317C GLU* 1.4 72.4 - - + +
319C GLU* 1.3 74.1 + - - +
320C ASN 3.1 1.6 - - - -
321C ILE* 3.2 33.1 + - + +
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Residues in contact with GLU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C LEU* 3.1 15.0 + - + +
316C LYS* 3.6 12.6 - - - +
317C GLU 3.3 0.4 - - - -
318C ILE* 1.3 87.2 - - - +
320C ASN* 1.3 63.2 + - - +
321C ILE* 3.2 4.8 + - - +
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Residues in contact with ASN 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LYS* 4.0 18.4 + - - +
316C LYS* 3.5 18.3 + - - +
317C GLU* 2.9 21.2 + - - +
319C GLU* 1.3 82.3 - - - +
321C ILE* 1.3 61.1 + - - +
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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