Contacts of the helix formed by residues 299 - 316 (chain I) in PDB entry 6RAR
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 THR 299 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296I ASP* 3.3 28.7 + - + +
297I LEU 3.3 0.2 - - - -
298I ASP* 1.3 86.2 - - + +
300I ILE* 1.3 64.5 + - - +
301I GLN* 3.6 15.9 + - - +
302I GLY* 3.1 17.2 + - - -
303I GLN* 3.0 28.3 + - - +
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Residues in contact with ILE 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299I THR* 1.3 72.1 - - - +
301I GLN* 1.3 81.3 + - - +
303I GLN* 3.4 21.0 + - + +
304I LYS* 2.9 58.7 + - + +
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Residues in contact with GLN 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299I THR* 3.7 16.1 - - - +
300I ILE* 1.3 95.7 - - - +
302I GLY* 1.3 57.3 + - - +
304I LYS* 3.3 9.6 + - + +
305I ARG* 2.9 29.0 + - - +
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Residues in contact with GLY 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295I VAL* 4.1 6.5 - - - +
296I ASP* 3.2 28.7 - - - -
297I LEU* 4.4 4.3 - - - -
299I THR* 3.1 10.9 + - - -
301I GLN* 1.3 73.3 - - - +
303I GLN* 1.3 60.1 + - - +
305I ARG* 3.1 7.6 + - - +
306I PHE* 2.8 30.8 + - - +
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Residues in contact with GLN 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296I ASP 3.9 0.8 + - - -
297I LEU* 2.8 41.2 + - + +
298I ASP* 3.8 4.6 + - - +
299I THR 3.0 25.3 + - - +
300I ILE* 3.4 28.0 + - + +
302I GLY* 1.3 78.1 - - - +
304I LYS* 1.3 61.8 + - - +
306I PHE* 3.4 3.3 + - - +
307I VAL* 3.3 25.4 + - - +
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Residues in contact with LYS 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300I ILE* 2.9 50.9 + - + +
301I GLN* 3.5 8.5 - - + +
303I GLN* 1.3 78.2 - - - +
305I ARG* 1.3 62.7 + - - +
307I VAL* 3.4 8.4 + - - +
308I GLU* 3.1 21.0 + - - +
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Residues in contact with ARG 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293I GLU* 2.9 40.3 + - - +
295I VAL* 4.0 14.1 - - + -
301I GLN 2.9 17.6 + - - +
302I GLY* 3.1 8.3 + - - +
304I LYS* 1.3 74.3 - - - +
306I PHE* 1.3 66.8 + - - +
308I GLU* 3.2 29.4 + - - +
309I LEU* 2.9 38.8 + - + +
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Residues in contact with PHE 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158I MET* 4.3 11.9 - - + -
164I ILE* 3.8 25.4 - - + -
295I VAL* 4.5 4.9 - - + +
297I LEU* 4.0 20.4 - - + -
302I GLY 2.8 16.1 + - - +
303I GLN* 3.7 5.2 - - - +
304I LYS 3.3 0.2 - - - -
305I ARG* 1.3 76.8 - - - +
307I VAL* 1.3 73.6 + - + +
309I LEU* 3.1 9.6 + - - +
310I ASN* 2.9 30.1 + - + +
321I VAL* 3.9 20.0 - - + -
323I ILE* 3.7 39.5 - - + -
341I ALA* 4.6 7.4 - - + -
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Residues in contact with VAL 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303I GLN 3.3 13.9 + - - +
304I LYS* 3.7 8.3 - - - +
305I ARG 3.3 0.2 - - - -
306I PHE* 1.3 86.3 - - + +
308I GLU* 1.3 64.0 + - - +
310I ASN* 3.3 7.6 + - + +
311I LYS* 3.0 23.5 + - + +
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Residues in contact with GLU 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304I LYS 3.1 13.2 + - - +
305I ARG* 3.2 34.3 + - - +
307I VAL* 1.3 78.4 - - - +
309I LEU* 1.3 54.5 + - - +
311I LYS* 3.4 10.4 + - - +
312I SER* 2.7 42.8 + - - +
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Residues in contact with LEU 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I ILE* 4.0 37.2 - - + -
166I ILE* 5.3 1.7 - - - +
293I GLU* 3.7 31.6 - - + +
295I VAL* 4.0 20.4 - - + -
305I ARG* 2.9 36.6 + - + +
306I PHE* 3.1 7.2 + - - +
308I GLU* 1.3 74.4 - - - +
310I ASN* 1.3 65.2 + - - +
312I SER* 3.4 8.3 + - - +
313I ALA* 3.0 24.6 + - - +
321I VAL* 4.1 3.3 - - + +
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Residues in contact with ASN 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306I PHE* 2.9 21.1 + - + +
307I VAL* 3.6 11.9 - - + +
309I LEU* 1.3 76.1 - - - +
311I LYS* 1.3 62.2 + - - +
313I ALA* 3.3 2.3 + - - +
314I VAL* 3.0 30.4 + - - +
320I GLY* 4.4 4.5 - - - -
321I VAL* 3.6 37.5 + - + +
341I ALA* 4.3 13.1 - - - +
342I LYS* 5.6 1.1 - - - -
343I PRO* 5.6 1.2 - - - +
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Residues in contact with LYS 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307I VAL* 3.0 17.9 + - + +
308I GLU* 3.8 12.8 - - - +
310I ASN* 1.3 76.8 - - - +
312I SER* 1.3 53.6 + - - +
314I VAL* 3.2 7.0 + - + +
315I GLU* 2.6 61.8 + - + +
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Residues in contact with SER 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I GLU* 2.7 29.1 + - - +
309I LEU* 3.8 9.0 - - - +
311I LYS* 1.3 76.7 - - - +
313I ALA* 1.3 54.8 + - - +
315I GLU* 3.7 10.0 - - - +
316I GLY* 2.6 35.2 + - - -
318I TYR* 5.1 0.3 - - - -
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Residues in contact with ALA 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166I ILE* 3.7 19.9 - - + +
309I LEU 3.0 18.1 + - - +
310I ASN 3.5 2.2 - - - +
311I LYS 3.2 0.2 - - - -
312I SER* 1.3 78.1 - - - +
314I VAL* 1.3 60.7 + - - +
316I GLY 3.5 0.3 + - - -
317I GLY 3.4 2.6 + - - -
318I TYR* 2.9 37.6 + - + +
320I GLY 3.3 26.5 - - - +
321I VAL* 3.5 13.0 - - + -
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Residues in contact with VAL 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310I ASN* 3.0 31.5 + - - +
311I LYS* 3.7 5.8 - - + +
313I ALA* 1.3 75.5 - - - +
315I GLU* 1.3 66.9 + - + +
317I GLY* 3.1 14.6 + - - -
318I TYR 4.0 9.9 + - - +
320I GLY* 4.7 6.7 - - - -
343I PRO* 4.1 38.1 - - + -
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Residues in contact with GLU 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311I LYS* 2.6 41.8 + - + +
312I SER* 3.7 8.0 - - - +
314I VAL* 1.3 76.6 - - + +
316I GLY* 1.3 57.6 + - - +
317I GLY* 3.0 5.9 + - - -
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Residues in contact with GLY 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312I SER 2.6 20.6 + - - -
313I ALA 3.8 1.6 - - - -
314I VAL 3.3 0.2 - - - -
315I GLU* 1.3 71.3 - - - +
317I GLY* 1.3 58.2 + - - +
318I TYR* 3.5 24.7 - - - -
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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