Contacts of the strand formed by residues 214 - 224 (chain H) in PDB entry 1RFU
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 VAL 214 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H ARG* 3.5 30.3 - - + +
207H THR 3.0 9.2 - - - +
208H ARG* 3.6 44.9 - - + +
212H GLY 3.8 2.7 - - - +
213H SER* 1.3 74.0 - - - +
215H VAL* 1.3 63.9 + - - +
216H THR* 3.5 7.2 + - - +
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Residues in contact with VAL 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H GLN 4.0 0.3 - - - +
206H ARG* 3.6 1.0 - - - -
207H THR* 2.7 68.8 + - + +
209H ALA* 5.0 8.1 - - + +
213H SER* 3.9 2.6 - - - +
214H VAL* 1.3 72.4 - - - +
216H THR* 1.3 67.9 + - - +
217H GLN* 5.4 10.6 - - + +
250H ASN* 6.0 0.2 - - - +
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Residues in contact with THR 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H SER* 5.0 2.5 - - - +
205H GLN 3.4 8.1 - - - +
206H ARG* 4.0 30.9 + - + +
214H VAL* 3.5 8.3 + - - +
215H VAL* 1.3 81.2 + - - +
217H GLN* 1.3 67.8 + - - +
218H ARG* 4.0 29.5 + - + +
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Residues in contact with GLN 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203H GLY 4.5 0.9 - - - -
204H SER* 3.3 5.5 + - - -
205H GLN* 2.7 71.9 + - + +
207H THR* 5.3 1.9 + - - -
215H VAL* 4.2 10.7 + - + +
216H THR* 1.3 76.6 - - - +
218H ARG* 1.3 65.2 + - - +
219H ILE* 4.4 4.2 - - + +
250H ASN* 3.5 24.5 + - - +
251H ASN* 3.6 4.2 + - - +
252H LEU* 3.2 32.0 - - + +
253H LYS* 4.3 4.6 - - - +
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Residues in contact with ARG 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H LEU* 3.4 46.7 + - + +
173H ASP* 2.8 35.8 + - - -
203H GLY 3.7 2.0 - - - -
204H SER* 3.7 27.1 + - - +
216H THR* 4.0 17.9 + - + +
217H GLN* 1.3 76.6 - - - +
219H ILE* 1.3 67.5 + - - +
311H VAL* 3.6 10.1 - - - +
312H LEU* 3.0 49.2 + - + +
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Residues in contact with ILE 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H LEU* 6.0 0.2 - - - +
201H ALA 3.9 0.3 - - - +
202H LEU* 3.4 3.6 - - - +
203H GLY 2.8 52.2 + - - +
217H GLN* 5.3 2.9 - - + +
218H ARG* 1.3 83.5 - - - +
220H ARG* 1.3 58.6 + - - +
221H MET* 3.9 10.3 - - + -
252H LEU* 3.5 18.2 - - + +
253H LYS* 3.6 28.3 - - + +
256H CYS* 3.3 39.7 - - + -
309H ALA* 4.4 7.9 - - + -
310H THR 3.2 11.0 - - - +
311H VAL* 4.6 10.1 - - + -
312H LEU* 4.2 6.2 - - - +
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Residues in contact with ARG 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H GLN* 2.5 32.2 + - - +
193H PRO* 3.0 31.5 - - - +
200H MET* 3.0 32.9 - - + +
201H ALA 3.4 3.4 - - - -
202H LEU* 3.2 23.6 - - + -
219H ILE* 1.3 73.6 - - - +
221H MET* 1.3 70.5 + - - +
222H GLU* 3.6 15.5 + - - -
310H THR* 2.8 53.7 + - - +
312H LEU* 3.7 17.3 - - + +
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Residues in contact with MET 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H VAL* 5.7 3.8 - - + -
199H LEU 3.6 0.3 - - - +
200H MET* 3.1 9.5 - - - +
201H ALA* 2.7 60.6 + - + +
202H LEU 5.1 0.4 - - - -
203H GLY* 4.8 3.1 - - - +
219H ILE* 3.9 25.8 - - + +
220H ARG* 1.3 82.6 - - - +
222H GLU* 1.3 66.0 + - - +
223H MET* 4.0 6.3 - - + -
237H PHE* 6.4 0.9 - - + -
256H CYS* 3.9 24.0 - - + -
257H GLU 4.8 0.4 - - - -
260H VAL* 4.0 21.5 - - + -
307H VAL* 4.9 10.3 - - + -
308H GLN 4.8 2.9 - - - +
309H ALA* 3.4 31.2 - - + +
310H THR* 4.8 0.4 - - - -
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Residues in contact with GLU 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H SER* 4.4 9.2 - - - +
193H PRO* 3.6 23.3 - - + +
194H ARG* 3.0 53.4 + - - +
198H TYR* 4.3 14.3 - - + -
199H LEU 3.4 4.0 - - - +
200H MET* 4.8 1.6 - - + -
220H ARG* 3.6 26.4 + - - -
221H MET* 1.3 76.6 - - - +
223H MET* 1.3 62.1 + - - +
307H VAL* 4.5 14.6 - - - +
308H GLN 5.4 2.6 + - - -
310H THR* 5.4 5.7 - - - +
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Residues in contact with MET 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H THR 3.4 22.2 - - - +
187H SER* 3.9 4.3 - - - -
198H TYR* 3.1 11.4 - - - -
199H LEU* 2.5 74.1 + - + +
201H ALA* 3.9 17.0 - - + -
221H MET* 4.5 7.2 - - + +
222H GLU* 1.3 78.1 - - - +
224H HIS* 1.3 63.1 + - - +
260H VAL* 3.6 26.2 - - + -
307H VAL* 5.0 7.2 - - + -
7402H ADP 3.0 38.8 - - + +
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Residues in contact with HIS 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H ASP* 3.5 20.1 + - + -
198H TYR* 3.4 41.0 + + + -
222H GLU 4.3 0.2 + - - -
223H MET* 1.3 72.6 - - - +
225H LYS* 1.3 72.2 + - - +
226H VAL* 3.7 5.5 + - - +
264H HIS* 4.6 26.9 - - + +
268H GLN* 4.9 9.0 - - - +
7402H ADP 3.2 14.5 - - - -
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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