Contacts of the strand formed by residues 221 - 231 (chain H) in PDB entry 2PUQ
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 GLN 221 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206H ALA 3.5 1.6 - - - +
207H VAL* 3.5 3.3 - - - -
208H LEU* 2.8 35.7 + - + +
219H ASP 3.8 7.2 + - - +
220H GLU* 1.3 79.1 - - - +
222H SER* 1.3 62.3 + - - +
223H ARG* 3.6 20.1 + - - +
252H VAL* 3.4 15.6 - - + +
253H VAL* 2.7 53.7 + - - +
255H THR* 3.7 12.9 - - - +
258H VAL* 3.5 18.1 - - + +
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Residues in contact with SER 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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205H ILE* 3.9 19.3 - - - -
206H ALA 3.2 5.4 - - - -
207H VAL* 4.2 12.6 - - - +
220H GLU* 5.2 2.1 - - - +
221H GLN* 1.3 74.9 + - - +
223H ARG* 1.3 83.0 + - - +
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Residues in contact with ARG 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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205H ILE* 3.2 7.0 - - - -
206H ALA* 2.9 32.7 + - + +
221H GLN* 3.6 25.0 + - - +
222H SER* 1.3 102.3 + - - +
224H ARG* 1.3 69.7 + - - +
248H LEU* 4.1 19.1 - - + -
249H HIS* 4.9 1.3 - - - +
250H GLN* 3.2 28.8 + - - +
251H PRO 2.9 26.6 + - - -
252H VAL* 3.6 31.4 - - + +
253H VAL* 4.3 8.7 - - - +
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Residues in contact with ARG 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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202H ARG 5.0 9.9 - - - +
204H LEU 3.4 10.5 - - - +
205H ILE* 4.4 6.3 - - + +
223H ARG* 1.3 74.3 - - - +
225H VAL* 1.3 63.3 - - - +
226H ALA 3.8 0.2 - - - -
248H LEU* 3.5 4.0 - - - -
249H HIS* 2.9 43.1 + - + +
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Residues in contact with VAL 225 (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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170H LEU* 4.7 0.4 - - + -
201H TRP 4.8 4.2 - - - +
204H LEU* 3.1 45.4 + - + +
205H ILE 4.2 0.2 - - - -
206H ALA* 4.1 15.0 - - + +
224H ARG* 1.3 76.3 - - - +
226H ALA* 1.3 60.8 + - - +
227H GLN 3.6 22.4 - - - +
228H VAL* 3.9 12.8 - - + -
246H LEU* 3.8 27.4 - - + -
247H ARG 3.7 7.2 - - - +
248H LEU* 4.2 12.3 - - + +
399H VAL* 4.5 9.0 - - - +
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Residues in contact with ALA 226 (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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224H ARG 3.6 3.0 + - - -
225H VAL* 1.3 72.2 - - - +
227H GLN* 1.3 60.2 + - + +
247H ARG* 2.7 26.0 + - - +
248H LEU 4.1 2.2 - - - +
249H HIS* 3.9 35.4 - - + +
398H GLY 4.2 2.4 - - - +
399H VAL* 3.6 18.8 - - - +
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Residues in contact with GLN 227 (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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225H VAL* 3.5 4.7 - - - +
226H ALA* 1.3 82.0 - - + +
228H VAL* 1.3 64.8 + - - +
229H ILE* 4.0 23.8 - - + +
245H LEU 3.7 0.6 - - - +
246H LEU* 3.1 5.9 - - - -
247H ARG* 2.9 67.3 + - + +
396H ARG* 3.3 23.2 + - - +
397H PRO 4.1 3.0 + - - -
398H GLY 3.1 20.2 + - - +
399H VAL* 3.1 16.2 - - - +
401H LEU* 3.7 25.2 - - + +
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Residues in contact with VAL 228 (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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195H PHE* 3.8 39.9 - - + -
201H TRP* 4.3 20.2 - - + -
204H LEU* 4.7 4.0 - - + -
225H VAL* 3.9 17.0 - - + -
227H GLN* 1.3 75.0 - - - +
229H ILE* 1.3 57.0 + - - +
230H ILE* 4.3 2.2 - - + -
244H ALA* 4.1 6.7 - - + -
245H LEU 3.6 1.8 - - - -
246H LEU* 4.0 16.4 - - + -
399H VAL* 2.7 14.1 + - + +
400H LEU* 3.3 19.2 - - + +
401H LEU 2.7 33.4 + - - +
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Residues in contact with ILE 229 (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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187H TRP* 4.2 27.6 - - + -
227H GLN* 4.0 29.4 - - + +
228H VAL* 1.3 76.0 - - - +
230H ILE* 1.3 61.6 + - - +
244H ALA* 3.2 4.0 - - - -
245H LEU* 2.6 55.1 + - + +
247H ARG* 4.8 3.1 - - - +
386H TRP* 4.0 4.1 - - + -
390H LEU* 3.8 24.7 - - + +
401H LEU* 3.3 21.5 - - + +
403H ALA* 3.7 29.6 - - + -
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Residues in contact with ILE 230 (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 ALA* 3.9 24.5 - - + +
195H PHE* 4.9 1.6 - - + -
228H VAL* 4.3 3.8 - - + -
229H ILE* 1.3 77.7 - - - +
231H PRO* 1.4 82.4 - - + +
234H TYR* 3.9 24.0 - - + +
236H PRO* 6.4 1.1 - - + -
243H ILE 3.9 1.1 - - - +
244H ALA* 3.9 12.1 - - + -
386H TRP* 3.7 4.0 - - - -
400H LEU* 4.1 29.8 - - + -
401H LEU 2.9 12.8 + - - +
402H ARG* 3.4 19.2 - - + -
403H ALA 3.2 19.8 + - - -
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Residues in contact with PRO 231 (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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230H ILE* 1.4 86.0 - - + +
232H SER* 1.3 61.4 + - - +
233H THR* 3.2 17.5 - - - +
234H TYR* 3.3 19.3 + - + +
241H HIS* 3.8 15.0 - - + +
243H ILE* 3.0 48.7 - - + +
383H TYR* 4.4 7.0 - - + -
386H TRP* 3.4 24.8 - - + -
402H ARG* 4.7 0.9 + - - +
403H ALA 3.7 0.4 - - - +
405H PHE* 4.1 11.2 - - + -
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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