Contacts of the strand formed by residues 244 - 248 (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 ALA 244 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H VAL* 3.5 7.4 - - - +
190H SER 2.8 31.7 + - - +
191H ALA 4.0 1.3 - - - -
192H ALA 3.9 7.6 - - - +
195H PHE* 3.7 30.3 - - + -
228H VAL* 4.1 1.3 - - + -
229H ILE 3.2 10.3 - - - +
230H ILE* 3.9 11.0 - - + -
243H ILE* 1.3 79.7 - - - +
245H LEU* 1.3 61.1 + - - +
246H LEU* 4.0 7.6 - - + -
386H TRP* 5.3 0.7 - - - -
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Residues in contact with LEU 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H ILE* 4.2 13.0 - - + -
187H TRP* 3.5 34.8 - - + -
188H VAL 3.5 13.9 - - - +
189H VAL* 3.8 19.1 - - + -
227H GLN 3.7 0.9 - - - +
228H VAL* 3.6 0.9 - - - -
229H ILE* 2.6 52.2 + - + +
244H ALA* 1.3 75.0 - - - +
246H LEU* 1.3 61.4 + - - +
386H TRP* 4.7 3.8 - - + -
387H LEU* 4.2 19.7 - - + +
390H LEU* 3.8 32.3 - - + -
391H MET* 4.2 10.8 - - + -
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Residues in contact with LEU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H LEU* 3.9 36.8 - - + -
186H ILE 3.4 1.4 - - - +
187H TRP* 3.3 10.5 - - - -
188H VAL* 2.7 55.7 + - + +
190H SER* 4.2 7.2 - - - -
195H PHE* 4.1 10.1 - - + -
204H LEU* 5.3 0.4 - - + -
225H VAL* 3.8 26.7 - - + -
227H GLN 3.1 4.0 - - - +
228H VAL* 4.0 22.0 - - + -
244H ALA* 4.0 15.3 - - + +
245H LEU* 1.3 81.8 - - - +
247H ARG* 1.3 59.7 + - - +
248H LEU* 3.8 4.2 + - + +
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Residues in contact with ARG 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H ILE* 3.5 28.4 - - + +
187H TRP* 3.6 38.7 - - + -
225H VAL* 3.6 3.3 - - - +
226H ALA* 2.7 43.7 + - - -
227H GLN* 2.9 43.2 + - + +
229H ILE* 4.8 4.0 - - - +
246H LEU* 1.3 70.1 - - - +
248H LEU* 1.3 61.2 + - - +
390H LEU 5.0 2.8 + - - -
393H SER 4.9 5.3 + - - -
394H GLU 4.7 1.8 + - - -
395H PRO* 3.3 50.0 - - - +
396H ARG 4.4 0.4 - - - +
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Residues in contact with LEU 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H LEU* 4.6 2.7 - - + -
185H THR 4.0 18.4 - - - +
186H ILE* 3.0 28.9 + - - +
188H VAL* 4.4 21.3 - - + -
206H ALA* 3.9 26.9 - - + -
208H LEU* 4.9 1.1 - - + -
223H ARG* 4.1 10.5 - - + -
224H ARG 3.5 6.7 - - - +
225H VAL* 4.2 15.9 - - + -
226H ALA* 4.1 2.2 - - - +
246H LEU* 4.7 4.3 - - + +
247H ARG* 1.3 88.3 - - - +
249H HIS* 1.4 64.2 + - - +
250H GLN* 3.4 13.8 + - - +
252H VAL* 4.1 20.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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