Contacts of the strand formed by residues 234 - 241 (chain H) in PDB entry 4NQD
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 234 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H PRO* 3.7 27.8 - - - +
213H VAL 3.7 0.7 - - - +
214H GLN* 3.3 8.2 + - - +
215H PHE* 2.7 48.1 + - + +
230H LYS 4.6 2.0 + - - -
231H PRO* 4.3 1.0 - - - +
232H VAL* 2.9 38.7 + - + +
233H THR* 1.3 76.0 - - - +
235H ILE* 1.3 58.6 + - - +
236H VAL* 3.5 22.9 - - + +
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Residues in contact with ILE 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210H ARG* 5.0 1.1 - - - +
212H GLN* 3.3 44.9 - - + +
213H VAL 3.4 4.0 - - - +
214H GLN* 3.2 35.9 - - + +
234H GLN* 1.3 73.3 - - - +
236H VAL* 1.3 61.9 + - - +
237H SER* 3.9 9.0 + - - +
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Residues in contact with VAL 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H PRO* 4.9 0.9 - - + -
124H PRO* 3.7 30.7 - - + +
125H GLU* 5.1 0.7 - - - -
126H VAL* 3.5 34.3 - - + +
211H CYS 4.1 0.2 - - - +
213H VAL 2.8 34.4 + - - +
234H GLN* 3.5 31.4 - - + +
235H ILE* 1.3 74.2 - - - +
237H SER* 1.3 67.3 + - - +
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Residues in contact with SER 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H VAL* 4.1 9.1 - - - +
210H ARG* 3.4 39.2 + - - -
211H CYS 3.2 10.8 - - - -
212H GLN* 3.8 10.0 - - - +
235H ILE* 3.9 6.6 + - - +
236H VAL* 1.3 82.0 + - - +
238H ALA* 1.3 61.1 - - - +
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Residues in contact with ALA 238 (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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126H VAL* 3.7 24.2 - - + +
127H ALA* 3.8 15.9 - - - -
128H VAL* 3.7 18.2 - - + +
210H ARG* 3.4 5.9 - - - +
211H CYS 2.9 29.0 + - - +
237H SER* 1.3 74.6 - - - +
239H GLU* 1.3 62.4 + - - +
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Residues in contact with GLU 239 (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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128H VAL* 4.0 9.9 - - - +
208H HIS* 2.7 36.8 + - + +
209H PHE 3.3 12.1 - - - +
210H ARG* 4.3 10.5 - - + -
238H ALA* 1.3 77.1 - - - +
240H ALA* 1.3 65.3 + - - +
241H TRP* 4.9 9.0 + - + +
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Residues in contact with ALA 240 (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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123G ASP 6.0 0.2 - - - +
128H VAL* 4.1 20.0 - - + +
130H GLU* 3.8 28.0 - - + +
144H LEU* 4.7 3.6 - - + -
202H TRP* 4.5 7.6 - - + -
208H HIS* 3.9 2.2 - - - -
209H PHE* 2.9 37.4 + - - +
239H GLU* 1.3 77.6 - - - +
241H TRP* 1.3 66.3 + - - +
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Residues in contact with TRP 241 (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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130H GLU* 4.5 4.3 + - - +
202H TRP* 3.3 19.7 - - - -
205H PRO 3.7 18.8 - - - +
206H ARG* 3.6 18.2 - - - -
207H ASN 3.6 13.2 - - - -
208H HIS* 3.4 43.3 + + + -
209H PHE* 4.5 0.2 - - - -
239H GLU* 4.9 8.5 + - + +
240H ALA* 1.3 78.4 - - - +
242H GLY* 1.3 69.3 + - - +
243H ARG* 4.3 6.8 + - - +
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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