Contacts of the strand formed by residues 234 - 240 (chain D) in PDB entry 1NPP
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 ARG 234 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C VAL* 3.8 19.0 - - + +
171C PRO* 2.7 57.5 + - - +
172C LEU* 3.7 16.4 + - + -
173C LYS* 3.4 34.3 - - - +
229D ILE 3.2 0.3 - - - +
230D SER* 3.9 0.9 - - - -
231D ILE* 2.6 47.5 + - + +
233D GLY* 1.3 71.2 - - - +
235D MET* 1.3 63.7 + - - +
236D THR* 3.0 19.9 + - - +
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Residues in contact with MET 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LYS* 4.9 9.7 - - - +
228D MET* 3.7 39.2 - - + +
229D ILE 3.4 6.1 - - - +
230D SER* 3.6 26.0 - - - -
233D GLY 3.5 7.0 + - - +
234D ARG* 1.3 71.0 + - - +
236D THR* 1.3 60.5 + - - +
237D PRO* 4.0 5.5 - - - +
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Residues in contact with THR 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 3.6 33.4 - - + -
170C VAL* 4.6 7.2 - - + +
208D PHE* 5.3 0.9 - - + -
227D VAL 3.3 1.0 - - - +
228D MET* 3.8 2.9 - - - -
229D ILE* 2.6 38.4 + - + +
231D ILE* 3.6 16.8 - - + +
234D ARG* 3.0 20.3 + - - +
235D MET* 1.3 73.6 + - - +
237D PRO* 1.3 83.1 - - + +
238D VAL* 3.4 8.2 + - + +
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Residues in contact with PRO 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D GLU* 6.4 0.4 - - + -
226D THR* 6.2 3.4 - - - -
227D VAL 3.4 6.3 - - - +
228D MET* 3.7 28.2 - - + -
235D MET 4.0 5.2 - - - +
236D THR* 1.3 90.2 - - + +
238D VAL* 1.3 66.6 + - - +
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 5.2 1.6 - - + -
208D PHE* 3.6 35.7 - - + -
226D THR* 4.4 1.3 - - - -
227D VAL* 2.5 49.4 + - - +
229D ILE* 4.0 11.2 - - + -
236D THR* 3.7 19.5 - - + +
237D PRO* 1.3 84.9 - - - +
239D GLU* 1.3 75.8 + - - +
240D LEU* 3.7 21.1 - - + -
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Residues in contact with GLU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D LYS* 4.8 18.1 - - + +
225D LEU 3.0 11.2 - - - +
226D THR* 4.2 19.2 - - + +
238D VAL* 1.3 76.5 - - - +
240D LEU* 1.3 72.7 + - - +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D VAL* 3.5 28.9 - - + -
205D GLU 5.4 5.8 - - - +
207D PRO* 6.5 0.7 - - + -
208D PHE* 4.8 10.1 - - + -
224D LYS* 3.1 4.9 - - - -
225D LEU* 2.7 42.4 + - - +
227D VAL* 4.1 10.5 - - + -
229D ILE* 5.4 0.9 - - + -
238D VAL* 3.7 18.4 + - + +
239D GLU* 1.3 84.6 - - - +
241D ASP* 1.3 63.7 + - - +
243D ASP 5.7 0.2 - - - +
244D GLN* 2.8 40.7 + - + +
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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