Contacts of the strand formed by residues 230 - 237 (chain P) in PDB entry 2D2I
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 LEU 230 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305O MET* 4.7 1.1 - - - -
160P LEU* 4.9 9.0 - - + -
164P ALA* 4.5 10.1 - - + -
173P ILE* 4.4 9.2 - - + -
176P GLY* 3.5 22.0 - - - +
177P THR* 5.4 0.2 - - - -
178P MET* 6.2 1.3 - - + -
216P ALA* 3.5 22.2 - - + +
217P LYS* 3.8 11.4 + - - +
219P VAL* 4.0 35.9 - - + -
226P LEU* 4.0 19.5 + - + +
228P GLY* 3.6 3.7 - - - +
229P LYS* 1.3 92.1 - - + +
231P ASN* 1.3 71.6 + - - +
247P LEU* 4.4 8.7 - - + -
249P VAL* 4.2 15.0 - - + -
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Residues in contact with ASN 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303O LEU* 3.5 38.1 - - + +
305O MET* 3.7 24.0 - - + +
176P GLY 3.3 7.0 + - - +
177P THR* 3.2 6.1 - - - +
178P MET* 2.8 23.0 + - - +
216P ALA* 3.4 10.7 - - - +
217P LYS* 3.8 27.9 - - - +
228P GLY 5.8 1.0 + - - -
230P LEU* 1.3 83.0 + - - +
232P GLY* 1.3 61.3 + - - +
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Residues in contact with GLY 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303O LEU* 5.5 1.7 - - - +
311O LYS* 5.4 1.1 - - - -
177P THR* 4.4 2.9 - - - -
178P MET* 2.9 20.9 - - - -
212P THR* 5.4 0.7 - - - -
213P THR* 3.7 19.1 + - - +
216P ALA* 3.7 6.2 - - - +
231P ASN* 1.3 81.0 - - - +
233P ILE* 1.3 71.4 + - - +
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Residues in contact with ILE 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301O LEU* 4.7 33.9 - - + +
303O LEU* 6.2 2.9 - - + -
311O LYS* 4.1 12.6 - - + -
313O ILE* 3.6 37.7 - - + -
178P MET* 3.0 7.6 + - - +
179P THR* 3.1 26.1 - - + +
180P THR 3.0 21.0 + - - -
210P PRO* 6.0 0.4 - - + -
211P THR 4.2 4.9 - - - +
212P THR* 5.1 2.5 - - - +
213P THR* 3.6 9.8 - - - +
232P GLY* 1.3 81.2 - - - +
234P ALA* 1.3 65.0 + - - +
235P LEU* 4.8 10.5 - - + -
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Residues in contact with ALA 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180P THR* 3.2 26.5 - - + +
182P HIS* 5.2 4.5 - - + -
200P ARG* 5.8 0.2 - - - +
210P PRO* 3.4 5.7 - - - +
211P THR* 2.9 51.7 + - + +
212P THR 4.5 0.2 - - - +
213P THR* 4.2 9.9 - - - -
233P ILE* 1.3 79.1 - - - +
235P LEU* 1.3 68.3 + - - +
236P ARG* 4.1 1.8 - - - +
4339P SO4 6.0 0.7 - - - +
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Residues in contact with LEU 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181O THR* 3.8 24.9 - - + +
244O VAL* 4.2 20.6 - - + -
246O ASP* 5.9 4.5 - - + -
301O LEU* 5.4 2.2 - - + -
313O ILE* 5.5 7.6 - - + -
315O TRP* 5.1 1.6 - - + -
179P THR* 4.0 20.6 - - + -
180P THR 2.7 11.4 + - - +
181P THR* 3.3 9.8 - - - +
182P HIS 2.9 23.7 + - - -
208P ILE* 4.4 14.4 - - + -
209P VAL 3.5 2.7 - - - -
210P PRO* 3.9 26.7 - - + -
233P ILE* 4.8 11.2 - - + -
234P ALA* 1.3 81.9 - - - +
236P ARG* 1.3 64.8 + - - +
237P VAL* 3.6 4.9 + - + +
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Residues in contact with ARG 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P HIS* 3.2 32.0 + - - +
183P SER 3.3 18.8 - - - -
184P TYR* 5.1 0.9 - - - -
185P THR* 3.2 29.1 + - - +
188P GLN* 2.8 63.3 + - + +
200P ARG* 3.6 19.4 - - - +
204P ALA 5.8 0.4 - - - -
207P ASN 3.6 1.8 - - - +
208P ILE* 3.3 2.8 - - - -
209P VAL* 2.7 40.3 + - + +
211P THR* 3.9 20.5 - - + +
234P ALA* 5.2 2.0 - - - +
235P LEU* 1.3 73.3 - - - +
237P VAL* 1.3 63.7 + - - +
4339P SO4 5.4 5.1 + - - -
4340P SO4 2.7 28.3 + - - -
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Residues in contact with VAL 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181O THR* 4.4 3.4 - - + -
208O ILE* 3.7 33.4 - - + -
237O VAL* 4.3 14.1 - - + -
181P THR* 3.8 18.2 - - + -
182P HIS 2.7 20.1 + - - +
183P SER* 3.9 0.2 - - - -
184P TYR* 3.6 14.0 + - - +
204P ALA 4.4 1.3 - - - -
207P ASN 4.1 1.1 - - - -
208P ILE* 4.3 21.3 - - + -
235P LEU* 3.7 11.2 - - + +
236P ARG* 1.3 81.0 - - - +
238P PRO* 1.3 62.0 - - + +
239P THR* 2.7 28.9 + - + +
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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