Contacts of the strand formed by residues 210 - 215 (chain D) in PDB entry 1J0B
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 210 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D ASP* 3.4 19.3 + - - +
184D SER* 3.2 6.0 - - - -
185D ILE* 2.8 28.4 + - - -
202D LEU* 4.1 2.6 - - - +
208D ASP 4.3 5.6 - - - +
209D ILE* 1.3 80.1 - - - +
211D PRO* 1.3 68.2 - - + +
212D VAL* 3.5 1.6 + - + -
247D GLU* 2.8 45.1 + - - +
249D TYR* 4.7 1.6 + - - -
298D GLU 2.9 28.1 + - - -
299D LEU* 3.0 33.9 + - - +
300D GLY 4.2 0.6 - - - +
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Residues in contact with PRO 211 (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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185D ILE 3.7 4.3 - - - +
195D LEU* 4.1 7.6 - - + -
198D LEU* 4.4 5.8 - - + -
199D SER* 3.9 31.6 - - - +
202D LEU* 4.0 21.8 - - + -
209D ILE 4.2 3.1 - - - +
210D ARG* 1.3 85.1 - - + +
212D VAL* 1.3 62.2 + - - +
213D GLY 4.1 0.2 - - - -
246D PRO* 3.5 25.0 - - + +
247D GLU* 3.3 23.3 + - + +
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Residues in contact with VAL 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D SER* 4.3 13.5 - - - -
185D ILE 2.7 12.3 + - - +
186D VAL* 3.1 30.2 - - + +
187D VAL* 2.9 28.5 + - - +
195D LEU* 4.6 2.9 - - - +
198D LEU* 4.9 0.6 - - - +
210D ARG* 4.4 2.2 - - + +
211D PRO* 1.3 76.2 - - - +
213D GLY* 1.3 62.3 + - - +
214D ILE* 4.2 11.2 - - + -
247D GLU* 3.5 27.6 - - + +
249D TYR* 4.1 16.6 - - + -
299D LEU* 3.6 26.5 - - + -
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Residues in contact with GLY 213 (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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187D VAL* 3.2 8.7 - - - -
189D ALA* 4.6 1.8 - - - -
195D LEU* 4.0 18.9 - - - +
211D PRO 4.0 0.2 + - - -
212D VAL* 1.3 74.8 - - - +
214D ILE* 1.3 64.7 + - - +
215D ALA 3.7 0.9 - - - -
247D GLU 3.0 13.2 + - - -
248D LEU* 3.0 32.4 - - - +
249D TYR* 3.0 6.6 + - - -
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Residues in contact with ILE 214 (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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186D VAL* 3.7 17.9 - - + -
187D VAL 3.1 5.9 + - - -
188D ALA* 3.7 1.0 - - - -
189D ALA 3.1 16.9 + - - +
212D VAL* 4.2 14.6 - - + -
213D GLY* 1.3 75.6 - - - +
215D ALA* 1.3 64.3 + - - +
216D VAL* 3.5 7.8 + - + +
249D TYR* 3.6 12.3 - - + -
251D TYR* 3.3 56.1 - - + -
285D LYS 3.8 1.3 - - - +
286D ALA* 3.5 41.7 - - + +
289D GLY 4.1 8.3 - - - +
290D LEU* 5.3 0.2 - - - -
293D LEU* 4.5 1.6 - - + -
299D LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 215 (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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189D ALA* 3.8 10.8 - - - -
213D GLY 3.7 3.4 + - - -
214D ILE* 1.3 74.1 - - - +
216D VAL* 1.3 59.5 + - - +
217D GLY 3.6 4.9 - - - +
218D ARG 5.2 1.1 - - - +
219D PHE* 4.0 20.2 - - + -
223D MET* 4.0 16.2 - - + -
248D LEU* 3.8 15.9 - - + +
249D TYR 2.8 16.1 + - - +
250D ASP* 4.3 2.9 - - - +
251D TYR 3.2 24.3 + - - -
252D SER* 3.6 3.0 + - - -
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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