Contacts of the strand formed by residues 210 - 214 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183L ASP* 3.0 19.5 + - - +
184L SER* 3.6 11.7 - - - -
185L ILE* 3.1 26.9 + - - +
202L LEU* 3.6 5.8 - - - +
208L ASP 5.4 2.0 - - - +
209L ILE* 1.3 71.6 - - - +
211L PRO* 1.3 65.6 - - + +
212L VAL* 3.7 5.1 + - + -
247L GLU* 2.8 34.3 + - - +
298L GLU 2.7 22.9 + - - -
299L LEU* 2.8 39.4 + - - +
300L GLY* 3.2 6.9 - - - +
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Residues in contact with PRO 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185L ILE 4.3 1.8 - - - +
195L LEU* 4.1 7.6 - - + -
198L LEU* 4.6 6.5 - - + -
199L SER* 3.1 38.8 - - - +
202L LEU* 3.8 20.9 - - + -
209L ILE 3.7 4.0 - - - +
210L ARG* 1.3 85.6 - - + +
212L VAL* 1.3 61.7 + - - +
244L VAL 6.0 0.9 - - - +
245L ARG 5.6 0.9 - - - +
246L PRO* 3.1 15.4 - - + +
247L GLU* 2.9 25.9 + - + +
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Residues in contact with VAL 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L SER* 4.9 3.4 - - - -
185L ILE 3.2 17.3 + - - +
186L VAL* 4.3 15.3 - - + -
187L VAL* 2.9 33.2 + - - +
195L LEU* 3.8 4.6 - - - +
198L LEU* 5.6 0.2 - - - +
210L ARG* 4.5 10.5 - - + +
211L PRO* 1.3 75.1 - - - +
213L GLY* 1.3 64.1 + - - +
214L ILE* 4.2 10.3 - - + -
247L GLU* 3.2 41.5 - - + +
249L TYR* 3.7 20.6 - - + -
299L LEU* 4.4 16.6 - - + -
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Residues in contact with GLY 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L VAL 2.9 10.3 - - - -
189L ALA* 4.1 6.3 - - - -
195L LEU* 4.1 8.1 - - - +
212L VAL* 1.3 74.4 - - - +
214L ILE* 1.3 65.0 + - - +
247L GLU 2.7 11.7 + - - +
248L LEU* 3.1 20.2 - - - +
249L TYR* 2.9 25.5 + - - -
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Residues in contact with ILE 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L VAL* 4.2 14.4 - - + -
187L VAL 3.0 6.7 + - - -
188L ALA* 3.8 3.5 - - - -
189L ALA 3.1 14.8 + - - +
212L VAL* 4.2 6.3 - - + -
213L GLY* 1.3 72.8 - - - -
215L ALA* 1.3 58.1 + - - +
216L VAL* 3.0 13.6 + - - +
249L TYR* 3.7 31.2 - - + -
251L TYR* 3.1 42.6 - - + +
285L LYS* 4.1 1.6 - - + +
286L ALA* 3.4 41.7 - - + +
289L GLY* 4.2 2.2 - - - -
293L LEU* 4.2 16.2 - - + -
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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