Contacts of the strand formed by residues 211 - 216 (chain A) in PDB entry 1RI4
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 GLU 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.1 37.5 + - + +
209A VAL* 3.2 22.1 - - - +
210A ARG* 1.3 80.7 - - + +
212A TYR* 1.3 70.2 + - - +
224A ILE* 3.3 35.9 - - + +
225A GLU 3.2 15.3 - - - +
226A TYR* 3.6 18.6 - - + +
227A PHE* 4.0 0.6 - - - -
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Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A HIS* 4.9 0.9 - - - -
175A PRO* 3.5 30.7 - - - +
180A ILE* 3.8 7.9 - - + +
196A ILE* 3.6 27.6 - - + -
197A GLU 2.9 22.2 - - - +
198A LEU* 4.1 11.4 - - + +
199A GLU* 5.4 0.2 - - - -
211A GLU* 1.3 81.9 - - - +
213A ARG* 1.3 67.4 + - - +
214A PHE* 3.8 11.4 - + + -
223A CYS 3.5 1.0 - - - +
224A ILE* 3.5 6.6 - - - +
225A GLU* 2.9 65.6 + - + +
226A TYR 4.6 2.1 + - - -
227A PHE* 3.6 43.7 - + - -
283A ILE* 5.7 0.7 - - - +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 3.3 2.3 - - - +
196A ILE* 3.2 8.0 - - - +
197A GLU* 2.8 53.4 + - + +
198A LEU 5.6 2.5 - - - +
212A TYR* 1.3 74.8 - - - +
214A PHE* 1.3 59.2 + - - +
215A THR* 5.0 0.8 + - - +
222A ASN* 2.6 63.8 + - - +
223A CYS 3.4 1.8 - - - -
224A ILE* 3.0 35.2 - - - +
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Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A TYR* 4.0 13.9 - - + -
195A LYS 3.6 0.7 - - - -
196A ILE* 3.7 20.9 - - + -
212A TYR* 3.8 8.4 + + + -
213A ARG* 1.3 71.7 - - - +
215A THR* 1.3 74.9 + - - +
216A LEU* 4.1 29.2 - - + -
220A VAL* 3.7 25.0 - - + +
222A ASN 3.3 1.0 + - - -
223A CYS* 2.7 42.5 + - - +
225A GLU* 3.6 33.2 - - + -
280A VAL* 5.2 1.3 - - + -
283A ILE* 4.3 19.1 - - + -
284A TYR* 3.5 28.3 - + - -
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Residues in contact with THR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A PHE 4.6 0.2 - - - -
194A TYR* 3.1 12.0 - - - +
195A LYS* 3.1 50.5 + - + +
213A ARG* 5.0 1.2 + - - +
214A PHE* 1.3 75.9 - - - +
216A LEU* 1.3 67.6 + - - +
217A LEU* 5.8 0.4 - - - -
220A VAL* 3.6 11.4 - - - +
221A ASN* 4.3 6.5 - - + +
222A ASN* 2.9 27.5 + - - +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A THR* 5.6 4.7 - - + -
46A ILE* 5.3 10.1 - - + -
50A ASN* 6.2 1.8 - - - +
193A PHE* 3.6 15.5 - - + +
194A TYR* 4.3 3.1 - - + -
214A PHE* 4.1 19.5 - - + -
215A THR* 1.3 78.0 - - - +
217A LEU* 1.3 70.8 + - + +
218A ASP 3.2 0.3 + - - -
219A SER* 2.9 40.3 + - - +
220A VAL* 3.0 23.5 + - + +
221A ASN* 4.9 1.9 - - - +
280A VAL* 3.6 32.3 - - + -
284A TYR* 5.3 3.6 - - + +
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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