Contacts of the strand formed by residues 213 - 223 (chain C) in PDB entry 2BG9
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 GLN 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C THR* 2.5 31.0 + - - -
155C ALA* 3.5 6.2 - - - +
158C ILE* 3.2 14.8 + - - +
159C SER* 2.8 24.4 + - - +
160C MET* 2.7 49.1 - - - +
161C ASP* 5.2 1.7 - - - +
199C LYS* 5.3 0.2 - - + -
200C ASN 3.1 11.7 - - - +
201C ILE* 2.7 39.5 - - - +
211C ASN 3.1 21.4 + - - -
212C TYR* 1.4 68.7 - - - +
214C ASP* 1.3 58.1 + - - +
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Residues in contact with ASP 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLN* 2.9 30.6 + - - +
147C LYS* 2.5 43.6 + - + +
148C PHE 3.1 3.6 - - - -
149C THR* 2.9 13.7 - - + -
160C MET* 3.8 4.6 + - - -
199C LYS* 3.0 27.3 - - - +
200C ASN 2.8 18.2 + - - +
201C ILE* 4.2 2.1 - - - -
202C TYR* 4.7 2.1 + - - +
212C TYR* 3.2 17.6 - - - +
213C GLN* 1.3 75.9 - - - +
215C VAL* 1.3 62.2 + - - +
216C THR* 3.5 2.0 + - - -
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.2 48.7 - - + +
37C LEU* 3.4 3.4 - - + -
146C LEU 3.3 3.3 - - - +
147C LYS* 3.1 4.5 - - - -
148C PHE* 2.5 81.0 + - + +
160C MET* 5.6 2.2 - - + -
161C ASP 4.5 6.3 - - - +
162C LEU* 4.0 15.0 - - + -
199C LYS* 5.0 0.2 - - + -
214C ASP* 1.3 70.5 - - - +
216C THR* 1.3 61.1 + - - +
217C PHE* 3.5 15.8 + - + -
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Residues in contact with THR 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LEU 3.3 5.4 - - - +
147C LYS* 2.7 46.8 + - + +
196C PRO 4.1 0.9 - - - +
197C ALA* 3.8 0.7 - - - -
198C LYS* 3.2 40.7 + - + +
199C LYS 4.6 2.1 - - - -
200C ASN* 4.6 1.4 - - - +
214C ASP 4.0 4.0 + - - -
215C VAL* 1.3 68.3 - - - +
217C PHE* 1.3 72.4 + - - +
218C TYR* 3.4 36.0 + - + +
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Residues in contact with PHE 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 2.8 55.6 - - + -
144C CYS 3.5 3.1 - - - +
146C LEU* 2.6 38.8 + - + +
148C PHE* 5.1 2.7 - - + -
162C LEU* 2.6 55.9 - - + -
178C ILE* 5.1 4.5 - - + -
195C LYS* 3.3 30.1 - - - +
196C PRO 3.6 2.9 - - - -
197C ALA* 3.6 15.0 - - + -
215C VAL* 3.5 19.5 - - + -
216C THR* 1.3 99.0 - - - +
218C TYR* 1.3 65.8 + - - +
219C LEU* 5.1 0.3 - - - +
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Residues in contact with TYR 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ASN* 5.0 8.7 - - + -
144C CYS 3.3 3.6 - - - +
145C SER* 3.5 31.4 - - - -
147C LYS* 5.7 0.9 - - - -
195C LYS* 3.2 9.5 - - - +
196C PRO* 2.9 43.3 + - + +
198C LYS* 5.6 12.9 - - - -
216C THR* 3.4 29.4 + - + +
217C PHE* 1.3 75.9 - - - +
219C LEU* 1.3 58.7 + - - +
220C ILE* 3.9 8.3 - - + -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 5.3 0.4 - - + -
42C LEU* 5.1 9.6 - - + -
136C TYR* 5.3 2.4 - - - +
143C ASN* 4.0 0.2 - - - -
144C CYS* 2.3 69.1 + - + +
146C LEU* 5.3 0.7 - - + -
180C ASP* 2.6 52.7 - - + +
190C TRP* 5.5 0.9 - - - +
192C ILE* 3.4 11.9 - - + -
194C HIS 3.5 11.2 - - - +
195C LYS* 4.2 2.5 - - + -
217C PHE 3.8 1.3 + - - +
218C TYR* 1.3 72.3 - - - +
220C ILE* 1.3 58.4 + - - +
221C ILE* 3.1 34.7 + - + -
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Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ASP 5.6 1.8 - - - +
142C GLN 3.4 1.6 - - - +
143C ASN* 2.4 44.4 - - + +
193C ILE* 3.4 19.0 + - + +
194C HIS* 3.1 53.7 + - + +
196C PRO* 4.7 13.5 - - + -
218C TYR* 4.8 3.8 - - + -
219C LEU* 1.3 74.3 - - - +
221C ILE* 1.3 62.0 + - - +
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Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 5.0 1.8 - - + -
136C TYR* 3.2 38.8 - - + +
140C ASP 2.6 29.1 - - - +
141C TRP* 2.7 17.1 - - + +
142C GLN 3.5 4.6 + - - -
190C TRP* 2.8 40.2 - - + +
191C GLU 3.1 11.4 - - - +
192C ILE* 2.9 30.1 - - + -
193C ILE* 4.1 4.9 - - - +
219C LEU* 3.1 30.1 + - + +
220C ILE* 1.3 74.5 - - - +
222C ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C PHE* 2.6 45.4 - - - +
141C TRP* 3.1 15.3 - - + -
190C TRP* 3.1 3.3 - - - +
191C GLU* 2.2 83.8 + - + +
193C ILE* 3.4 13.2 - - + -
221C ILE* 1.3 74.9 - - - +
223C ARG* 1.3 101.6 + - - +
224C LYS* 2.8 33.6 + - - +
226C LEU* 6.1 3.0 - - - +
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Residues in contact with ARG 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 4.2 11.5 + - - +
47C GLU* 3.0 31.0 + - - +
141C TRP* 2.6 56.2 + - + -
189C GLU* 2.4 64.1 + - - +
190C TRP* 2.8 27.8 - - + +
191C GLU* 4.1 1.1 - - - +
222C ARG* 1.3 85.0 + - - +
224C LYS* 1.3 77.3 + - - +
225C PRO* 5.2 6.1 - - - +
285C VAL* 3.9 25.1 - - - +
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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