Contacts of the strand formed by residues 208 - 215 (chain C) in PDB entry 2BDI
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 TYR 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C ILE* 4.3 0.9 - - - -
122C SER* 3.7 21.5 - - - -
123C ILE 4.2 3.8 - - - -
124C ALA* 3.7 36.3 - - + -
125C SER 5.4 2.0 - - - -
200C ILE* 2.9 10.0 - - - +
201C CYS 2.7 32.3 + - - +
202C ASN* 2.9 30.1 + - + -
203C GLY* 1.3 82.7 - - - +
209C LEU* 1.4 59.0 + - - +
210C GLN* 3.2 2.4 + - - +
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Residues in contact with LEU 209 (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 VAL* 3.6 31.0 - - + -
47C VAL* 3.7 20.0 - - + -
53C LEU* 4.1 4.7 - - + -
121C ILE* 4.2 9.7 - - + +
122C SER 2.9 18.8 + - - +
123C ILE* 3.5 16.1 - - + +
124C ALA* 2.8 23.8 + - - +
198C PRO* 3.9 24.2 - - + -
199C LEU 4.1 0.2 - - - +
200C ILE* 3.9 10.3 - - + -
208C TYR* 1.4 68.1 - - - +
210C GLN* 1.3 57.5 + - - +
211C GLY 3.7 20.4 - - - +
212C LEU* 5.3 0.4 - - + -
231C LEU* 3.6 16.7 - - + +
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Residues in contact with GLN 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ALA* 3.7 15.4 - - - +
127C GLN 2.9 25.7 + - - +
128C CYS 3.7 0.6 + - - -
129C PRO* 3.4 39.7 - - + +
136C CYS* 5.6 0.2 - - - -
162C VAL* 6.0 0.2 - - + -
181C PHE* 3.9 13.1 - - + -
199C LEU* 2.7 19.1 + - + +
201C CYS* 3.5 39.4 + - + +
208C TYR* 3.2 2.4 + - - +
209C LEU* 1.3 72.6 - - - +
211C GLY* 1.4 56.6 - - - +
229C THR 3.8 0.9 - - - +
230C ASN* 4.7 0.9 - - - +
231C LEU* 3.4 24.9 + - - +
232C CYS* 4.3 4.5 + - - +
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Residues in contact with GLY 211 (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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181C PHE* 4.1 7.4 - - - -
197C GLY 3.5 2.4 - - - +
198C PRO* 3.6 2.9 - - - +
199C LEU* 2.9 40.2 + - - +
209C LEU* 3.7 6.1 - - - +
210C GLN* 1.4 80.2 - - - +
212C LEU* 1.3 65.0 + - - +
229C THR 3.3 12.6 - - - -
231C LEU* 3.5 6.8 - - - +
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Residues in contact with LEU 212 (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 VAL* 4.2 14.1 - - + -
53C LEU* 4.0 11.2 - - + +
54C SER* 3.5 31.4 - - - +
55C ALA* 5.2 1.1 - - + +
102C ASP 4.5 1.1 - - - +
103C LEU* 4.2 9.4 - - + -
196C GLY* 3.0 34.3 - - - +
197C GLY 3.0 8.5 - - - +
209C LEU* 5.3 0.4 - - + -
211C GLY* 1.3 79.7 - - - +
213C VAL* 1.3 65.6 + - - +
214C SER 3.0 1.6 + - - -
228C TYR* 3.0 8.5 - - - +
229C THR* 2.9 40.0 + - - +
231C LEU* 3.8 29.4 - - + -
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Residues in contact with VAL 213 (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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55C ALA* 4.2 4.0 - - - +
138C VAL* 4.3 15.9 - - + -
139C SER 5.3 0.2 - - - +
190C SER* 4.1 9.4 - - - +
194C ASP* 3.0 44.4 - - + +
195C SER* 3.2 7.8 - - - +
196C GLY* 2.5 28.7 + - - +
197C GLY* 2.8 18.7 + - - +
198C PRO 4.8 0.2 - - - +
212C LEU* 1.3 70.1 - - - +
214C SER* 1.3 56.5 + - - +
227C VAL 4.5 0.9 - - - +
228C TYR* 3.6 23.8 - - + -
703C PBZ 4.0 20.2 - - + -
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Residues in contact with SER 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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186B GLN* 3.1 7.8 - - - -
55C ALA* 5.3 0.2 - - - -
57C HIS* 3.0 23.3 + - - -
99C LEU 4.5 1.2 + - - -
102C ASP* 2.8 32.9 + - - +
180C MET* 6.2 0.4 - - - -
195C SER* 3.9 4.3 + - - -
212C LEU 3.0 4.6 + - - -
213C VAL* 1.3 74.6 - - - +
215C PHE* 1.3 79.1 + - - +
227C VAL* 3.2 17.1 + - - -
228C TYR 4.3 0.9 - - - -
229C THR* 4.0 17.3 - - - -
703C PBZ 4.4 1.2 + - - -
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Residues in contact with PHE 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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186B GLN* 2.8 33.0 - + + +
222B VAL* 4.2 7.6 - - + -
99C LEU* 3.9 37.9 - - + -
172C TYR* 3.9 18.6 - + + -
175C LEU* 5.2 8.1 - - + -
180C MET* 3.6 30.5 - - + -
214C SER* 1.3 89.3 - - - +
216C GLY* 1.3 61.1 + - - +
226C GLY* 3.8 1.2 - - - -
227C VAL* 2.7 64.7 + - + +
703C PBZ 3.9 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