Contacts of the strand formed by residues 208 - 215 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I ILE* 4.3 0.7 - - - -
122I SER* 3.6 24.5 - - - -
123I ILE 4.2 4.5 - - - -
124I ALA* 3.7 34.3 - - + -
125I SER 5.4 1.6 - - - -
200I ILE* 2.9 9.0 - - - +
201I CYS 2.7 36.1 + - - +
202I ASN* 3.0 28.5 - - + -
203I GLY* 1.3 82.9 - - - +
209I LEU* 1.3 60.4 + - - +
210I GLN 3.2 1.8 + - - -
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Residues in contact with LEU 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I VAL* 3.6 29.4 - - + -
47I VAL* 3.8 9.0 - - + -
53I LEU* 4.1 5.4 - - + -
121I ILE* 4.1 8.8 - - + +
122I SER 2.8 19.4 + - - +
123I ILE* 3.5 28.3 - - + +
124I ALA* 2.8 27.0 + - - +
198I PRO* 3.9 13.5 - - + -
199I LEU 4.1 0.2 - - - +
200I ILE* 3.8 21.1 - - + -
208I TYR* 1.3 68.9 - - - +
210I GLN* 1.3 58.3 + - - +
211I GLY 3.7 19.7 - - - +
212I LEU* 5.4 0.7 - - + -
231I LEU* 3.7 17.4 - - + +
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Residues in contact with GLN 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I ALA* 3.6 15.3 - - - +
127I GLN 2.9 26.6 + - - +
128I CYS* 4.0 0.6 - - - -
129I PRO* 3.4 36.5 - - + +
181I PHE* 3.8 10.1 - - + -
199I LEU* 2.7 17.0 + - + +
201I CYS* 3.3 47.1 + - + +
208I TYR 3.2 1.6 + - - -
209I LEU* 1.3 72.6 - - - +
211I GLY* 1.3 57.7 + - - +
229I THR 3.7 1.0 - - - +
230I ASN* 4.4 1.2 - - - +
231I LEU* 3.5 24.1 + - - +
232I CYS* 4.4 4.7 + - - +
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Residues in contact with GLY 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181I PHE* 4.1 7.4 - - - -
197I GLY 3.5 2.1 - - - +
198I PRO* 3.6 3.1 - - - +
199I LEU* 2.9 39.3 + - - +
209I LEU* 3.7 6.6 - - - +
210I GLN* 1.3 81.0 - - - +
212I LEU* 1.3 62.2 + - - +
228I TYR* 4.6 0.2 - - - -
229I THR 3.3 13.0 - - - -
231I LEU* 3.4 9.8 - - - +
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Residues in contact with LEU 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I VAL* 4.2 15.5 - - + -
53I LEU* 4.0 12.3 - - + +
54I SER* 3.5 31.2 - - - +
55I ALA* 4.4 1.1 - - + +
102I ASP 5.1 0.9 - - - +
103I LEU* 4.1 9.9 - - + -
196I GLY* 3.0 33.9 - - - +
197I GLY 2.9 7.0 - - - +
211I GLY* 1.3 79.9 - - - +
213I VAL* 1.3 66.6 + - - +
214I SER 2.9 1.2 + - - -
228I TYR* 3.0 8.7 - - - +
229I THR* 2.9 38.2 + - - +
231I LEU* 3.8 28.5 - - + -
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Residues in contact with VAL 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ALA* 4.2 4.3 - - - +
138I VAL* 4.3 11.7 - - + -
190I SER* 4.1 17.5 - - - +
194I ASP* 3.0 46.7 - - + +
195I SER* 3.3 7.0 - - - +
196I GLY* 2.7 26.0 + - - +
197I GLY* 2.8 23.0 + - - +
198I PRO 4.9 0.7 - - - +
212I LEU* 1.3 71.1 - - - +
214I SER* 1.3 57.8 + - - +
227I VAL 5.3 0.9 - - - +
228I TYR* 3.7 23.3 - - + -
709I PBZ 4.4 15.9 - - + +
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Residues in contact with SER 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I ALA* 5.3 0.2 - - - -
57I HIS* 3.1 23.3 - - - -
99I LEU 4.5 1.4 + - - -
102I ASP* 2.8 32.9 + - - +
180I MET* 6.1 0.6 - - - +
195I SER* 4.0 0.3 + - - -
212I LEU 2.9 4.1 + - - -
213I VAL* 1.3 72.1 - - - +
215I PHE* 1.3 82.7 + - - +
227I VAL* 3.2 14.6 + - - -
228I TYR* 4.1 0.7 - - - -
229I THR* 4.0 20.6 - - - -
709I PBZ 3.5 10.3 - - - -
186L GLN* 3.6 1.6 - - - -
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Residues in contact with PHE 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I LEU* 4.0 39.7 - - + -
172I TYR* 3.8 18.4 - + - -
175I LEU* 5.2 8.1 - - + -
180I MET* 3.5 32.1 - - + -
214I SER* 1.3 95.2 - - - +
216I GLY* 1.3 61.8 + - - +
226I GLY* 3.8 1.0 - - - -
227I VAL* 2.7 63.4 + - + +
709I PBZ 3.4 19.6 - - + -
186L GLN* 3.5 21.5 - + + +
222L VAL* 4.7 6.5 - - + -
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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