Contacts of the strand formed by residues 208 - 213 (chain R) in PDB entry 5A31
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 SER 208 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204R ALA* 3.5 0.9 - - - -
205R LEU 2.9 31.7 + - - -
206R GLY 3.4 0.8 + - - -
207R LYS* 1.3 82.2 + - - +
209R ILE* 1.3 69.2 + - - +
210R PHE* 3.7 26.4 - - - -
221R HIS* 4.2 4.5 + - - -
223R CYS 3.7 4.7 - - - -
224R ASP* 2.6 22.2 + - - -
229R TYR* 3.9 2.9 - - - -
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Residues in contact with ILE 209 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203R VAL 3.5 9.0 - - - +
204R ALA* 4.1 15.0 - - + -
208R SER* 1.3 82.4 - - - +
210R PHE* 1.3 72.3 + - - +
211R LEU* 4.4 1.1 - - + -
221R HIS* 3.8 2.6 + - - -
222R LEU* 2.8 48.6 + - + +
223R CYS* 3.3 24.8 + - - -
229R TYR* 3.7 17.5 - - + -
231R SER 5.7 0.2 - - - +
232R LEU* 4.7 6.3 - - + -
241R LEU* 4.0 16.8 - - + -
243R VAL* 3.4 44.2 - - + -
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Residues in contact with PHE 210 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201R LEU 3.7 0.5 - - - +
202R ALA* 3.5 2.3 - - - -
203R VAL* 2.9 38.5 + - + +
205R LEU* 3.6 29.4 - - + -
208R SER* 3.7 23.8 - - - -
209R ILE* 1.3 77.2 - - - +
211R LEU* 1.3 64.0 + - - +
219R VAL* 4.2 11.7 - - + -
220R VAL 3.3 5.6 - - - -
221R HIS* 3.5 43.3 - + + -
324V ALA* 3.3 29.6 - - + -
325V LEU* 3.9 19.3 - - + -
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Residues in contact with LEU 211 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200R VAL* 3.8 11.2 - - + -
201R LEU 3.3 2.2 - - - -
202R ALA* 3.6 25.8 - - + -
209R ILE* 4.4 0.7 - - + -
210R PHE* 1.3 81.1 - - - +
212R THR* 1.3 63.1 + - - +
218R ASP 3.7 0.2 - - - +
219R VAL* 3.3 7.6 - - - +
220R VAL* 2.7 55.2 + - + +
222R LEU* 3.6 32.5 - - + -
234R TRP* 4.0 12.6 - - + -
241R LEU* 4.3 6.7 - - + -
255R VAL* 3.8 32.3 - - + +
325V LEU* 4.7 1.1 - - - -
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Residues in contact with THR 212 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177R ARG* 4.1 22.4 - - - +
179R LEU* 4.6 7.4 - - + +
200R VAL* 3.3 8.7 - - - -
201R LEU* 2.9 43.9 + - - +
211R LEU* 1.3 73.8 + - - +
213R ASP* 1.3 77.2 + - - +
214R ASN* 3.6 1.9 + - - +
217R GLY 4.3 10.5 - - - +
218R ASP 3.2 10.1 - - - +
219R VAL* 4.1 6.5 - - + +
465R TYR* 5.3 0.9 - - - +
325V LEU* 3.1 30.1 - - - +
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Residues in contact with ASP 213 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177R ARG* 5.2 0.2 + - - -
198R THR 5.2 0.6 - - - +
199R ASP 4.1 3.9 - - - +
200R VAL* 4.6 15.7 - - + +
212R THR* 1.3 79.7 - - - +
214R ASN* 1.3 61.2 + - - +
215R ASN* 3.0 37.0 + - - +
216R THR* 3.5 28.4 + - - +
217R GLY* 2.8 24.8 + - - -
218R ASP* 2.9 16.5 + - + +
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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