Contacts of the strand formed by residues 216 - 222 (chain I) in PDB entry 5G04
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 216 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209I CYS 3.8 0.7 - - - +
210I LEU* 3.2 7.2 - - - +
211I SER* 3.0 37.9 + - - -
214I LEU 3.3 0.4 - - - -
215I LYS* 1.4 77.5 - - - +
217I LEU* 1.3 61.4 + - - +
218I SER 4.0 0.9 - - - -
235I GLN* 3.7 23.1 + - - -
236I LEU 3.2 14.1 - - - -
238I THR* 3.8 2.9 - - - -
584I HIS* 4.0 6.5 + - - -
605I THR* 2.5 30.4 + - - -
607I ILE* 3.8 5.2 - - - -
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Residues in contact with LEU 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I VAL* 4.4 17.0 - - + -
185I ILE* 4.7 7.4 - - + -
187I LEU* 4.2 33.2 - - + -
198I VAL* 4.9 4.7 - - + -
208I LEU* 4.7 0.4 - - + -
209I CYS 3.1 30.3 - - - +
210I LEU* 4.0 18.4 - - + -
216I SER* 1.3 72.8 - - - +
218I SER* 1.3 64.8 + - - +
219I VAL* 3.7 11.7 - - + +
234I PHE 3.7 2.4 - - - +
235I GLN* 4.5 0.2 - - - -
236I LEU* 2.8 50.1 + - + +
238I THR* 4.1 14.6 - - + +
548I MET* 5.1 0.4 - - - -
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Residues in contact with SER 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I LEU* 3.6 0.5 - - - -
209I CYS* 2.8 38.1 + - - +
216I SER* 4.0 0.8 + - - -
217I LEU* 1.3 71.3 - - - +
219I VAL* 1.3 64.1 + - - +
233I TYR* 3.4 34.1 - - - -
234I PHE 3.3 4.3 - - - -
235I GLN* 3.7 11.0 - - - +
575I LEU* 3.8 6.1 - - - +
584I HIS* 2.4 37.9 + - - +
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Residues in contact with VAL 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I ILE* 3.8 29.2 - - + -
201I ILE* 5.0 2.5 - - + -
205I CYS* 3.8 27.6 - - - -
207I ALA 3.3 9.9 - - - +
208I LEU* 3.8 17.3 - - + -
217I LEU* 3.7 19.3 - - + +
218I SER* 1.3 81.5 - - - +
220I VAL* 1.3 65.9 + - - +
221I THR* 4.1 1.6 - - - +
233I TYR* 3.4 5.4 - - - -
234I PHE* 2.4 55.8 + - + +
236I LEU* 4.6 2.0 - - + -
575I LEU* 4.2 1.8 - - - +
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Residues in contact with VAL 220 (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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205I CYS* 3.0 27.2 - - - +
206I LEU* 3.2 11.0 + - + +
207I ALA* 2.9 35.3 + - + +
219I VAL* 1.3 77.0 - - - +
221I THR* 1.3 63.4 + - - +
222I GLU* 5.2 2.0 - - + +
231I VAL* 4.1 20.0 - - + -
232I SER 3.2 10.3 - - - +
233I TYR* 4.6 2.0 - - + -
556I LEU* 5.0 2.0 - - + -
573I PRO* 5.1 13.5 - - + -
575I LEU* 3.8 10.3 - - + -
586I LEU* 4.2 26.9 - - + -
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Residues in contact with THR 221 (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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201I ILE* 4.6 4.0 - - + -
202I ALA* 2.3 43.8 + - + +
203I GLY 3.9 0.2 - - - -
204I THR 3.4 4.8 + - - -
205I CYS* 3.2 23.4 - - - -
219I VAL* 4.1 2.0 - - - -
220I VAL* 1.3 73.1 - - - +
222I GLU* 1.3 58.4 + - - +
223I VAL* 5.4 0.4 - - + -
232I SER* 2.8 48.8 + - - +
234I PHE* 3.3 40.6 - - + -
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Residues in contact with GLU 222 (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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203I GLY* 3.5 1.2 - - - -
204I THR* 2.6 40.1 + - - +
206I LEU* 4.7 10.7 - - + +
220I VAL* 5.2 2.2 - - + +
221I THR* 1.3 72.7 + - - +
223I VAL* 1.3 60.9 + - - +
224I SER* 5.3 0.7 - - - +
229I SER* 3.8 26.0 + - - -
230I GLU 3.4 20.9 - - - +
231I VAL* 4.5 10.7 - - + +
562I SER* 4.4 6.4 + - - -
568I ARG* 3.3 29.8 + - - -
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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