Contacts of the strand formed by residues 203 - 211 (chain O) in PDB entry 3Q2K
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 VAL 203 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196O LEU* 4.6 7.2 - - + +
197O ASP* 4.4 6.1 + - + +
201O GLY 3.4 2.8 + - - +
202O PRO* 1.3 74.6 - - - +
204O GLU* 1.3 63.6 + - - +
205O SER 3.6 23.1 - - - +
206O VAL* 4.1 2.9 - - + -
227O LEU* 4.8 6.5 - - + -
228O ARG 3.7 9.9 - - - +
229O TRP* 3.7 29.2 - - + +
230O ARG* 3.7 14.0 + - - -
331O LEU* 4.1 28.5 - - + -
347O LEU* 3.6 31.6 - - + +
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Residues in contact with GLU 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228M ARG* 5.6 3.6 + - - -
203O VAL* 1.3 74.4 - - - +
205O SER* 1.3 86.3 + - - +
228O ARG* 2.8 51.2 + - - +
229O TRP 3.9 2.6 - - - +
230O ARG* 3.6 43.2 - - + +
344O ARG* 4.6 4.6 + - - -
346O PRO* 3.5 3.9 - - + +
347O LEU* 2.9 28.3 + - - +
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Residues in contact with SER 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203O VAL* 3.6 4.7 - - - +
204O GLU* 1.3 102.2 + - - +
206O VAL* 1.3 67.2 + - - +
228O ARG* 3.2 24.9 + - - +
344O ARG* 3.3 18.9 - - - -
345O ILE 3.3 14.8 - - - -
346O PRO* 3.5 10.8 - - - -
347O LEU* 4.5 2.0 - - - +
209P TYR* 2.9 18.1 + - - -
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Residues in contact with VAL 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203O VAL* 4.1 2.7 - - + -
205O SER* 1.3 76.8 - - - +
207O TYR* 1.3 64.6 + - - +
225O ALA* 4.8 0.7 - - + -
226O ALA 3.3 9.2 - - - +
227O LEU* 3.2 30.3 - - + -
331O LEU* 3.6 21.5 - - + -
334O ALA* 3.7 41.1 - - + +
335O ILE* 3.9 12.6 - - + +
338O SER* 3.9 1.5 + - - -
344O ARG* 3.4 4.2 - - - +
345O ILE* 2.7 37.2 + - + +
347O LEU* 5.2 0.4 - - + -
209P TYR* 3.5 6.5 - - - -
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Residues in contact with TYR 207 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206O VAL* 1.3 74.2 - - - +
208O ALA* 1.3 80.6 + - - +
209O TYR* 4.0 21.7 - + - -
225O ALA* 3.3 1.9 - - - -
226O ALA* 2.7 36.9 + - + +
338O SER* 3.1 4.3 - - - -
342O GLY* 3.4 19.6 - - - -
343O VAL* 3.5 22.9 - - - -
344O ARG 3.4 15.7 - - - -
207P TYR* 3.1 62.4 - + + -
209P TYR* 3.8 1.2 + - - +
226P ALA* 4.8 3.2 - - + +
344P ARG* 3.0 37.8 + - + -
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Residues in contact with ALA 208 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207O TYR* 1.3 93.5 - - - +
209O TYR* 1.3 64.0 + - - +
210O THR* 4.6 0.9 - - + -
224O VAL 3.1 13.0 - - - +
225O ALA* 3.7 13.9 - - + -
335O ILE* 3.6 36.6 - - + +
338O SER* 2.8 9.5 + - - +
339O ALA* 3.3 20.3 + - + +
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Residues in contact with TYR 209 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207O TYR* 4.0 17.3 - + - -
208O ALA* 1.3 73.9 - - - +
210O THR* 1.3 67.8 + - - +
223O GLY* 3.1 1.9 - - - -
224O VAL* 2.8 34.2 + - + +
339O ALA* 4.6 2.7 - - - +
205P SER* 2.7 37.6 + - - -
206P VAL* 3.4 8.7 - - - -
207P TYR 3.7 1.1 + - - -
226P ALA* 3.8 33.4 - - + -
227P LEU 3.8 17.5 - - - -
228P ARG* 3.3 51.4 - - + +
234P MET* 3.7 19.1 - - + -
344P ARG* 3.3 17.0 - - - -
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Residues in contact with THR 210 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O TRP* 5.7 2.8 - - - -
185O PHE* 4.1 23.1 - - + -
208O ALA* 4.6 7.0 - - + -
209O TYR* 1.3 82.1 - - - +
211O ALA* 1.3 67.5 + - - +
220O GLU* 3.7 22.6 + - + +
222O THR 3.3 12.1 - - - -
335O ILE* 4.7 5.2 - - + -
336O TYR* 5.0 3.2 - - + -
339O ALA* 3.3 31.3 + - + +
228P ARG* 4.7 9.4 + - - +
234P MET* 3.7 4.5 - - - +
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Residues in contact with ALA 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230I ARG* 5.5 4.7 - - - +
210O THR* 1.3 80.0 - - - +
212O THR* 1.3 61.8 + - - +
213O LEU* 3.6 16.8 - - + -
220O GLU* 3.9 6.2 - - - +
221O ASP* 3.2 14.2 + - - +
222O THR* 3.0 21.4 + - - +
228P ARG* 6.2 2.2 - - - +
232P GLY 5.2 0.7 - - - +
234P MET* 3.5 19.3 - - + +
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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