Contacts of the strand formed by residues 226 - 230 (chain A) in PDB entry 3RLG
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 LYS 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO* 4.6 7.5 + - - +
8A TRP* 3.7 32.2 - - + -
192A ILE 3.2 2.8 + - - -
193A TRP* 3.3 29.9 - - + +
194A GLN 2.8 30.0 + - - -
217A ARG* 4.2 0.7 - - - +
224A ILE* 3.2 5.2 - - - +
225A ASN* 1.3 85.1 - - + +
227A VAL* 1.3 59.1 + - - +
247A ASP* 3.2 33.0 + - + +
278A ASN 4.0 2.4 + - - -
279A PRO* 3.3 29.2 - - - +
281A VAL* 2.9 25.9 + - - +
282A THR* 5.1 0.2 - - - -
283A PHE* 4.0 16.0 - - - +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TRP* 5.4 0.2 - - - -
194A GLN 3.4 10.5 - - - +
196A ASP* 5.5 2.0 - - + -
210A VAL* 4.7 9.4 - - + +
213A ALA* 3.9 37.2 - - + +
214A VAL* 4.0 10.5 - - + +
217A ARG* 4.1 19.1 - - - +
224A ILE* 3.8 16.2 - - + -
226A LYS* 1.3 77.7 - - - +
228A TYR* 1.3 67.9 + - - +
246A VAL* 3.7 18.4 - - + +
247A ASP* 2.8 31.7 + - - +
248A GLY 3.1 4.5 + - - -
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Residues in contact with TYR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 3.8 17.9 - - + -
89A VAL* 3.7 24.2 - - + +
130A VAL* 5.5 0.4 - - + -
132A SER* 4.0 1.7 + - - -
164A ASP* 2.7 28.1 + - + +
166A SER* 5.5 0.3 - - - -
193A TRP* 3.4 34.5 - + + -
194A GLN 3.0 12.1 + - - +
195A SER* 3.2 37.7 - - - -
196A ASP* 2.9 26.3 + - - +
227A VAL* 1.3 79.6 - - - +
229A TYR* 1.3 61.5 + - - +
230A TRP* 4.7 3.4 - + - -
246A VAL* 4.8 0.7 - - - -
248A GLY* 3.1 24.0 - - - +
250A MET* 3.5 34.7 - - + +
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Residues in contact with TYR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ASP* 3.2 32.8 - - - -
197A GLY* 4.5 2.0 - - - -
204A ARG* 3.6 26.4 + - + +
205A GLY 3.2 18.9 + - - -
207A LEU* 3.7 22.2 - - + +
210A VAL* 3.4 20.2 - - + -
228A TYR* 1.3 75.7 - - - +
230A TRP* 1.3 64.6 + - - +
232A VAL* 3.6 26.4 - - + +
237A THR* 4.3 14.1 - - + +
241A ALA* 3.7 19.7 - - + -
246A VAL* 4.3 13.5 - - + -
248A GLY 3.0 9.6 + - - +
249A ILE* 3.5 6.0 - - + +
250A MET* 2.9 24.2 + - - +
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Residues in contact with TRP 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ASP* 5.3 0.9 - - - -
166A SER* 4.6 17.4 + - - -
173A ASN* 4.8 3.9 + - - -
195A SER* 3.9 19.1 + - - -
196A ASP* 3.0 28.7 + - - +
197A GLY* 3.0 49.8 - - - +
198A ILE* 3.0 34.6 + - + +
199A THR* 3.4 7.6 - - - -
228A TYR* 4.5 7.0 - + + -
229A TYR* 1.3 80.0 - - - +
231A THR* 1.3 81.0 + - - +
232A VAL* 4.6 3.4 - - - -
250A MET* 3.5 29.6 - - + -
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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