Contacts of the helix formed by residues 208 - 214 (chain A) in PDB entry 3LRB
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 GLU 208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 4.0 31.7 + - + +
73A SER* 4.7 2.8 + - - -
93A TYR* 2.6 49.6 + - - +
205A ILE* 4.3 3.3 - - - +
206A GLY* 2.5 13.2 + - - +
207A VAL* 1.3 79.2 - - - +
209A SER* 1.3 57.2 + - - +
210A ALA 3.1 0.2 - - - -
211A SER* 2.6 32.6 + - - -
212A VAL* 3.0 17.2 + - + +
293A TRP* 3.6 16.3 - - - -
296A LEU* 5.3 0.7 - - + -
361A THR* 4.5 3.6 - - - +
364A PRO* 4.9 1.0 - - - +
365A TYR* 3.3 29.2 + - + +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 6.0 0.2 - - - -
18A MET* 4.9 6.1 - - - +
19A VAL* 3.5 27.3 - - - +
22A ASN* 3.8 13.4 + - - -
23A ILE* 4.1 2.4 - - - +
206A GLY* 2.6 21.9 + - - -
207A VAL 3.3 0.2 - - - -
208A GLU* 1.3 72.2 - - - +
210A ALA* 1.3 56.9 + - - +
212A VAL* 3.0 4.5 + - - +
213A ALA* 2.9 28.9 + - - +
293A TRP* 6.6 0.2 - - - -
296A LEU* 3.1 37.6 - - - +
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.6 7.9 - - + -
19A VAL* 3.4 25.7 - - + +
207A VAL 4.3 0.8 + - - -
208A GLU 2.7 5.7 + - - -
209A SER* 1.3 73.3 + - - +
211A SER* 1.3 58.7 + - - +
212A VAL 3.0 5.6 + - - -
213A ALA* 3.6 8.7 + - - +
214A ALA 3.8 2.8 + - - -
224A VAL* 3.4 35.4 - - + +
227A ALA* 3.7 5.8 - - + -
228A THR* 3.3 27.4 - - + -
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.2 33.2 + - - -
64A SER* 3.8 12.3 - - - -
68A PRO* 6.3 0.4 - - - -
69A SER* 3.5 9.6 + - - -
71A GLY 3.5 0.5 - - - -
72A GLY* 2.5 27.4 + - - -
76A TYR* 2.3 43.3 + - - -
208A GLU 2.6 8.2 + - - -
210A ALA* 1.3 75.1 - - - +
212A VAL* 1.3 51.6 + - - +
213A ALA 3.6 0.2 - - - -
214A ALA* 4.7 1.3 - - - -
224A VAL* 4.1 8.4 - - - +
228A THR* 4.4 2.3 - - - +
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Residues in contact with VAL 212 (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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71A GLY* 2.3 42.5 + - - +
72A GLY 3.0 4.0 - - - +
73A SER* 4.9 5.4 - - - -
93A TYR* 3.8 15.5 - - + +
208A GLU* 3.0 36.0 + - + +
209A SER* 3.0 13.6 + - - +
211A SER* 1.3 77.7 - - - +
213A ALA* 1.3 64.3 + - - +
296A LEU* 3.6 32.3 - - + +
299A GLN* 3.8 9.6 - - - +
300A THR* 3.0 14.6 - - - +
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Residues in contact with ALA 213 (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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15A VAL* 5.1 3.6 - - + -
18A MET* 5.9 3.1 - - - -
70A PRO* 5.0 1.2 - - - +
71A GLY 4.8 1.4 + - - -
209A SER 2.9 12.9 + - - +
210A ALA* 4.0 5.6 - - - +
212A VAL* 1.3 78.9 - - - +
214A ALA* 1.3 60.2 + - - +
215A GLY* 2.7 17.5 + - - -
216A VAL* 3.7 13.3 + - + +
217A VAL* 3.5 24.5 - - + -
295A LEU* 5.6 6.3 - - + -
296A LEU* 4.9 6.7 - - + +
299A GLN* 4.2 19.0 + - - +
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Residues in contact with ALA 214 (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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68A PRO* 3.8 7.6 - - + +
69A SER* 2.9 41.3 - - - +
70A PRO* 3.8 9.2 - - + -
71A GLY 4.3 0.7 - - - +
210A ALA 3.8 8.0 + - - -
211A SER 4.7 1.3 - - - +
212A VAL 3.8 0.2 - - - -
213A ALA* 1.3 75.8 - - - +
215A GLY* 1.3 69.2 + - - +
216A VAL 2.9 1.6 + - - -
217A VAL* 2.9 23.0 + - - +
220A PRO* 4.0 12.2 - - - +
224A VAL* 4.6 12.8 - - - -
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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