Contacts of the strand formed by residues 205 - 211 (chain A) in PDB entry 3DLX
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 GLY 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A THR* 3.6 11.4 - - - -
60A LEU* 3.8 21.8 - - - +
204A THR* 1.3 77.8 - - - +
206A ASP* 1.3 63.5 + - - -
207A PHE 3.3 1.3 - - - -
237A ALA 2.8 10.9 + - - -
238A ALA* 3.3 1.9 - - - -
239A GLU* 3.1 23.0 + - - +
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Residues in contact with ASP 206 (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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54A PRO* 5.5 5.1 - - + +
57A ALA* 3.5 12.3 - - + -
58A THR* 2.8 37.9 + - - +
205A GLY* 1.3 73.5 - - - -
207A PHE* 1.3 81.5 + - + +
239A GLU* 3.4 10.5 + - - +
240A THR* 3.1 23.7 + - - -
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Residues in contact with PHE 207 (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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49A ALA 5.0 0.4 - - - -
52A ASP* 3.5 32.1 - - - -
53A ILE* 3.6 54.5 - - + -
54A PRO* 3.9 11.0 - - + -
57A ALA* 4.8 0.7 - - + -
58A THR 3.4 2.3 + - - +
59A VAL* 3.5 13.6 - - + -
60A LEU* 2.9 28.1 + - - +
206A ASP* 1.3 91.3 - - + +
208A ALA* 1.3 60.3 + - - +
209A LEU* 5.0 1.3 - - + -
238A ALA* 3.5 6.3 - - - -
240A THR* 3.2 41.7 - - + -
242A VAL* 4.4 9.9 - - + -
268A ARG* 3.9 4.7 - - - -
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Residues in contact with ALA 208 (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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60A LEU* 3.2 12.1 - - + -
207A PHE* 1.3 72.7 - - - +
209A LEU* 1.3 66.3 + - - +
210A VAL* 3.9 7.4 - - + -
234A MET* 3.1 33.0 - - + +
238A ALA* 3.4 10.5 - - + +
240A THR 3.1 7.1 + - - +
241A THR* 3.8 11.0 - - + -
242A VAL* 2.9 28.8 + - - +
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Residues in contact with LEU 209 (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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50A VAL* 4.1 25.4 - - + -
53A ILE* 4.3 13.0 - - + -
59A VAL* 3.8 17.9 - - + -
60A LEU 2.6 11.5 + - - +
61A VAL* 4.6 11.0 - - + -
62A GLY 3.0 26.3 + - - -
70A PRO* 3.4 17.8 - - + +
73A LEU* 4.1 22.9 - - + +
74A ILE* 4.8 8.7 - - + +
77A LEU* 3.8 32.8 - - + -
102A LEU* 5.8 0.4 - - + -
207A PHE* 5.0 2.0 - - + -
208A ALA* 1.3 78.2 - - - +
210A VAL* 1.3 59.3 - - - +
242A VAL* 3.6 9.4 - - + -
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Residues in contact with VAL 210 (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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62A GLY 5.6 0.4 - - - +
70A PRO* 4.0 3.4 - - - -
73A LEU* 4.0 1.7 - - - +
208A ALA* 4.0 22.4 - - + -
209A LEU* 1.3 76.4 - - - +
211A LYS* 1.3 63.2 + - - +
223A PHE* 4.2 7.2 - - + -
231A ASN* 3.5 36.6 - - + +
234A MET* 4.4 5.4 - - + -
235A CYS* 3.9 26.9 - - - +
241A THR* 5.2 1.1 - - - -
242A VAL 2.9 14.0 + - - +
243A VAL* 3.2 20.0 - - + -
244A GLU* 2.7 34.5 + - - +
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Residues in contact with LYS 211 (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 GLY* 3.6 31.4 - - - +
69A ILE 3.6 22.9 - - - +
70A PRO* 3.7 5.2 - - + +
71A GLU* 5.6 0.2 - - - -
210A VAL* 1.3 71.0 - - - +
212A ALA* 1.3 81.3 + - - +
213A TRP* 5.0 0.2 - - - +
223A PHE* 3.4 11.4 - - - -
227A ALA* 4.5 4.6 - - + +
231A ASN* 3.0 23.5 + - - -
244A GLU* 3.4 14.4 - - + +
246A GLU* 2.6 28.3 + - - -
275A TYR* 2.9 44.4 - - + -
277A LYS* 4.2 10.7 - - - +
362A ASP* 5.2 1.8 + - - -
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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