Contacts of the strand formed by residues 238 - 245 (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 ALA 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.3 0.9 - - + -
205A GLY* 3.3 10.5 - - - +
207A PHE* 3.5 10.5 - - - +
208A ALA* 3.4 42.0 - - + +
234A MET 4.1 0.2 + - - -
236A LYS 3.7 3.2 + - - +
237A ALA* 1.3 80.4 + - - +
239A GLU* 1.3 66.0 + - - +
240A THR 3.3 1.5 + - - +
241A THR* 4.0 9.1 - - + +
267A HIS* 4.0 11.3 - - - -
393B HIS* 5.5 3.5 - - - -
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Residues in contact with GLU 239 (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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205A GLY 3.1 12.4 + - - +
206A ASP* 3.4 13.9 + - - +
238A ALA* 1.3 72.7 - - - +
240A THR* 1.3 64.5 + - - +
267A HIS* 3.4 14.8 + - - -
434B LYS* 6.0 4.9 - - - +
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Residues in contact with THR 240 (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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206A ASP 3.1 7.0 + - - -
207A PHE* 3.2 33.0 - - + -
208A ALA 3.1 20.0 + - - -
238A ALA* 4.3 0.2 - - - -
239A GLU* 1.3 81.6 + - - +
241A THR* 1.3 64.7 + - - +
242A VAL* 3.9 2.3 + - + -
267A HIS* 3.4 8.5 - - + -
268A ARG* 3.5 48.0 + - + +
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Residues in contact with THR 241 (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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208A ALA* 3.7 22.0 - - + -
210A VAL* 5.2 0.7 - - - -
235A CYS* 2.9 40.8 - - - +
236A LYS 5.2 0.2 - - - -
238A ALA* 4.0 17.5 - - + +
240A THR* 1.3 73.4 - - - +
242A VAL* 1.3 62.1 + - - +
243A VAL* 4.1 1.6 - - - -
265A TYR 2.5 23.7 + - - +
266A VAL* 3.8 1.5 - - - -
267A HIS* 2.9 20.2 + - + +
268A ARG* 3.0 26.7 + - - +
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Residues in contact with VAL 242 (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* 3.7 38.4 - - + +
50A VAL* 4.5 1.3 - - + -
73A LEU* 3.5 33.3 - - + +
207A PHE* 4.4 9.4 - - + -
208A ALA 2.9 14.7 + - - +
209A LEU* 4.4 8.7 - - + -
210A VAL* 2.9 26.2 + - - +
240A THR* 4.4 10.3 - - + +
241A THR* 1.3 77.0 - - - +
243A VAL* 1.3 65.4 + - - +
268A ARG* 3.3 20.9 - - + +
270A ILE* 5.0 2.5 - - + -
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Residues in contact with VAL 243 (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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73A LEU* 4.4 2.0 - - - -
210A VAL* 3.2 28.3 - - + +
212A ALA* 3.8 18.2 - - + -
221A VAL* 4.3 6.1 - - + -
235A CYS* 4.0 15.3 - - - -
241A THR 5.0 1.3 - - - -
242A VAL* 1.3 76.9 - - - +
244A GLU* 1.3 62.6 + - - +
245A VAL* 3.8 23.6 - - + -
266A VAL* 3.7 23.8 - - + -
268A ARG 2.9 7.4 + - - +
269A LEU* 3.4 16.4 - - + +
270A ILE* 2.9 27.3 + - - +
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Residues in contact with GLU 244 (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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70A PRO* 3.0 22.3 - - + +
71A GLU 3.7 0.7 + - - -
72A ASN* 2.9 26.4 + - - -
73A LEU* 2.9 36.2 + - + +
210A VAL 2.7 17.2 + - - +
211A LYS* 3.6 9.3 - - + +
212A ALA 2.8 32.6 + - - +
243A VAL* 1.3 74.2 - - - +
245A VAL* 1.3 56.5 + - - +
270A ILE* 3.3 23.8 - - + +
272A GLY 4.6 0.2 - - - +
275A TYR* 2.8 28.7 + - - +
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Residues in contact with VAL 245 (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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212A ALA* 3.5 14.6 - - + -
213A TRP 3.8 7.6 - - - +
214A LYS 3.9 8.3 - - - +
215A ALA* 3.8 23.8 - - + +
221A VAL* 4.6 0.9 - - + -
243A VAL* 3.8 17.7 - - + -
244A GLU* 1.3 78.6 - - - +
246A GLU* 1.3 59.8 + - - +
247A GLU 3.6 19.1 - - - +
248A ILE* 3.9 20.6 - - + -
269A LEU* 4.0 4.9 - - + -
270A ILE 3.0 17.6 + - - +
271A LYS* 3.4 4.9 - - - -
272A GLY 3.0 24.1 + - - -
275A TYR* 3.1 7.1 + - - -
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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