Contacts of the strand formed by residues 245 - 251 (chain A) in PDB entry 6TAV
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 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU* 2.9 27.7 + - - +
244A GLU* 1.3 89.8 - - + +
246A MET* 1.4 67.0 + - - +
247A ASN* 5.5 0.2 - - - +
303A GLN* 3.1 39.2 - - - +
304A VAL 3.2 20.3 - - - +
305A LYS* 3.8 5.4 + - + +
306A THR 4.0 2.0 - - - +
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Residues in contact with MET 246 (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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235A VAL* 6.4 1.3 - - - -
236A PRO* 4.5 22.7 - - + -
239A ILE* 5.1 17.7 - - + -
245A GLU* 1.4 77.2 - - - +
247A ASN* 1.3 67.5 + - - +
248A VAL* 3.9 19.7 + - + -
268A ILE* 5.1 18.2 - - + -
270A ARG* 5.8 3.8 - - - -
302A GLN 4.1 0.2 - - - +
303A GLN* 3.4 4.9 - - - -
304A VAL* 3.1 42.4 + - + +
306A THR* 3.4 28.7 - - + -
309A PHE* 6.0 2.7 - - + -
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Residues in contact with ASN 247 (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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234A THR 4.6 0.3 - - - +
236A PRO* 3.3 26.0 - - - +
245A GLU* 5.5 0.3 - - - +
246A MET* 1.3 75.8 - - - +
248A VAL* 1.3 59.2 + - - +
302A GLN 3.9 5.2 - - - +
303A GLN* 3.1 36.0 + - + +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A THR 3.5 15.0 - - - +
235A VAL* 3.7 19.7 - - + -
236A PRO* 5.2 0.9 - - + -
246A MET* 4.0 22.2 - - + -
247A ASN* 1.3 75.6 - - - +
249A SER* 1.3 73.1 + - - +
266A VAL* 5.8 8.5 - - + -
300A PHE 4.7 0.2 - - - +
302A GLN* 2.9 47.0 + - + +
304A VAL* 4.1 11.7 - - + -
320A LEU* 4.5 9.4 - - + -
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Residues in contact with SER 249 (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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233A VAL* 3.8 0.2 - - - -
234A THR* 2.8 51.6 + - - -
247A ASN* 6.0 0.3 - - - +
248A VAL* 1.3 82.8 + - - +
250A VAL* 1.3 60.9 + - - +
251A CYS* 5.2 5.6 - - - -
300A PHE 3.8 8.7 - - - -
301A TYR* 3.1 38.5 - - - +
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Residues in contact with VAL 250 (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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231A VAL* 3.9 27.1 - - + -
232A GLN 3.3 11.9 - - - +
233A VAL* 4.4 3.6 - - + -
248A VAL* 6.3 0.2 - - + -
249A SER* 1.3 76.7 - - - +
251A CYS* 1.4 65.0 + - - +
264A VAL* 4.0 30.3 - - + -
266A VAL* 4.8 15.9 - - + -
294A LEU* 3.5 7.1 - - + +
299A CYS* 3.3 13.0 - - - +
300A PHE* 3.4 20.9 + - + +
322A THR* 4.0 17.9 - - + -
324A ALA* 6.0 1.3 - - + -
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Residues in contact with CYS 251 (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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231A VAL* 3.6 8.0 - - - +
232A GLN* 2.9 43.2 + - + +
234A THR* 5.4 3.6 - - - -
249A SER* 5.2 4.5 - - - -
250A VAL* 1.4 80.1 - - - +
252A GLY* 1.3 61.3 + - - +
253A LEU* 5.5 4.0 - - + -
294A LEU* 4.3 7.0 - - - -
298A GLY 4.9 1.1 - - - +
299A CYS* 2.0 48.2 - - - -
301A TYR* 5.5 0.7 - - - -
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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