Contacts of the helix formed by residues 342 - 347 (chain A) in PDB entry 1TE6
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 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLU* 5.0 0.2 + - - -
317A ASP* 2.9 29.3 + - - +
322A THR* 2.9 24.6 + - - +
340A LEU* 3.3 21.9 - - + +
341A LEU* 1.3 75.8 - - - +
343A VAL* 1.3 66.3 + - - +
344A ASN 3.2 0.7 - - - -
345A GLN* 3.0 42.3 + - + +
346A ILE 3.8 0.2 + - - -
369A SER* 3.6 22.4 - - - +
370A HIS 3.8 4.5 - - - +
371A ARG* 3.4 35.5 - - - +
393A LYS* 5.2 1.5 - - - +
640A MG 3.9 2.4 - - - -
641A MG 3.9 0.2 - - - -
642A PO4 3.3 25.7 + - - -
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Residues in contact with VAL 343 (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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35A PRO* 4.9 11.0 - - + -
111A LEU* 3.7 28.7 - - + +
115A LEU* 5.0 8.3 - - + -
341A LEU* 4.0 2.7 + - + -
342A LYS* 1.3 71.6 - - - +
344A ASN* 1.3 61.7 + - + +
346A ILE* 3.6 4.0 + - - +
347A GLY* 2.9 25.6 + - - -
348A SER 3.9 4.2 + - - +
349A VAL* 5.1 3.6 - - - -
352A ALA* 3.9 24.6 - - + +
369A SER 5.2 2.2 + - - +
379A PHE* 4.8 10.3 - - + -
380A ILE* 4.8 15.7 - - + -
383A LEU* 3.8 28.7 - - + -
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Residues in contact with ASN 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.4 6.6 - - + +
35A PRO* 3.5 27.6 + - + +
36A SER* 4.4 4.8 - - - +
37A GLY 4.7 0.6 - - - +
44A GLU* 4.9 2.6 + - - +
45A ALA* 4.5 6.1 - - - +
47A GLU* 4.4 11.1 + - - +
107A ALA* 4.5 14.0 - - + +
108A ASN* 6.2 1.1 - - - +
111A LEU* 3.4 21.5 - - + -
342A LYS* 3.2 2.1 - - - +
343A VAL* 1.3 77.4 - - - +
345A GLN* 1.3 61.3 + - - +
346A ILE 3.3 1.5 + - - -
347A GLY* 4.1 5.1 + - - +
371A ARG* 2.9 48.4 + - - +
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Residues in contact with GLN 345 (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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43A TYR 4.8 0.3 - - - +
44A GLU* 3.1 34.7 + - + +
45A ALA* 2.8 27.9 + - - +
317A ASP* 2.9 33.2 + - - +
318A ASP* 3.9 3.6 + - - -
321A VAL* 3.1 34.7 - - - +
322A THR* 2.9 17.5 + - - +
340A LEU 4.2 2.6 - - - +
342A LYS* 3.0 33.8 + - + +
344A ASN* 1.3 79.4 + - - +
346A ILE* 1.3 60.4 + - - +
371A ARG* 3.5 12.8 - - - +
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Residues in contact with ILE 346 (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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45A ALA* 3.6 8.8 - - + +
102A LYS* 2.9 27.3 + - - +
321A VAL 4.7 0.7 - - - +
322A THR* 3.4 36.6 - - + +
323A ASN* 3.8 31.4 - - + +
324A PRO* 4.2 6.3 - - + -
343A VAL 3.6 8.7 - - - +
345A GLN* 1.3 83.4 - - - +
347A GLY* 1.3 61.4 + - - +
348A SER 3.8 17.9 - - - +
351A GLU* 3.6 29.6 - - + +
352A ALA* 3.9 14.8 - - + +
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Residues in contact with GLY 347 (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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102A LYS* 3.7 12.6 - - - -
107A ALA* 4.2 15.5 - - - -
110A ILE* 3.4 9.2 - - - +
111A LEU* 3.2 32.5 + - - -
343A VAL 2.9 13.3 + - - -
344A ASN* 4.1 3.0 - - - -
345A GLN 3.8 0.4 - - - -
346A ILE* 1.3 78.2 - - - +
348A SER* 1.3 60.5 + - - +
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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