Contacts of the helix formed by residues 348 - 362 (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 SER 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ASP* 4.0 21.5 - - - +
94A LEU* 4.8 3.7 - - - +
102A LYS* 4.7 0.7 - - - -
110A ILE* 4.6 7.2 - - - -
111A LEU* 4.0 8.5 - - - -
114A SER* 3.9 5.4 - - - -
343A VAL* 3.9 3.1 + - - +
346A ILE* 3.7 4.6 - - - +
347A GLY* 1.3 80.1 - - - +
349A VAL* 1.3 64.0 + - - +
350A THR* 3.7 3.6 + - - -
351A GLU* 2.6 39.5 + - - +
352A ALA* 3.1 20.6 + - - +
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Residues in contact with VAL 349 (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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86A GLN* 3.8 14.1 - - + +
111A LEU* 4.3 2.0 - - + +
114A SER* 3.0 33.0 + - - +
115A LEU* 3.8 29.6 - - + -
118A CYS* 4.3 13.9 - - + -
133A ILE* 4.3 3.1 - - + -
136A LEU* 5.2 1.3 - - + -
343A VAL* 5.1 3.4 - - + -
348A SER* 1.3 71.9 - - - +
350A THR* 1.3 57.9 + - - +
352A ALA* 3.1 4.7 + - - +
353A ILE* 2.7 55.3 + - + +
379A PHE* 4.0 21.1 - - + -
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Residues in contact with THR 350 (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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86A GLN* 3.5 5.4 + - - +
87A GLU* 3.3 41.2 + - + -
90A ASP* 2.7 31.1 + - + -
91A ASN* 4.9 7.9 - - - +
94A LEU* 6.3 0.7 - - + -
348A SER* 4.1 1.1 - - - -
349A VAL* 1.3 80.4 - - - +
351A GLU* 1.3 61.0 + - + +
353A ILE* 3.3 6.9 + - - +
354A GLN* 2.9 54.4 + - + +
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Residues in contact with GLU 351 (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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94A LEU* 3.6 21.6 - - + +
102A LYS* 2.9 32.6 + - - -
322A THR 4.7 0.7 - - - +
324A PRO* 4.8 6.5 - - + +
346A ILE* 3.6 31.3 - - + +
348A SER* 2.6 31.1 + - - +
350A THR* 1.3 74.8 - - + +
352A ALA* 1.3 60.3 + - - +
354A GLN* 3.3 17.9 + - - +
355A ALA* 2.8 30.0 + - - +
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Residues in contact with ALA 352 (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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322A THR* 4.3 11.0 - - + -
341A LEU* 3.4 18.7 - - + +
343A VAL* 3.9 28.7 - - + -
346A ILE* 3.9 12.7 - - + +
348A SER 3.1 14.0 + - - +
349A VAL 3.1 9.3 + - - +
351A GLU* 1.3 72.9 - - - +
353A ILE* 1.3 72.2 + - + +
355A ALA 3.3 0.5 + - - -
356A CYS* 2.9 19.8 + - - +
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Residues in contact with ILE 353 (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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133A ILE* 5.2 5.4 - - + -
136A LEU* 4.5 10.8 - - + +
137A ALA* 4.0 27.1 - - + +
343A VAL* 5.7 0.2 - - + -
349A VAL* 2.7 46.8 + - + +
350A THR* 3.7 7.0 - - - +
352A ALA* 1.3 84.2 - - + +
354A GLN* 1.3 55.8 + - + +
356A CYS* 3.2 7.0 + - - +
357A LYS* 2.9 48.4 + - + +
383A LEU* 3.8 24.7 - - + -
387A LEU* 4.1 15.0 - - + -
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Residues in contact with GLN 354 (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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87A GLU* 4.2 13.7 + - - +
91A ASN* 5.9 0.8 + - - -
324A PRO* 5.1 10.3 - - + +
350A THR* 2.9 38.1 + - + +
351A GLU* 3.5 26.4 - - - +
353A ILE* 1.3 76.4 - - + +
355A ALA* 1.3 62.2 + - - +
357A LYS* 3.4 21.4 + - - +
358A LEU* 2.9 25.2 + - - +
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Residues in contact with ALA 355 (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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322A THR* 3.7 27.6 - - + +
324A PRO* 4.4 8.2 - - + +
327A ILE* 3.6 25.7 - - + +
339A LEU* 3.4 12.6 - - + +
351A GLU 2.8 17.6 + - - +
352A ALA 3.6 4.7 - - - +
354A GLN* 1.3 75.2 - - - +
356A CYS* 1.3 63.2 + - - +
358A LEU* 3.3 6.4 + - - +
359A ALA 3.1 17.3 + - - -
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Residues in contact with CYS 356 (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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339A LEU* 4.3 4.0 - - - -
341A LEU* 3.8 18.3 - - + +
352A ALA 2.9 13.9 + - - +
353A ILE* 3.2 9.4 + - - +
355A ALA* 1.3 76.9 - - - +
357A LYS* 1.3 62.7 + - - +
359A ALA* 3.2 4.5 + - - +
360A GLN* 3.0 52.4 + - - +
366A VAL* 4.0 18.4 - - - -
387A LEU* 3.9 30.3 - - + -
389A THR* 4.2 0.7 - - - -
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Residues in contact with LYS 357 (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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136A LEU 4.4 10.3 + - - -
137A ALA* 3.6 24.8 + - + +
353A ILE* 2.9 39.6 + - + +
354A GLN* 3.8 19.9 - - - +
356A CYS* 1.3 76.3 - - + +
358A LEU* 1.3 57.2 + - - +
360A GLN* 3.7 17.2 - - - +
361A GLU* 2.8 53.0 + - + +
387A LEU* 5.9 0.7 - - + -
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Residues in contact with LEU 358 (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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324A PRO* 3.9 28.0 - - + +
327A ILE* 3.6 33.2 - - + -
328A GLU* 4.2 23.8 - - + +
331A VAL* 6.4 0.2 - - + -
354A GLN 2.9 17.9 + - - +
355A ALA 3.5 4.9 - - - +
357A LYS* 1.3 77.5 - - - +
359A ALA* 1.3 60.2 + - - +
361A GLU* 3.6 11.8 + - - +
362A ASN* 2.7 45.9 + - - +
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Residues in contact with ALA 359 (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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327A ILE* 4.8 3.8 - - + +
339A LEU* 3.9 13.2 - - + -
355A ALA 3.1 9.5 + - - +
356A CYS 3.2 8.0 + - - +
358A LEU* 1.3 81.2 - - - +
360A GLN* 1.3 60.7 + - - +
362A ASN* 3.0 9.8 + - - -
363A GLY 3.3 0.2 + - - -
364A TRP* 2.9 54.1 + - + +
366A VAL* 3.7 18.6 - - + -
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Residues in contact with GLN 360 (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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139A ASN* 5.3 7.5 + - - +
356A CYS* 3.0 37.2 + - - +
357A LYS* 3.7 17.9 - - - +
359A ALA* 1.3 77.1 - - - +
361A GLU* 1.3 57.6 + - + +
363A GLY* 3.0 19.2 + - - -
364A TRP 3.8 10.7 - - - +
366A VAL* 3.9 13.0 - - + +
387A LEU* 3.2 23.0 + - - +
388A CYS 4.3 2.6 - - - +
389A THR* 4.2 11.3 - - - +
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Residues in contact with GLU 361 (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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357A LYS* 2.8 47.1 + - - +
358A LEU* 3.9 12.8 - - - +
360A GLN* 1.3 72.0 - - + +
362A ASN* 1.3 62.8 + - - +
363A GLY 3.4 1.1 + - - -
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Residues in contact with ASN 362 (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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328A GLU* 5.3 1.2 + - - -
331A VAL* 4.3 35.0 - - + +
332A GLU* 5.7 0.3 - - - +
358A LEU* 2.7 43.1 + - - +
359A ALA 3.0 7.0 + - - +
361A GLU* 1.3 84.0 - - - +
363A GLY* 1.3 57.5 + - - +
364A TRP* 3.2 14.6 + - + -
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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