Contacts of the helix formed by residues 358 - 366 (chain A) in PDB entry 6T2C
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 THR 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A GLN* 2.9 31.7 + - - +
356A LYS* 2.8 17.3 + - + +
357A LYS* 1.3 79.7 - - - +
359A ASN* 1.3 66.4 + - - +
360A HIS* 3.2 18.9 + - + +
361A LEU* 3.3 14.8 - - - +
362A LYS* 3.3 24.1 + - - +
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Residues in contact with ASN 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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333A ASN* 4.9 0.4 - - - -
358A THR* 1.3 75.0 - - - +
360A HIS* 1.3 62.8 + - - +
362A LYS* 3.1 9.8 + - - +
363A TRP* 3.0 26.7 + - - +
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Residues in contact with HIS 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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333A ASN* 3.5 41.4 + - + +
336A MET* 3.4 47.2 + - + +
337A ILE* 3.4 29.7 - - + +
340A GLN* 2.5 32.1 + - + -
358A THR* 3.2 14.5 + - + -
359A ASN* 1.3 80.0 + - - +
361A LEU* 1.3 74.1 + - - +
363A TRP* 3.8 1.4 - - - +
364A GLY 2.9 23.4 + - - -
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Residues in contact with LEU 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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337A ILE* 4.0 18.8 - - + -
340A GLN* 3.7 22.4 - - - +
355A LEU* 3.8 19.3 - - + -
356A LYS 3.8 4.9 - - - +
358A THR* 3.3 18.5 + - - +
359A ASN 3.2 0.6 - - - -
360A HIS* 1.3 86.2 - - + +
362A LYS* 1.3 56.8 + - - +
364A GLY 3.4 0.3 + - - -
365A LEU* 2.9 44.7 + - + +
475A TYR* 3.6 32.1 - - + -
500A ILE* 4.1 14.6 - - + -
516A ILE* 4.0 10.8 - - + -
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Residues in contact with LYS 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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357A LYS* 3.8 34.4 + - - +
358A THR 3.3 16.9 + - - +
359A ASN* 3.1 8.6 + - - +
361A LEU* 1.3 77.4 - - - +
363A TRP* 1.3 59.1 + - - +
365A LEU* 3.8 0.6 - - - -
366A GLY 2.9 7.1 + - - -
367A GLU* 2.8 72.7 + - + +
475A TYR* 3.5 12.8 - - + +
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Residues in contact with TRP 363 (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 LYS 4.9 0.7 - - - -
329A GLY* 3.8 12.3 - - - -
330A VAL* 3.3 53.4 - - + +
333A ASN* 3.4 39.5 - - + +
334A TYR* 4.0 31.9 - + - -
359A ASN 3.0 11.6 + - - +
360A HIS 3.8 0.7 - - - +
362A LYS* 1.3 78.3 - - - +
364A GLY* 1.3 76.3 + - - +
366A GLY* 3.0 17.5 + - - -
369A GLN* 4.8 16.1 - - - +
562A THR* 5.5 0.2 - - - -
1V A 4.2 36.4 + + - +
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Residues in contact with GLY 364 (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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334A TYR* 5.0 0.9 - - - -
337A ILE* 4.1 4.5 - - - -
360A HIS 2.9 16.2 + - - -
361A LEU 3.4 2.0 + - - -
363A TRP* 1.3 91.7 - - - +
365A LEU* 1.3 57.0 + - - +
516A ILE* 3.4 23.4 - - - +
562A THR* 3.2 33.0 + - - +
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Residues in contact with LEU 365 (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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361A LEU* 2.9 35.0 + - + +
362A LYS* 4.5 2.2 - - - +
364A GLY* 1.3 76.9 - - - +
366A GLY* 1.3 59.1 + - - +
367A GLU* 5.1 1.1 - - + +
475A TYR* 3.6 28.7 - - + +
500A ILE* 3.8 8.5 - - + +
501A LYS 3.3 21.3 - - - +
502A GLY* 4.0 5.4 - - - -
514A ASN* 2.8 45.3 + - + +
515A PHE* 3.7 30.1 - - - -
516A ILE* 3.7 15.9 - - + -
1V A 4.1 3.6 - - - -
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Residues in contact with GLY 366 (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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362A LYS 2.9 9.4 + - - -
363A TRP* 3.0 12.2 + - - -
364A GLY 3.5 0.2 - - - -
365A LEU* 1.3 79.8 - - - +
367A GLU* 1.3 58.7 + - - -
368A GLY 4.0 0.3 + - - -
369A GLN* 4.2 11.6 + - - -
514A ASN* 4.0 0.7 + - - -
1V A 3.4 21.9 - - - -
10V A 3.0 28.4 + - - +
11V A 3.7 0.5 + - - -
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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