Contacts of the helix formed by residues 320 - 333 (chain A) in PDB entry 1KTW
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A VAL* 6.1 2.0 - - + -
319A HIS* 1.3 79.8 - - - +
321A ARG* 1.3 68.4 + - - +
322A GLN* 3.8 4.0 + - - +
323A SER* 2.8 32.6 + - - -
324A TRP* 3.2 18.9 + - - +
350A TRP* 4.3 13.9 - - - +
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Residues in contact with ARG 321 (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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320A THR* 1.3 79.1 - - - +
322A GLN* 1.3 65.7 + - + +
323A SER 3.2 0.2 + - - -
324A TRP* 3.4 6.6 + - - +
325A LYS* 3.4 8.7 + - - +
339A THR* 3.9 19.7 - - + +
340A PRO* 2.9 45.6 + - + +
341A TYR* 3.7 0.8 - - - +
350A TRP* 3.0 46.2 - - + -
1D G4S 2.8 49.4 + - - -
2D DGS 3.5 21.8 + - - -
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Residues in contact with GLN 322 (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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320A THR* 3.8 3.7 + - - +
321A ARG* 1.3 83.1 - - + +
323A SER* 1.3 57.2 + - - +
324A TRP 3.4 0.2 - - - -
325A LYS* 3.6 25.9 + - - +
326A GLN* 2.8 60.4 + - + +
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL 4.8 1.0 + - - -
319A HIS* 2.8 25.8 + - - -
320A THR* 2.8 35.0 + - - -
321A ARG 3.1 0.2 - - - -
322A GLN* 1.3 77.3 - - - +
324A TRP* 1.3 63.4 + - - +
326A GLN* 4.0 5.0 - - - +
327A ALA* 3.3 18.4 + - - +
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Residues in contact with TRP 324 (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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311A LEU* 2.8 32.6 + - + -
312A PHE 3.0 26.7 - - - -
313A SER* 3.5 21.1 - - - +
314A PRO* 3.7 20.4 - - + -
317A GLU* 5.0 1.3 - - - -
319A HIS* 3.7 27.5 + + + +
320A THR 3.2 16.1 + - - +
321A ARG 4.1 2.9 - - - +
323A SER* 1.3 75.2 - - - +
325A LYS* 1.3 67.3 + - - +
327A ALA* 3.2 14.9 + - + +
328A VAL* 3.1 36.2 + - + +
340A PRO* 4.6 3.6 - - + -
350A TRP* 4.0 22.9 - - + -
352A ALA* 3.5 26.8 - - + +
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Residues in contact with LYS 325 (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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321A ARG 3.4 4.7 + - - +
322A GLN* 3.6 28.2 + - - +
324A TRP* 1.3 78.9 - - - +
326A GLN* 1.3 58.4 + - + +
328A VAL* 3.2 7.3 + - - +
329A GLU* 3.0 51.4 + - - +
337A ALA* 3.3 33.8 + - + +
338A GLN* 4.6 0.4 - - - +
339A THR* 4.1 18.8 + - + +
340A PRO* 3.8 32.6 - - + +
352A ALA* 5.3 0.2 - - - -
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Residues in contact with GLN 326 (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 GLN* 2.8 49.5 + - + +
323A SER* 4.0 6.1 - - - +
324A TRP 3.2 0.2 - - - -
325A LYS* 1.3 75.2 - - + +
327A ALA* 1.3 65.1 + - - +
329A GLU* 3.4 8.7 + - - +
330A SER* 3.0 26.5 + - - -
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Residues in contact with ALA 327 (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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319A HIS* 4.3 7.4 - - + -
323A SER 3.3 13.8 + - - +
324A TRP* 3.2 31.1 + - + +
326A GLN* 1.3 79.4 - - - +
328A VAL* 1.3 58.9 + - - +
330A SER* 2.6 20.2 + - - -
331A LYS* 4.1 13.0 - - - +
368A TYR* 5.1 0.3 + - - -
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Residues in contact with VAL 328 (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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311A LEU* 4.0 20.4 - - + -
324A TRP* 3.1 40.3 + - + +
325A LYS 3.6 6.5 - - - +
326A GLN 3.1 0.2 - - - -
327A ALA* 1.3 75.8 - - - +
329A GLU* 1.3 59.9 + - - +
330A SER 3.0 1.8 - - - -
331A LYS* 2.9 20.4 + - - +
332A LEU* 3.0 37.5 + - + +
337A ALA* 3.9 18.4 - - + -
352A ALA* 4.1 13.7 - - + +
354A VAL* 5.5 2.5 - - + -
368A TYR* 4.9 5.8 - - - +
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Residues in contact with GLU 329 (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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325A LYS* 3.0 38.2 + - - +
326A GLN* 4.1 8.0 - - - +
328A VAL* 1.3 75.7 - - - +
330A SER* 1.3 57.1 + - - +
331A LYS 3.0 1.1 - - - -
332A LEU* 4.9 0.9 - - - -
333A GLY* 2.8 44.8 + - - +
334A ARG* 4.0 10.3 + - - +
335A GLY* 3.0 32.4 + - - -
336A CYS* 5.4 0.2 - - - -
337A ALA* 3.6 26.6 + - + +
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Residues in contact with SER 330 (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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326A GLN 3.0 12.7 + - - -
327A ALA* 2.6 29.1 + - - -
329A GLU* 1.3 77.0 - - - +
331A LYS* 1.3 61.5 + - - +
334A ARG* 6.0 1.8 - - - +
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Residues in contact with LYS 331 (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 ALA 4.1 10.1 - - - +
328A VAL 2.9 7.2 + - - +
330A SER* 1.3 86.5 - - - +
332A LEU* 1.3 66.0 + - + +
333A GLY 3.6 0.2 - - - -
363A LYS* 5.4 2.1 - - - +
367A GLU* 4.0 33.8 + - + +
368A TYR* 3.3 32.5 + - + +
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Residues in contact with LEU 332 (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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311A LEU* 4.5 4.0 - - + -
328A VAL* 3.0 37.3 + - + +
331A LYS* 1.3 79.4 - - - +
333A GLY* 1.3 59.4 + - - +
336A CYS* 3.7 20.3 - - + +
354A VAL* 3.8 36.3 - - + -
360A CYS 4.7 1.3 - - - +
363A LYS* 2.9 40.8 + - + +
364A ALA* 3.5 34.5 - - + +
367A GLU* 5.0 2.0 - - + -
368A TYR* 3.8 19.7 - - + -
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Residues in contact with GLY 333 (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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329A GLU* 2.8 34.1 + - - +
330A SER 4.9 0.2 - - - -
331A LYS 3.6 0.6 - - - -
332A LEU* 1.3 80.1 - - - +
334A ARG* 1.3 82.8 - - - -
336A CYS* 3.3 15.7 + - - +
363A LYS* 4.8 3.6 - - - -
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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