Contacts of the helix formed by residues 339 - 355 (chain D) in PDB entry 1TLF
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 PRO 339 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A VAL* 3.4 27.9 - - - +
354A SER 3.8 4.7 - - - +
356A LEU* 3.5 37.9 - - + +
356C LEU* 4.5 13.0 - - + -
337D ALA 4.9 0.2 - - - +
338D SER* 1.3 86.9 - - - +
340D ARG* 1.3 63.4 + - - +
342D LEU* 3.1 18.6 + - + +
343D ALA* 3.1 10.2 + - - +
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Residues in contact with ARG 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ARG* 4.7 7.9 - - - +
354A SER* 3.9 30.1 + - - +
238B VAL* 5.8 5.9 - - - +
327D LYS* 5.2 9.0 - - - +
338D SER* 3.4 5.5 + - - +
339D PRO* 1.3 77.8 - - - +
341D ALA* 1.3 63.7 + - - +
343D ALA* 2.9 35.0 + - - +
344D ASP* 2.9 52.4 + - - +
347D MET* 3.4 26.3 - - - +
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Residues in contact with ALA 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D ALA* 4.0 16.8 - - + -
338D SER* 3.0 23.1 + - - +
340D ARG* 1.3 79.2 - - - +
342D LEU* 1.3 61.7 + - - +
344D ASP* 3.3 10.4 + - - +
345D SER* 3.0 28.3 + - - -
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Residues in contact with LEU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A VAL* 3.7 15.0 - - + -
349C LEU* 3.4 29.4 - - + +
352C GLN* 4.3 21.8 - - + +
353C VAL* 4.3 15.3 - - + -
356C LEU* 4.4 14.6 - - + -
337D ALA* 3.7 26.7 - - + +
338D SER 2.9 37.3 + - - +
339D PRO* 3.1 8.5 + - + +
341D ALA* 1.3 77.0 - - - +
343D ALA* 1.3 58.2 + - - +
345D SER* 3.5 3.4 + - - +
346D LEU* 2.8 36.9 + - + +
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Residues in contact with ALA 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ALA* 2.8 30.5 - - + +
353A VAL* 4.1 1.5 - - - +
354A SER* 3.6 14.4 - - - +
339D PRO 3.1 6.7 + - - +
340D ARG* 2.9 29.7 + - - +
342D LEU* 1.3 76.4 - - - +
344D ASP* 1.3 57.1 + - - +
346D LEU* 3.2 6.0 + - - +
347D MET* 2.8 35.9 + - + +
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Residues in contact with ASP 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C GLU* 5.4 3.1 - - - +
327D LYS* 4.1 22.8 - - - -
340D ARG* 2.9 47.5 + - - +
341D ALA* 3.3 11.2 + - - +
343D ALA* 1.3 77.5 - - - +
345D SER* 1.3 62.9 + - - +
347D MET* 3.4 13.3 + - - +
348D GLN* 3.0 36.2 + - - +
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Residues in contact with SER 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C LEU* 4.0 24.0 - - - +
341D ALA 3.0 17.1 + - - -
342D LEU* 3.7 5.6 - - - +
344D ASP* 1.3 76.0 - - - +
346D LEU* 1.3 63.8 + - - +
348D GLN* 3.2 13.7 + - - +
349D LEU* 3.2 26.6 + - - +
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Residues in contact with LEU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A LEU* 3.4 16.7 - - + +
350A ALA* 3.6 21.1 - - + +
353A VAL* 4.8 4.7 - - + -
346B LEU* 4.0 30.3 - - + -
346C LEU* 3.4 31.9 - - + -
349C LEU* 4.3 17.9 - - + -
353C VAL* 4.3 9.9 - - + -
342D LEU* 2.8 31.6 + - + +
343D ALA* 3.4 5.6 - - - +
345D SER* 1.3 75.9 - - - +
347D MET* 1.3 58.2 + - - +
349D LEU* 2.9 11.2 + - + +
350D ALA* 2.8 27.7 + - - +
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Residues in contact with MET 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A MET* 3.6 22.2 - - + -
350A ALA* 3.6 16.6 - - + -
351A ARG* 3.8 37.5 - - - -
340D ARG* 3.4 35.9 - - - +
343D ALA* 2.8 17.7 + - - +
344D ASP* 3.9 14.4 - - - +
346D LEU* 1.3 72.3 - - - +
348D GLN* 1.3 63.5 + - + +
350D ALA* 3.0 9.2 + - - +
351D ARG* 2.9 29.7 + - + +
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Residues in contact with GLN 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C THR 3.6 12.1 + - - +
259C GLU* 3.8 23.6 + - - +
260C SER 4.2 0.3 - - - +
261C GLY* 3.5 24.7 - - - +
344D ASP* 3.0 26.1 + - - +
345D SER* 3.5 11.5 + - - +
346D LEU 3.2 0.2 - - - -
347D MET* 1.3 74.8 - - + +
349D LEU* 1.3 52.4 + - + +
351D ARG* 3.1 7.0 + - - +
352D GLN* 2.8 41.9 + - - +
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A LEU* 5.0 1.1 - - + -
342C LEU* 4.1 28.7 - - + +
345C SER* 3.9 32.1 - - - +
346C LEU* 3.8 35.7 - - + +
349C LEU* 4.1 16.6 - - + -
345D SER* 3.2 14.5 + - - +
346D LEU* 2.9 9.4 + - - +
348D GLN* 1.3 77.7 - - + +
350D ALA* 1.3 56.7 + - - +
352D GLN* 3.0 16.6 + - - +
353D VAL* 2.8 36.2 + - + +
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Residues in contact with ALA 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ARG* 5.4 0.7 - - - -
343A ALA* 3.3 35.7 - - - +
346A LEU* 3.6 21.0 - - + +
347A MET* 4.1 11.4 - - + +
346D LEU 2.8 9.0 + - - +
347D MET* 3.0 13.9 + - - +
349D LEU* 1.3 74.2 - - - +
351D ARG* 1.3 59.9 + - - +
353D VAL* 3.0 5.8 + - - +
354D SER* 2.8 26.3 + - - -
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Residues in contact with ARG 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ARG* 5.0 4.5 - - - +
347A MET* 5.1 9.2 - - + -
230C MET* 3.7 27.6 + - - +
233C LEU* 4.0 5.5 - - - +
234C ASN* 2.5 36.1 - - - +
259C GLU* 3.8 22.4 - - - -
260C SER* 3.0 35.6 + - - +
347D MET* 2.9 19.4 + - + +
348D GLN* 3.4 7.6 - - - +
350D ALA* 1.3 76.2 - - - +
352D GLN* 1.3 61.2 + - - +
354D SER* 2.5 28.5 + - - -
355D ARG* 3.3 32.2 + - - +
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Residues in contact with GLN 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C SER 3.6 14.8 - - - +
261C GLY* 3.5 28.5 + - - +
262C LEU* 5.1 4.9 - - - +
337C ALA* 4.7 9.3 - - - +
342C LEU* 4.1 29.8 - - + +
348D GLN* 2.8 28.7 + - - +
349D LEU* 3.2 22.9 + - - +
350D ALA 3.0 0.2 - - - -
351D ARG* 1.3 80.0 - - - +
353D VAL* 1.3 57.0 + - - +
355D ARG* 4.0 20.2 + - - +
356D LEU* 4.2 6.9 + - - +
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Residues in contact with VAL 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A PRO* 3.4 29.1 - - + +
342A LEU* 4.5 10.1 - - + -
343A ALA* 4.4 9.0 - - + +
346A LEU* 4.8 9.6 - - + -
353B VAL* 4.4 18.6 - - + -
342C LEU* 3.8 25.1 - - + -
346C LEU* 5.2 3.8 - - + -
349D LEU* 2.8 19.8 + - + +
350D ALA* 3.5 7.6 - - - +
352D GLN* 1.3 73.7 - - - +
354D SER* 1.3 68.8 + - - +
355D ARG 3.2 0.2 - - - -
356D LEU* 2.7 34.9 + - + +
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Residues in contact with SER 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A PRO* 4.1 9.1 - - - +
340A ARG* 3.1 41.5 + - - +
343A ALA* 3.8 8.9 - - - +
234C ASN* 5.6 5.0 + - - -
350D ALA 2.8 10.5 + - - -
351D ARG* 2.5 26.6 + - - +
353D VAL* 1.3 77.1 - - - +
355D ARG* 1.3 61.9 + - - +
356D LEU 2.6 21.7 + - - +
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Residues in contact with ARG 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 3.7 34.3 - - - +
234C ASN* 5.5 1.3 - - - +
236C GLY* 4.4 13.5 - - - -
238C VAL* 4.5 23.4 - - + +
260C SER* 2.4 36.1 + - - -
262C LEU* 3.6 30.3 - - - +
351D ARG* 3.3 41.1 + - - +
352D GLN* 4.1 14.8 + - - +
353D VAL 3.2 1.0 - - - -
354D SER* 1.3 80.9 + - - +
356D LEU* 1.3 56.4 + - - +
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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