Contacts of the helix formed by residues 339 - 355 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A LEU* 3.6 27.1 - - + -
336B THR* 6.1 0.4 - - + -
337B ALA 4.1 4.5 - - - +
338B SER* 1.3 84.1 - - - +
340B ARG* 1.3 56.7 + - - +
342B LEU* 4.8 0.7 - - + -
343B ALA* 2.8 32.9 + - - +
353C VAL* 3.0 24.9 - - + +
354C SER* 3.2 16.1 - - - +
356C LEU 3.5 26.9 - - - +
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Residues in contact with ARG 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B SER* 3.8 10.3 - - - +
339B PRO* 1.3 81.4 - - - +
341B ALA* 1.3 61.2 + - - +
343B ALA* 3.4 0.5 - - - +
344B ASP* 2.6 56.6 + - - +
354C SER* 4.0 21.9 + - - +
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Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ALA* 4.7 6.1 - - + -
338B SER* 2.8 32.0 + - - +
340B ARG* 1.3 72.9 - - - +
342B LEU* 1.3 58.2 + - - +
344B ASP* 3.3 9.5 + - - +
345B SER* 2.7 30.2 + - - -
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LEU* 3.8 15.6 - - + +
352A GLN* 3.1 50.5 - - + +
353A VAL* 3.8 22.0 - - + +
356A LEU* 4.3 14.6 - - + -
336B THR 3.4 19.1 - - - +
337B ALA* 3.5 14.6 - - + +
338B SER 2.7 19.2 + - - +
341B ALA* 1.3 70.1 - - - +
343B ALA* 1.3 67.1 + - - +
345B SER* 2.8 19.5 + - - +
346B LEU* 2.9 17.5 + - + +
353C VAL* 4.2 9.4 - - + -
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B PRO 2.8 22.7 + - - +
340B ARG 3.4 3.8 - - - +
342B LEU* 1.3 76.5 - - - +
344B ASP* 1.3 65.3 + - - +
346B LEU* 3.0 9.4 + - - +
347B MET* 3.0 21.3 + - + +
350C ALA* 3.3 22.1 - - - +
353C VAL* 4.0 7.1 - - - +
354C SER* 3.3 29.2 - - - +
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Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ARG* 2.6 50.7 + - - +
341B ALA* 3.4 10.5 - - - +
343B ALA* 1.3 77.8 - - - +
345B SER* 1.3 63.4 + - - +
347B MET* 3.0 11.8 + - - +
348B GLN* 3.0 27.0 + - - +
354C SER* 4.8 1.7 + - - -
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Residues in contact with SER 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.7 22.3 - - - +
341B ALA 2.7 18.1 + - - -
342B LEU* 2.8 12.6 + - - +
344B ASP* 1.3 74.9 - - - +
346B LEU* 1.3 65.5 + - - +
348B GLN* 3.0 43.0 + - - +
349B LEU* 3.2 10.0 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.8 3.8 - - + -
349A LEU* 3.4 38.8 - - + -
353A VAL* 4.9 3.4 - - + -
342B LEU 2.9 15.7 + - - +
343B ALA 3.0 7.2 + - - +
345B SER* 1.3 76.5 - - - +
347B MET* 1.3 52.7 + - - +
349B LEU* 2.9 17.9 + - + +
350B ALA* 2.8 32.3 + - - +
346C LEU* 5.0 8.5 - - + +
350C ALA* 3.9 20.9 - - + +
353C VAL* 3.8 31.0 - - + -
346D LEU* 4.0 33.2 - - + -
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Residues in contact with MET 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ALA* 3.0 9.7 + - + +
344B ASP* 3.0 12.9 + - - +
346B LEU* 1.3 75.3 - - - +
348B GLN* 1.3 66.8 + - - +
350B ALA* 3.1 6.5 + - - +
351B ARG* 3.1 33.5 + - - +
347C MET* 2.9 64.4 - - + +
350C ALA* 3.6 12.6 - - + -
351C ARG* 3.9 29.2 - - + +
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ASP* 3.0 19.6 + - + +
345B SER* 3.0 30.6 + - - +
347B MET* 1.3 77.1 - - - +
349B LEU* 1.3 75.0 + - + +
351B ARG* 2.8 20.8 + - - +
352B GLN* 2.9 22.6 + - + +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.5 11.0 - - + +
345A SER* 3.8 31.6 - - - +
346A LEU* 3.9 31.9 - - + +
349A LEU* 4.1 20.9 - - + -
345B SER 3.2 15.7 + - - +
346B LEU* 2.9 11.1 + - + +
348B GLN* 1.3 88.6 - - - +
350B ALA* 1.3 52.8 + - - +
352B GLN* 3.0 26.1 + - - +
353B VAL* 2.7 42.0 + - + +
346C LEU* 5.0 1.6 - - + -
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B LEU 2.8 11.2 + - - +
347B MET* 3.1 14.1 - - - +
348B GLN 3.0 0.2 + - - -
349B LEU* 1.3 76.9 - - - +
351B ARG* 1.3 58.7 + - - +
353B VAL* 3.2 5.6 + - - +
354B SER* 2.9 26.6 + - - -
343C ALA* 3.4 22.4 - - - +
346C LEU* 4.2 14.8 - - + +
347C MET* 3.8 28.3 - - + +
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Residues in contact with ARG 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B MET* 3.1 19.8 + - - +
348B GLN* 2.8 13.0 + - - +
350B ALA* 1.3 72.1 - - - +
352B GLN* 1.3 67.5 + - + +
354B SER* 2.7 18.1 + - - -
355B ARG* 2.9 52.8 + - - +
347C MET* 3.7 32.7 - - - +
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A THR* 4.4 19.8 - - - +
337A ALA* 5.4 1.6 + - - +
342A LEU* 3.2 33.2 - - + +
348B GLN* 2.9 19.0 + - + +
349B LEU* 3.2 28.6 + - - +
351B ARG* 1.3 77.6 - - + +
353B VAL* 1.3 60.0 + - - +
355B ARG* 3.5 19.1 + - - +
356B LEU* 3.6 11.1 + - - +
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.0 19.7 - - + -
346A LEU* 4.9 1.6 - - + -
349B LEU* 2.7 34.5 + - + +
350B ALA 3.5 5.4 - - - +
352B GLN* 1.3 71.8 - - - +
354B SER* 1.3 62.6 + - - +
356B LEU* 2.9 44.5 + - + +
339C PRO* 3.3 22.1 - - + +
342C LEU* 4.6 5.6 - - + -
343C ALA* 4.5 4.5 - - + +
346C LEU* 4.1 16.6 - - + -
353D VAL* 4.4 26.0 - - + -
356D LEU* 4.6 1.3 - - + -
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Residues in contact with SER 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B ALA 2.9 9.8 + - - -
351B ARG* 2.7 28.0 + - - -
353B VAL* 1.3 72.9 - - - +
355B ARG* 1.3 85.7 + - - +
356B LEU 3.5 3.2 + - - -
339C PRO* 4.5 7.5 - - - +
340C ARG* 3.7 31.6 + - - +
343C ALA* 3.7 17.7 - - - +
347C MET* 5.8 1.6 - - - -
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Residues in contact with ARG 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ARG* 2.9 57.6 + - - +
352B GLN* 3.6 14.4 - - - +
353B VAL 3.1 0.2 - - - -
354B SER* 1.3 101.8 + - - +
356B LEU* 1.3 59.2 + - - +
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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