Contacts of the helix formed by residues 341 - 355 (chain C) in PDB entry 4QGC
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 341 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303B ALA* 3.4 8.4 - - - +
333C SER* 4.0 19.3 - - - +
337C LYS* 6.5 0.9 - - + -
339C ARG 5.6 0.2 - - - +
340C PRO* 1.3 79.4 - - - +
342C ARG* 1.3 64.9 + - - +
343C ALA* 3.6 7.2 + - - +
344C GLU* 3.2 29.8 + - - +
345C GLY 3.3 15.8 + - - -
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Residues in contact with ARG 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG* 3.4 48.9 - - - +
295B GLY 6.1 0.2 - - - +
298B GLY* 4.5 9.2 - - - -
303B ALA* 3.8 14.3 - - + +
306B VAL* 3.7 45.8 - - + -
310B GLN* 4.8 2.2 + - - -
329B GLN* 2.8 41.5 + - - +
347B ASP* 3.1 25.5 + - - -
341C THR* 1.3 74.6 - - - +
343C ALA* 1.3 79.5 + - - +
345C GLY* 3.3 3.6 + - - -
346C SER* 3.1 45.1 + - - -
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Residues in contact with ALA 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLN* 4.8 3.1 + - + +
343B ALA* 6.4 1.8 - - + -
347B ASP* 5.1 10.1 - - + +
341C THR* 3.3 7.4 + - - +
342C ARG* 1.3 104.6 - - - +
344C GLU* 1.3 58.7 + - + +
346C SER* 3.3 2.9 + - - -
347C ASP* 2.9 29.3 + - - +
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Residues in contact with GLU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C GLN 5.7 1.3 - - - +
330C MET 3.4 20.0 - - - +
331C LEU* 4.0 10.2 - - + -
332C GLU* 3.5 7.8 + - - +
333C SER* 2.5 51.5 + - - -
340C PRO* 3.5 7.0 - - + +
341C THR* 3.2 25.8 + - - +
342C ARG 3.3 0.8 - - - -
343C ALA* 1.3 74.7 - - + +
345C GLY* 1.3 61.7 + - - +
347C ASP* 3.6 6.3 - - - +
348C VAL* 3.0 36.2 + - - +
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Residues in contact with GLY 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA* 4.3 16.2 - - - -
304B GLU* 5.3 0.4 - - - -
307B PHE* 4.3 3.5 - - - -
331C LEU* 4.9 0.2 - - - +
340C PRO* 5.2 0.9 - - - +
341C THR 3.3 7.8 + - - -
342C ARG 3.3 7.1 + - - -
344C GLU* 1.3 78.6 - - - +
346C SER* 1.3 57.2 + - - +
349C ALA* 3.1 29.1 + - - +
381C ILE* 3.6 28.8 - - - +
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Residues in contact with SER 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 4.9 0.7 + - - -
307B PHE* 3.5 28.9 + - - +
310B GLN* 5.6 0.5 + - - -
347B ASP* 4.4 7.2 - - - -
342C ARG* 3.1 39.9 + - - -
343C ALA 3.7 6.7 - - - -
344C GLU 3.3 0.2 - - - -
345C GLY* 1.3 74.1 - - - +
347C ASP* 1.3 61.0 + - - +
349C ALA* 3.9 0.6 - - - +
350C ASN* 3.0 44.5 + - - -
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Residues in contact with ASP 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 2.4 32.0 + - - -
343B ALA* 4.2 13.9 - - - +
346B SER* 4.6 7.2 + - - -
350B ASN* 6.0 0.7 - - - +
294C ARG* 2.8 35.3 + - - -
310C GLN* 5.4 0.5 + - - -
329C GLN 4.6 4.6 - - - +
330C MET 5.3 0.4 - - - +
343C ALA 2.9 17.5 + - - +
344C GLU* 3.3 9.6 + - - +
346C SER* 1.3 75.6 - - - +
348C VAL* 1.3 64.8 + - + +
350C ASN* 4.0 5.1 - - - +
351C ALA* 3.3 19.8 + - - +
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C MET* 3.6 43.7 - - + +
331C LEU* 3.9 14.8 - - + -
344C GLU 3.0 17.9 + - - +
347C ASP* 1.3 75.7 - - + +
349C ALA* 1.3 63.6 + - - +
351C ALA* 3.2 13.0 + - - +
352C VAL* 3.2 15.7 + - + +
359C ILE* 4.4 3.6 - - + -
378C GLN* 3.4 35.2 - - - +
381C ILE* 3.7 20.9 - - + -
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Residues in contact with ALA 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 3.5 46.0 - - + -
345C GLY 3.1 17.4 + - - +
346C SER 3.9 1.8 - - - +
347C ASP 3.4 0.2 - - - -
348C VAL* 1.3 81.2 - - - +
350C ASN* 1.3 57.0 + - - +
352C VAL* 3.2 6.2 + - - +
353C LEU* 2.9 32.6 + - - +
381C ILE* 3.9 6.0 - - + +
385C ALA* 4.0 10.3 - - + +
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Residues in contact with ASN 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 5.6 3.3 - - - +
311B LYS* 3.1 29.0 + - - +
347B ASP* 5.7 2.0 + - - +
350B ASN* 3.2 46.3 - - - +
354B ASP* 5.6 0.2 + - - -
310C GLN* 5.0 0.7 - - - +
311C LYS* 5.7 0.2 - - - +
346C SER* 3.0 32.8 + - - +
347C ASP* 4.0 4.7 - - - +
348C VAL 3.3 0.2 - - - -
349C ALA* 1.3 73.6 - - - +
351C ALA* 1.3 56.0 + - - +
353C LEU* 3.5 8.5 - - - +
354C ASP* 2.7 42.3 + - - +
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 4.8 0.2 - - - +
310C GLN* 3.9 16.5 - - - +
314C ILE* 4.2 0.4 - - + +
326C CYS* 3.6 33.4 - - + -
347C ASP 3.3 13.3 + - - +
348C VAL* 3.2 11.8 + - - +
350C ASN* 1.3 75.3 - - - +
352C VAL* 1.3 64.9 + - - +
354C ASP* 3.3 10.1 + - - +
355C GLY 3.3 0.7 + - - -
356C ALA* 3.1 24.3 + - - +
359C ILE* 4.1 9.2 - - + -
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Residues in contact with VAL 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C THR* 3.8 21.5 - - + +
348C VAL* 3.2 16.0 + - + +
349C ALA* 3.3 9.2 - - - +
351C ALA* 1.3 76.9 - - - +
353C LEU* 1.3 57.5 + - - +
355C GLY* 3.1 6.6 + - - -
356C ALA* 4.5 4.3 - - - +
359C ILE* 4.2 18.2 - - + -
382C ALA* 4.5 20.0 - - + +
385C ALA* 4.0 17.7 - - + -
386C GLU* 4.6 2.0 - - - +
389C ILE* 4.6 8.2 - - + +
467C ARG* 2.6 50.3 + - - +
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Residues in contact with LEU 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B PHE* 4.4 10.8 - - + -
311B LYS* 3.5 35.2 - - + +
349C ALA 2.9 21.9 + - - +
350C ASN* 3.8 11.0 - - - +
352C VAL* 1.3 71.5 - - - +
354C ASP* 1.3 65.0 + - - +
355C GLY* 3.1 1.2 + - - -
385C ALA* 3.2 26.9 - - + +
388C ALA* 3.7 21.8 - - + +
389C ILE* 3.6 22.2 - - + -
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Residues in contact with ASP 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 6.2 0.2 - - - -
350B ASN* 5.6 0.9 + - - -
310C GLN* 3.1 25.1 + - - -
311C LYS* 2.5 51.0 + - + +
314C ILE* 3.4 27.4 - - + +
315C GLY* 5.3 1.2 + - - -
318C ASN* 3.9 4.2 - - - +
350C ASN* 2.7 27.2 + - - +
351C ALA 3.3 7.9 - - - +
353C LEU* 1.3 75.9 - - - +
355C GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ILE* 3.5 7.3 - - - +
318C ASN* 3.1 31.8 + - - -
352C VAL 3.1 4.2 + - - -
353C LEU 3.1 1.1 - - - -
354C ASP* 1.3 79.4 - - - +
356C ALA* 1.3 67.8 + - - +
357C ASP* 3.5 0.9 + - - +
394C LEU* 5.9 5.8 - - - -
445C ARG* 3.4 10.2 + - - -
467C ARG* 3.5 13.5 - - - -
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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