Contacts of the helix formed by residues 349 - 362 (chain D) in PDB entry 4YCG
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 349 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LEU* 4.3 3.8 - - - -
376C LEU* 3.9 26.5 - - + +
398C GLY* 5.7 0.7 - - - -
347D THR 4.7 0.2 - - - +
348D PRO* 1.3 75.3 - - - +
350D LYS* 1.3 64.6 + - - +
351D HIS* 3.6 2.8 + - - +
352D ALA* 3.1 24.9 + - - +
353D ILE* 3.1 26.0 + - - +
406D CYS 4.1 0.4 + - - -
407D ARG* 3.6 38.2 + - - +
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Residues in contact with LYS 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A THR* 4.6 7.6 - - - +
248A GLU* 2.4 53.9 + - - +
249A LEU* 4.4 11.2 - - + +
252A MET* 3.6 35.3 - - + +
396C TYR* 3.5 26.9 - - + -
397C GLU* 3.1 28.0 + - - +
398C GLY* 3.3 13.5 + - - +
399C MET* 3.8 7.4 - - - -
349D THR* 1.3 74.3 - - - +
351D HIS* 1.3 57.9 + - - +
353D ILE* 3.3 4.0 + - - +
354D VAL* 2.9 34.2 + - - +
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Residues in contact with HIS 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU* 4.9 1.7 - - + +
331C ALA* 3.1 23.4 + - + +
332C TYR 2.7 29.0 + - - -
333C GLU* 4.7 2.9 - - - -
373C PRO* 4.2 13.0 - - + +
376C LEU* 4.0 11.4 - - + -
398C GLY 2.9 17.6 + - - +
399C MET 3.5 16.2 - - - +
400C SER* 4.1 2.7 - - - -
401C VAL* 3.3 19.8 - - + +
349D THR* 3.3 6.7 + - - +
350D LYS* 1.3 77.2 - - - +
352D ALA* 1.3 53.3 + - - +
354D VAL* 3.5 7.1 - - + +
355D GLN* 2.7 68.2 + - + +
407D ARG 4.2 2.2 + - - -
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Residues in contact with ALA 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D LEU* 3.8 14.4 - - + -
349D THR* 3.1 26.4 + - - +
350D LYS 3.3 0.2 - - - -
351D HIS* 1.3 77.0 + - - +
353D ILE* 1.3 55.5 + - - +
355D GLN* 3.8 4.6 - - - +
356D THR* 2.7 37.6 + - - -
369D ALA* 4.2 5.0 - - + +
406D CYS 3.6 24.2 - - - +
407D ARG 3.9 15.2 + - - +
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Residues in contact with ILE 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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249A LEU* 3.8 23.6 - - + -
252A MET* 3.8 21.3 - - + -
253A ILE* 3.9 18.6 - - + +
256A GLU* 3.8 31.2 - - + +
319C TRP* 3.8 24.2 - - + -
342D LEU* 4.2 8.5 - - + -
348D PRO* 4.2 12.6 - - + -
349D THR 3.1 15.1 + - - +
350D LYS 3.6 5.8 - - - +
351D HIS 3.2 0.2 - - - -
352D ALA* 1.3 74.0 - - - +
354D VAL* 1.3 66.4 + - - +
356D THR* 3.4 3.5 + - - -
357D LEU* 3.1 24.2 + - + +
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Residues in contact with VAL 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU* 6.1 0.4 - - + -
312C VAL* 3.8 37.7 - - + -
314C PHE* 5.2 0.2 - - + -
317C ILE* 4.8 3.6 - - + -
319C TRP* 3.5 31.4 - - + -
329C TYR* 3.8 24.0 - - + +
331C ALA* 4.8 3.4 - - + -
399C MET* 4.2 7.9 - - + -
350D LYS 2.9 21.2 + - - +
351D HIS* 3.5 9.4 - - + +
353D ILE* 1.3 76.5 - - - +
355D GLN* 1.3 58.9 + - - +
357D LEU* 3.1 8.5 + - - +
358D VAL* 2.8 31.7 + - + +
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Residues in contact with GLN 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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310C LEU* 4.9 6.5 - - + -
333C GLU* 4.2 18.3 + - - +
334C CYS 5.4 1.3 + - - -
373C PRO* 5.1 2.6 - - - +
351D HIS* 2.7 48.8 + - + +
352D ALA* 3.9 4.0 - - - +
354D VAL* 1.3 75.4 - - - +
356D THR* 1.3 53.4 + - - +
358D VAL* 3.6 6.6 - - - +
359D HIS* 2.7 36.1 + - - +
366D VAL* 4.0 10.3 - - + +
367D GLY 3.0 25.1 + - - +
368D LYS 3.4 19.0 + - - -
369D ALA* 3.6 10.0 - - - +
370D CYS* 6.1 0.6 - - - -
407D ARG* 4.1 8.5 + - - +
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Residues in contact with THR 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLU* 4.9 1.1 - - - +
338D CYS 4.2 11.7 + - - +
340D PHE* 4.0 42.8 - - + +
342D LEU* 3.3 22.1 - - + +
352D ALA 2.7 24.5 + - - -
353D ILE* 3.6 5.4 - - - -
354D VAL 3.2 0.2 - - - -
355D GLN* 1.3 77.4 - - - +
357D LEU* 1.3 57.1 + - - +
359D HIS* 3.4 8.7 + - + +
360D LEU* 2.8 28.1 + - + +
368D LYS* 5.1 6.3 - - + +
369D ALA* 4.2 8.7 + - - +
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Residues in contact with LEU 357 (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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256A GLU* 4.1 13.2 - - + +
317C ILE* 4.0 27.2 - - + +
319C TRP* 3.4 47.1 - - + +
340D PHE* 3.6 35.9 - - + -
353D ILE* 3.1 19.3 + - + +
354D VAL 3.6 6.1 - - - +
356D THR* 1.3 73.4 - - - +
358D VAL* 1.3 60.3 + - - +
360D LEU* 3.3 12.0 + - + +
361D LYS* 2.9 29.3 + - - +
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Residues in contact with VAL 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU* 4.4 9.0 - - + -
311C ARG 5.7 1.6 - - - +
312C VAL* 3.8 38.4 - - + -
317C ILE* 3.9 14.6 - - + -
354D VAL 2.8 21.4 + - - +
355D GLN* 3.7 7.2 - - - +
357D LEU* 1.3 75.6 - - - +
359D HIS* 1.3 52.2 + - - +
361D LYS* 3.1 4.0 + - - +
362D PHE* 2.5 48.9 + - + +
366D VAL* 3.6 30.1 - - + -
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Residues in contact with HIS 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D GLN 2.7 21.6 + - - +
356D THR* 3.6 6.5 - - + +
358D VAL* 1.3 74.0 - - - +
360D LEU* 1.3 64.6 + - + +
362D PHE 4.0 1.3 - - - -
363D PRO* 2.9 57.2 - - + +
366D VAL* 2.4 35.1 + - - +
367D GLY* 3.4 15.7 - - - +
368D LYS* 3.7 45.7 + - + +
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Residues in contact with LEU 360 (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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340D PHE* 3.9 45.3 - - + -
356D THR 2.8 20.8 + - - +
357D LEU* 3.5 13.2 - - + +
358D VAL 3.3 0.2 - - - -
359D HIS* 1.3 80.3 - - + +
361D LYS* 1.3 61.4 + - - +
363D PRO* 4.1 7.0 - - - +
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Residues in contact with LYS 361 (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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316C ASP* 3.4 33.0 + - - +
317C ILE* 4.7 4.0 - - + -
357D LEU 2.9 16.6 + - - +
358D VAL* 3.5 4.9 - - - +
360D LEU* 1.3 79.8 - - - +
362D PHE* 1.3 97.7 + - + +
363D PRO* 3.4 7.3 - - - +
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Residues in contact with PHE 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ASP* 3.8 31.2 - - + -
317C ILE* 5.8 1.3 - - + -
358D VAL* 2.5 35.1 + - + +
359D HIS 3.2 2.9 - - - +
361D LYS* 1.3 109.5 - - + +
363D PRO* 1.3 60.0 - - - +
364D THR* 3.2 6.0 + - + -
365D LYS* 3.3 19.7 + - + -
366D VAL* 3.1 26.8 + - + +
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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