Contacts of the helix formed by residues 428 - 438 (chain D) in PDB entry 6M04
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 GLN 428 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399D LYS* 5.1 1.4 + - - +
403D GLU* 5.5 1.9 - - - +
406D PHE* 6.2 3.8 - - + -
424D ASP* 2.8 41.2 + - - +
427D ASP* 1.3 71.4 - - - +
429D LEU* 1.3 60.3 + - - +
431D SER* 3.0 17.3 + - - -
432D LYS* 2.9 40.7 + - + +
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Residues in contact with LEU 429 (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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204D PHE* 5.1 14.1 - - + -
427D ASP* 3.3 7.5 - - + +
428D GLN* 1.3 79.0 - - - +
430D TYR* 1.3 66.2 + - + +
432D LYS* 4.3 12.6 - - + -
433D ARG* 3.0 38.7 + - + +
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Residues in contact with TYR 430 (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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19D ILE* 4.3 15.5 - - + -
200D LEU* 3.8 32.6 - - + +
204D PHE* 3.5 45.8 - + + -
420D LEU* 4.7 0.7 - - - +
423D VAL* 4.0 19.1 - - + -
426D TYR* 4.1 31.6 - + - -
427D ASP* 3.8 11.9 + - + +
428D GLN 3.3 0.6 - - - -
429D LEU* 1.3 89.4 - - + +
431D SER* 1.3 57.0 + - - +
433D ARG* 3.4 17.0 + - - +
434D PHE* 3.3 21.7 + - - +
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Residues in contact with SER 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399D LYS* 2.4 35.1 + - - +
403D GLU* 3.1 11.5 + - - +
420D LEU* 3.8 13.8 - - - +
423D VAL* 5.0 0.4 - - - +
424D ASP* 4.6 8.1 - - - -
427D ASP 4.0 5.6 + - - -
428D GLN* 3.0 22.5 + - - -
430D TYR* 1.3 80.2 - - - +
432D LYS* 1.3 59.1 + - - +
433D ARG 3.5 0.4 - - - -
434D PHE* 3.8 3.3 - - - +
435D GLY* 2.9 25.1 + - - -
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Residues in contact with LYS 432 (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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213D LEU* 5.5 10.5 - - + -
403D GLU* 3.0 29.5 - - + +
406D PHE* 3.3 36.9 - - - -
407D SER* 4.8 7.1 - - - +
428D GLN* 2.9 26.8 + - + +
429D LEU* 3.3 15.9 + - + +
431D SER* 1.3 75.9 - - - +
433D ARG* 1.3 59.3 + - - +
436D VAL* 3.0 43.7 + - + +
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Residues in contact with ARG 433 (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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200D LEU* 3.8 14.5 + - - +
203D CYS* 2.9 51.1 + - - +
204D PHE* 3.3 47.6 - - + +
209D THR* 3.9 30.1 - - - +
210D THR* 5.5 0.9 - - - +
213D LEU* 5.6 8.1 - - + -
429D LEU* 3.0 22.4 + - + +
430D TYR* 3.4 24.4 + - - +
432D LYS* 1.3 78.1 - - + +
434D PHE* 1.3 74.1 + - - +
436D VAL* 3.8 9.8 + - - +
437D PHE* 3.5 17.8 + - - +
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Residues in contact with PHE 434 (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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196D PHE* 4.6 16.2 - + - -
199D ILE* 4.0 27.1 - - + -
200D LEU* 5.1 9.6 - - + -
203D CYS* 3.6 23.3 - - + -
291D VAL* 4.5 21.8 - - + -
294D PHE* 5.4 4.9 - + - -
418D PHE* 4.9 10.3 - + - -
420D LEU* 3.9 29.8 - - + -
430D TYR 3.3 20.5 + - - +
431D SER* 3.5 3.5 + - - +
432D LYS 3.2 0.6 - - - -
433D ARG* 1.3 89.3 - - - +
435D GLY* 1.3 61.5 + - - +
437D PHE* 2.9 21.3 + + + +
438D LEU* 3.3 23.3 + - + +
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Residues in contact with GLY 435 (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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400D VAL* 5.2 8.3 - - - -
403D GLU* 3.3 23.1 - - - -
407D SER* 6.0 0.2 - - - -
411D ASP* 3.3 27.1 - - - +
420D LEU* 6.1 0.9 - - - -
431D SER 2.9 12.4 + - - -
434D PHE* 1.3 78.8 - - - +
436D VAL* 1.3 64.0 + - - +
438D LEU* 3.5 12.7 + - - +
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Residues in contact with VAL 436 (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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208D TRP* 5.5 7.0 - - + -
209D THR* 5.3 6.1 - - - +
212D ALA* 5.5 4.7 - - + -
213D LEU* 3.7 36.8 - - + -
407D SER* 4.1 20.0 - - - +
409D ILE* 5.4 15.7 - - + -
411D ASP* 5.6 0.2 - - - -
432D LYS* 3.0 28.9 + - + +
433D ARG* 3.8 7.2 - - + +
435D GLY* 1.3 77.2 - - - +
437D PHE* 1.3 61.9 + - - +
438D LEU 3.1 0.2 - - - -
439D SER* 3.1 22.7 + - - -
442D SER* 4.3 17.8 + - - +
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Residues in contact with PHE 437 (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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203D CYS* 3.8 26.9 - - - -
206D SER* 4.8 4.7 - - - -
208D TRP* 4.3 8.5 - + - -
209D THR* 3.7 25.6 - - + -
284D ALA* 3.4 39.0 - - + -
287D LEU* 3.5 35.9 - - + -
288D PHE* 3.1 57.2 - + - -
291D VAL* 4.0 15.4 - - + +
433D ARG 3.5 6.2 + - - +
434D PHE* 2.9 13.0 + + - +
436D VAL* 1.3 79.2 - - - +
438D LEU* 1.3 58.4 + - - +
439D SER 3.3 0.7 - - - -
442D SER* 6.2 0.2 - - - -
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Residues in contact with LEU 438 (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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291D VAL* 3.8 27.4 - - + -
292D ARG* 5.8 2.9 - - + -
295D ARG* 4.0 33.2 - - + +
400D VAL* 4.7 18.6 - - + -
411D ASP* 4.7 1.6 - - + -
412D VAL* 3.4 36.0 - - + +
413D LYS 5.0 0.7 - - - +
414D ASN 5.6 0.4 - - - +
415D ASP* 5.7 3.6 - - + +
434D PHE* 3.3 21.8 + - + +
435D GLY* 3.8 12.1 - - - +
436D VAL 3.1 1.0 - - - -
437D PHE* 1.3 79.5 - - - +
439D SER* 1.3 63.1 + - - +
440D GLU* 3.5 1.7 + - - +
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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