Contacts of the helix formed by residues 496 - 508 (chain E) in PDB entry 5MG3
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 LEU 496 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492E LEU* 3.5 20.4 - - + +
493E ASP* 3.3 3.7 + - - +
494E GLY 3.3 2.4 + - - -
495E ILE* 1.4 94.5 - - + +
497E VAL* 1.3 65.6 + - - +
498E ARG 3.3 0.4 - - - -
499E LEU* 3.2 14.4 + - - +
500E VAL* 3.2 19.6 + - - +
31Y ILE* 3.7 24.2 - - + -
35Y ILE* 4.3 19.1 - - + -
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Residues in contact with VAL 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493E ASP* 3.2 21.4 + - + +
496E LEU* 1.3 75.2 - - - +
498E ARG* 1.3 64.2 + - + +
500E VAL* 3.3 6.7 + - + +
501E SER* 2.9 43.5 + - - +
34Y ARG 4.4 2.2 - - - +
35Y ILE* 3.9 30.2 - - + +
38Y PHE* 3.5 38.8 - - + -
39Y ILE* 3.9 24.2 - - + -
208Y GLU* 5.3 1.1 - - + -
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Residues in contact with ARG 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490E TRP* 2.8 46.9 + - - +
493E ASP* 2.6 56.0 + - - +
494E GLY* 3.6 17.5 - - - +
497E VAL* 1.3 75.9 - - + +
499E LEU* 1.3 61.2 + - - +
501E SER* 4.1 2.3 - - - -
502E PHE* 3.4 19.8 + - - +
38Y PHE* 3.9 2.4 - - - -
205Y HIS* 3.2 15.8 + - - -
208Y GLU* 2.6 44.6 + - + +
212Y GLN* 4.6 6.0 - - - +
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Residues in contact with LEU 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494E GLY 3.9 11.0 + - - +
495E ILE* 3.3 31.6 - - + +
496E LEU 3.2 6.7 + - - +
498E ARG* 1.3 75.1 - - + +
500E VAL* 1.3 67.7 + - + +
502E PHE* 3.2 20.8 + - + +
503E ILE* 4.0 6.8 + - - +
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Residues in contact with VAL 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E LEU* 3.2 18.5 + - - +
497E VAL* 3.3 7.4 + - + +
499E LEU* 1.3 78.0 - - + +
501E SER* 1.3 60.9 + - - +
502E PHE 3.4 0.7 + - - -
503E ILE* 3.5 15.6 + - - +
504E THR* 3.9 8.4 + - - -
529G ILE* 3.5 31.6 - - + -
530G ILE* 4.5 16.8 - - + -
536G ASN* 4.6 10.5 + - - +
35Y ILE* 6.3 2.0 - - + -
39Y ILE* 4.5 5.6 - - + -
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Residues in contact with SER 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497E VAL* 2.9 24.3 + - - +
498E ARG 4.2 2.2 - - - -
500E VAL* 1.3 75.6 - - - +
502E PHE* 1.4 56.7 + - - +
503E ILE 3.4 0.2 - - - -
504E THR* 3.2 8.8 + - - -
505E GLY 3.0 24.3 + - - -
38Y PHE* 4.9 6.9 + - - +
39Y ILE* 3.6 18.5 - - - +
40Y PRO* 5.6 0.3 - - - +
206Y THR* 6.0 0.2 - - - +
208Y GLU* 3.8 17.6 - - - +
209Y GLN* 3.4 31.7 + - - +
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Residues in contact with PHE 502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498E ARG 3.4 12.8 + - - +
499E LEU* 3.2 16.3 + - + +
501E SER* 1.4 75.0 - - - +
503E ILE* 1.4 61.1 + - + +
505E GLY* 3.3 2.9 + - - -
506E LEU* 3.0 57.2 + - + +
212Y GLN* 3.6 39.5 + - + +
213Y GLY* 4.5 10.3 - - - -
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Residues in contact with ILE 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499E LEU 4.0 5.8 + - - +
500E VAL* 3.5 11.2 + - - +
501E SER 3.4 0.4 - - - -
502E PHE* 1.4 80.4 - - + +
504E THR* 1.4 51.2 + - - +
506E LEU* 3.1 14.0 + - + +
507E ARG* 2.8 56.4 + - + +
536G ASN* 3.6 36.8 - - + +
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Residues in contact with THR 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500E VAL 3.9 7.3 + - - -
501E SER* 3.2 13.6 + - - -
503E ILE* 1.4 70.9 - - - +
505E GLY* 1.4 63.1 + - - +
507E ARG 5.2 0.4 - - - -
508E PHE* 3.0 49.4 + - + +
533G VAL* 5.0 2.7 - - + -
536G ASN* 2.6 35.2 + - - +
39Y ILE* 4.5 5.5 - - - +
40Y PRO* 4.3 13.2 - - + -
209Y GLN* 3.6 33.2 + - - +
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Residues in contact with GLY 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D ARG* 2.9 25.7 + - - -
501E SER 3.0 11.7 + - - -
502E PHE 3.7 4.0 - - - -
503E ILE 3.3 0.2 - - - -
504E THR* 1.4 78.9 - - - +
506E LEU* 1.3 58.6 + - - +
507E ARG 3.7 0.2 + - - -
508E PHE 4.4 1.7 - - - +
209Y GLN* 3.3 31.5 - - - +
212Y GLN* 4.2 6.1 - - - -
215Y LEU* 4.1 7.8 - - - +
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Residues in contact with LEU 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D ARG* 3.3 23.5 + - - +
502E PHE* 3.0 49.5 + - + +
503E ILE* 3.1 15.2 + - + +
505E GLY* 1.3 77.1 - - - +
507E ARG* 1.4 65.1 + - + +
508E PHE 3.8 0.2 - - - -
212Y GLN* 4.8 0.9 - - - +
213Y GLY* 4.0 27.6 - - - +
214Y ASP* 5.1 6.1 - - - +
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Residues in contact with ARG 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D GLN* 3.9 29.4 - - - +
418D ARG* 3.6 10.9 - - - +
419D GLN* 3.7 13.5 + - - +
422D LEU* 5.8 2.7 - - - -
503E ILE* 2.8 38.5 + - + +
504E THR* 4.4 0.7 - - - -
506E LEU* 1.4 79.0 - - + +
508E PHE* 1.4 57.1 + - - +
535G GLY* 3.0 38.1 + - - +
536G ASN 2.6 27.1 + - - -
537G ILE* 4.6 6.2 + - - +
539G SER* 4.0 12.9 + - - +
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Residues in contact with PHE 508 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D ASN 4.9 2.1 - - - +
416D GLU* 3.6 46.8 - - + +
417D ALA 3.0 13.9 + - - -
418D ARG* 2.7 45.7 + - - +
419D GLN* 4.0 25.5 + - - +
504E THR* 3.0 35.2 + - + +
505E GLY* 4.4 1.4 - - - +
506E LEU 3.8 0.8 - - - -
507E ARG* 1.4 76.6 - - - +
533G VAL* 5.3 2.9 - - + -
534G LEU 3.4 29.2 - - - +
536G ASN* 5.6 0.2 - - - +
40Y PRO* 4.6 7.9 - - + -
41Y ILE 5.5 0.4 - - - -
43Y GLY 3.9 23.6 - - - -
44Y ILE 4.4 1.6 - - - -
46Y ALA* 4.1 13.5 - - + -
47Y ALA* 3.8 16.2 - - + -
209Y GLN* 3.8 21.1 + - - +
215Y LEU* 5.6 1.9 - - - +
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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