Contacts of the helix formed by residues 504 - 512 (chain E) in PDB entry 1M8V
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 ARG 504 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503E GLU* 1.3 82.2 - - - +
505E PRO* 1.3 76.9 - - + +
506E LEU 3.4 0.4 - - - -
507E ASP* 2.8 32.8 + - - +
508E VAL* 2.9 20.6 + - - +
633F GLY* 4.3 2.2 - - - -
634F TYR 3.9 2.9 - - - +
641F VAL* 3.9 0.7 - - - -
4Q U 3.5 49.6 + - + +
1R U 6.1 1.4 - - - -
5R U 3.2 12.7 + - - +
6R U 3.0 52.8 + - - +
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Residues in contact with PRO 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504E ARG* 1.3 84.3 - - + +
506E LEU* 1.3 60.2 + - + +
508E VAL* 3.1 2.9 + - - +
509E ILE* 2.9 36.8 + - + +
538E LEU* 6.0 0.9 - - + -
634F TYR 3.6 20.4 - - - +
635F ASP* 4.1 9.0 - - - +
639F ASN* 3.7 37.0 - - + +
640F VAL 4.4 0.2 - - - +
641F VAL* 3.5 21.5 - - + -
661F VAL* 3.9 17.7 - - + -
6R U 3.2 13.2 - - + +
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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
----------------------------------------------------------
505E PRO* 1.3 72.1 - - + +
507E ASP* 1.3 60.2 + - - +
509E ILE* 3.8 15.0 - - + +
510E HIS* 2.8 32.1 + - - +
534E TYR* 3.7 34.8 - - + -
535E ASP 4.3 8.7 - - - +
536E ILE* 4.8 17.0 - - + +
538E LEU* 4.5 10.5 - - + -
4R U 5.2 0.9 - - - +
5R U 3.2 30.0 - - - +
6R U 2.9 53.6 + - + +
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Residues in contact with ASP 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503E GLU* 3.7 12.3 + - - +
504E ARG* 2.8 54.4 + - - +
506E LEU* 1.3 78.6 - - - +
508E VAL* 1.3 57.6 + - - +
510E HIS* 3.6 2.1 - - - +
511E ARG* 2.9 41.4 + - - +
5R U 2.6 42.3 + - - +
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Residues in contact with VAL 508 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503E GLU* 3.6 26.2 - - - +
504E ARG 2.9 16.8 + - - +
505E PRO 3.6 5.8 - - - +
507E ASP* 1.3 77.0 - - - +
509E ILE* 1.3 60.3 + - - +
511E ARG* 3.0 23.5 - - - +
512E SER* 2.8 21.7 + - - +
572E PRO* 3.8 27.4 - - + -
641F VAL* 4.0 22.0 - - + -
659F LYS* 3.9 13.9 - - + -
661F VAL* 4.0 17.3 - - + -
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Residues in contact with ILE 509 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E PRO* 2.9 25.3 + - + +
506E LEU* 4.0 9.2 - - + +
508E VAL* 1.3 77.9 - - - +
510E HIS* 1.3 61.9 + - - +
512E SER* 3.1 14.1 + - - -
513E LEU 3.6 0.5 + - - -
531E LEU* 3.4 27.1 - - + +
534E TYR* 3.9 33.1 - - + -
538E LEU* 4.0 28.0 - - + -
540E VAL* 5.4 1.8 - - + -
570E ILE* 4.1 29.2 - - + -
661F VAL* 4.4 21.1 - - + -
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Residues in contact with HIS 510 (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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506E LEU 2.8 23.6 + - - +
507E ASP 3.4 4.9 + - - +
509E ILE* 1.3 74.1 - - - +
511E ARG* 1.3 59.7 + - - +
512E SER 3.2 0.2 - - - -
513E LEU* 3.2 42.5 + - + +
534E TYR* 2.6 36.5 + - - +
4R U 3.2 30.0 + + - -
5R U 3.4 38.5 + + + +
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Residues in contact with ARG 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503E GLU* 2.7 41.1 + - - +
507E ASP* 2.9 26.6 + - - +
508E VAL* 3.0 28.4 + - - +
510E HIS* 1.3 78.2 - - - +
512E SER* 1.3 55.6 + - - +
513E LEU 3.3 5.0 + - - +
515E LYS* 3.7 22.7 + - - +
572E PRO* 6.1 0.2 - - - +
659F LYS* 3.3 13.9 - - - +
5R U 5.9 0.7 - - - -
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Residues in contact with SER 512 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508E VAL* 2.8 14.0 + - - +
509E ILE* 3.1 13.0 + - - -
511E ARG* 1.3 76.9 + - - +
513E LEU* 1.3 67.3 + - - +
514E ASP 3.2 0.7 + - - -
515E LYS* 2.8 28.6 + - - +
517E VAL* 4.0 16.2 - - - -
531E LEU* 3.4 20.1 - - - +
572E PRO* 3.7 25.2 - - - +
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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
------------------------------------------------------------
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