Contacts of the helix formed by residues 583 - 591 (chain H) in PDB entry 3AOI
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 583 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H GLU* 6.0 0.4 - - - +
15H LEU* 3.5 36.1 - - + -
537H LYS* 4.6 10.1 - - + -
542H VAL* 4.4 18.8 - - + +
545H ASN* 3.3 46.0 - - + +
546H LEU* 4.8 5.6 - - + -
581H THR* 4.3 8.7 - - - +
582H GLY* 1.3 92.4 - - - +
584H GLU* 1.3 67.6 + - - +
585H GLU 3.3 2.5 - - - -
586H ARG* 2.8 20.9 + - + +
587H VAL* 2.8 25.7 + - + +
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Residues in contact with GLU 584 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546H LEU* 3.7 15.3 - - + +
577H PRO* 4.6 6.6 - - + +
580H MET* 3.1 55.4 - - + +
581H THR* 2.5 18.7 + - - -
582H GLY 2.4 31.3 + - - +
583H LEU* 1.3 78.5 + - - +
585H GLU* 1.3 62.5 + - - +
586H ARG 3.2 0.2 + - - -
587H VAL* 3.3 7.5 + - - -
588H VAL* 3.3 22.0 + - - +
665H PHE* 4.7 1.6 - - + -
666H LEU* 3.5 32.8 + - + +
842H ARG* 4.5 7.4 + - - -
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Residues in contact with GLU 585 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580H MET* 6.1 0.4 - - + -
582H GLY 5.2 3.1 + - - +
583H LEU 3.3 0.6 - - - -
584H GLU* 1.3 79.3 - - - +
586H ARG* 1.3 68.0 + - - +
588H VAL* 3.2 16.1 - - - +
589H ARG* 3.4 35.9 + - - +
596H TYR* 3.1 20.1 + - - -
664H GLY* 3.5 18.4 - - - +
665H PHE* 3.6 27.0 - - + -
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Residues in contact with ARG 586 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H PRO* 4.7 8.1 - - - +
15H LEU* 2.4 49.6 + - + +
16H PRO 3.4 5.9 + - - -
17H PRO* 5.0 0.6 - - - +
18H LEU* 2.6 27.3 - - + +
582H GLY 5.0 3.8 + - - +
583H LEU* 2.8 21.0 + - + +
585H GLU* 1.3 88.7 - - - +
587H VAL* 1.3 66.8 + - + +
589H ARG* 3.1 28.5 + - - +
590H ASP* 2.6 56.9 + - - +
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Residues in contact with VAL 587 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 4.1 8.1 - - + -
401H LEU* 3.4 36.3 - - + +
404H LEU* 3.8 19.7 - - + +
542H VAL* 4.4 14.4 - - + -
546H LEU* 4.6 8.3 - - + -
583H LEU* 2.8 30.1 + - + +
584H GLU* 3.3 8.0 + - - +
586H ARG* 1.3 74.3 - - - +
588H VAL* 1.3 54.8 - - - +
589H ARG 3.0 1.0 + - - -
590H ASP* 3.6 0.7 + - - +
591H SER* 2.2 38.7 + - - +
666H LEU* 4.5 11.2 - - + -
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Residues in contact with VAL 588 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400H PRO* 6.4 0.4 - - - -
584H GLU 3.3 14.8 - - - +
585H GLU 3.2 8.5 - - - +
587H VAL* 1.3 75.0 - - - +
589H ARG* 1.3 63.2 + - - +
591H SER* 2.9 13.7 + - - -
592H LEU* 4.2 0.3 - - - -
593H ALA* 3.4 23.4 + - + +
594H ALA* 4.0 8.0 + - + -
596H TYR* 3.4 14.7 + - + +
661H SER* 3.2 35.4 - - - +
664H GLY* 3.0 25.6 - - - +
665H PHE 3.6 0.4 - - - -
666H LEU* 3.4 23.1 - - + +
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Residues in contact with ARG 589 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585H GLU* 3.4 36.2 + - - +
586H ARG* 3.1 26.4 + - - +
587H VAL 3.0 2.4 + - - -
588H VAL* 1.3 77.2 - - - +
590H ASP* 1.3 66.0 + - - +
591H SER 2.9 8.3 + - - -
592H LEU* 3.3 20.1 + - - +
596H TYR* 3.1 47.9 + - + +
652H GLY* 4.1 18.8 + - - -
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Residues in contact with ASP 590 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H PRO* 4.1 8.1 - - - +
18H LEU* 2.6 58.2 + - + +
19H THR* 3.3 24.4 + - - +
124H ASP* 4.6 2.8 - - - +
404H LEU* 5.0 1.1 - - - -
586H ARG* 2.6 37.9 + - - +
589H ARG* 1.3 78.9 - - - +
591H SER* 1.3 58.1 + - - +
592H LEU* 3.5 7.8 - - - +
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Residues in contact with SER 591 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ASP* 3.8 10.7 - - - +
400H PRO* 5.0 15.7 - - - +
403H SER* 5.7 1.9 + - - -
404H LEU* 4.3 28.4 - - - +
407H LYS* 5.9 1.0 - - - -
587H VAL* 2.2 31.0 + - - +
588H VAL* 2.9 18.7 + - - -
590H ASP* 1.3 76.5 - - - +
592H LEU* 1.3 69.5 + - - +
593H ALA* 4.1 4.1 + - - +
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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