Contacts of the helix formed by residues 583 - 591 (chain M) in PDB entry 2O5J
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15M LEU* 3.4 39.0 - - + -
457M ALA* 5.9 1.6 - - + -
537M LYS* 5.1 11.9 - - + -
542M VAL* 5.4 11.0 - - + -
545M ASN* 4.2 27.1 - - + +
546M LEU* 4.4 15.3 - - + -
581M THR* 3.9 15.7 - - - +
582M GLY* 1.3 83.8 - - - +
584M GLU* 1.3 60.9 + - - +
585M GLU 3.2 3.1 - - - -
586M ARG* 3.1 14.7 + - + +
587M VAL* 2.8 40.2 + - + +
905M ILE* 5.5 1.3 - - + -
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Residues in contact with GLU 584 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546M LEU* 5.0 2.5 - - - +
577M PRO* 4.9 5.1 - - + +
580M MET* 2.9 57.7 - - + +
581M THR* 3.6 11.9 + - - +
582M GLY* 2.5 15.7 + - - -
583M LEU* 1.3 99.1 + - - +
585M GLU* 1.3 64.3 + - + +
587M VAL* 3.4 5.5 - - - +
588M VAL* 3.4 15.6 + - - +
665M PHE* 4.4 6.1 - - + -
666M LEU* 3.2 48.3 + - + +
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Residues in contact with GLU 585 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582M GLY 5.1 5.4 - - - +
583M LEU 3.2 0.9 - - - -
584M GLU* 1.3 81.5 - - + +
586M ARG* 1.3 94.0 + - - +
587M VAL 3.2 0.3 + - - -
588M VAL* 3.2 7.4 - - - +
589M ARG* 2.9 59.7 + - - +
664M GLY 3.6 15.0 - - - +
665M PHE* 4.4 16.5 - - + -
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Residues in contact with ARG 586 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M PRO* 4.2 11.5 - - - +
15M LEU* 2.6 56.4 + - + +
16M PRO 4.5 2.4 + - - -
17M PRO* 5.2 3.8 - - - +
18M LEU* 4.1 11.4 - - - -
582M GLY 5.1 1.5 + - - +
583M LEU* 3.1 23.2 + - + +
585M GLU* 1.3 94.7 + - - +
587M VAL* 1.3 55.2 + - - +
589M ARG* 4.6 4.3 - - - +
590M ASP* 2.7 82.6 + - - +
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Residues in contact with VAL 587 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M LEU* 5.5 2.0 - - + -
400M PRO* 5.9 0.4 - - + -
401M LEU* 3.9 30.3 - - + +
404M LEU* 4.3 9.9 - - + +
542M VAL* 4.5 21.8 - - + -
546M LEU* 4.8 7.2 - - + -
583M LEU* 2.8 21.0 + - + +
584M GLU* 3.4 9.2 - - - +
585M GLU 3.2 0.2 - - - -
586M ARG* 1.3 72.8 - - + +
588M VAL* 1.3 63.3 + - + +
590M ASP* 4.2 0.7 - - - +
591M SER* 2.7 36.9 + - - -
666M LEU* 3.7 35.0 - - + -
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Residues in contact with VAL 588 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400M PRO* 5.8 1.3 - - + -
584M GLU 3.6 2.9 - - - +
585M GLU 3.2 10.5 - - - +
587M VAL* 1.3 86.3 - - + +
589M ARG* 1.3 53.0 + - - +
591M SER* 2.6 32.8 + - - +
593M ALA* 3.4 25.4 + - + +
594M ALA* 4.0 7.8 + - + +
596M TYR* 3.8 10.5 - - - +
660M ALA 5.5 0.9 - - - +
661M SER* 4.1 15.3 - - - +
664M GLY* 3.1 32.1 - - - +
666M LEU* 3.7 31.0 - - + +
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Residues in contact with ARG 589 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585M GLU* 2.9 58.7 + - - +
586M ARG* 3.9 5.4 - - - +
587M VAL 3.1 0.6 - - - -
588M VAL* 1.3 73.8 - - - +
590M ASP* 1.3 63.8 + - - +
591M SER 2.6 15.8 - - - +
592M LEU* 4.3 7.3 - - - +
596M TYR* 3.0 63.5 + - + +
652M GLY* 4.0 10.9 + - - -
654M LEU* 4.5 8.5 - - - +
664M GLY* 5.5 0.8 + - - -
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Residues in contact with ASP 590 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M PRO* 3.6 23.4 - - - +
18M LEU* 3.5 34.4 + - + +
19M THR* 4.2 16.1 - - + +
124M ASP* 6.2 0.3 - - - -
404M LEU* 4.7 5.6 - - + -
586M ARG* 2.7 53.8 + - - +
587M VAL 4.2 0.4 - - - +
589M ARG* 1.3 74.7 - - - +
591M SER* 1.3 62.9 + - - +
592M LEU* 4.5 6.6 - - - +
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Residues in contact with SER 591 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400M PRO* 3.1 42.6 - - - +
401M LEU* 4.4 0.7 - - - -
403M SER* 5.7 0.4 - - - -
404M LEU* 4.2 17.1 - - - +
407M LYS* 5.7 2.7 - - - +
587M VAL 2.7 17.0 + - - -
588M VAL* 2.6 26.3 + - - +
589M ARG 2.6 17.8 - - - +
590M ASP* 1.3 79.3 - - - +
592M LEU* 1.3 62.2 + - - +
593M ALA 3.3 1.0 + - - -
594M ALA 5.4 0.3 - - - +
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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