Contacts of the helix formed by residues 536 - 543 (chain G) in PDB entry 4MNE
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 SER 536 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535G SER* 1.3 78.9 - - - +
537G LEU* 1.3 64.6 + - - +
538G TYR* 3.1 8.5 + - - +
539G HIS* 2.8 25.4 + - - +
540G HIS* 3.0 21.3 + - - -
579G SER 3.8 2.2 - - - -
580G ASN* 3.5 26.1 + - - -
582G ILE 3.2 8.3 - - - -
583G PHE* 3.9 14.8 - - - -
102H GLU* 4.5 3.3 + - - -
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Residues in contact with LEU 537 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535G SER 3.8 1.0 + - - -
536G SER* 1.3 71.9 - - - +
538G TYR* 1.3 61.7 + - - +
540G HIS* 4.3 3.8 - - + -
541G LEU* 3.0 44.8 + - + +
548G PHE* 4.5 5.8 - - + -
556G ILE* 3.7 30.1 - - + -
579G SER* 3.4 17.0 - - - +
582G ILE* 2.8 30.1 + - + +
583G PHE* 4.7 0.4 - - - +
584G LEU* 4.9 7.9 - - + +
645G VAL* 4.0 22.0 - - + -
649G LEU* 3.7 28.5 - - + -
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Residues in contact with TYR 538 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536G SER* 3.1 7.2 - - - +
537G LEU* 1.3 75.8 - - - +
539G HIS* 1.3 61.4 + - - +
541G LEU 3.2 0.2 + - - -
542G HIS* 2.8 74.4 + + + +
543G ILE* 4.3 3.6 - - + -
579G SER* 3.0 25.8 + - - +
580G ASN* 3.3 39.3 - - - +
619G TRP* 4.6 2.5 - + - -
648G GLU* 4.5 0.7 - - - -
654G LEU* 4.0 13.9 - - + +
102H GLU* 3.8 42.5 + - + -
103H ILE* 5.9 0.2 - - - +
221H ASN* 3.3 31.3 + - - +
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Residues in contact with HIS 539 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535G SER* 3.4 30.4 + - - -
536G SER* 2.8 21.8 + - - +
538G TYR* 1.3 78.3 - - - +
540G HIS* 1.3 62.7 + - - +
543G ILE* 3.0 46.2 + - + +
544G ILE* 3.1 50.4 + - + +
102H GLU* 3.9 15.9 + - - +
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Residues in contact with HIS 540 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535G SER* 3.7 29.9 + - - -
536G SER 3.0 23.5 + - - +
537G LEU* 3.7 7.6 - - - +
538G TYR 3.3 0.2 - - - -
539G HIS* 1.3 76.8 - - - +
541G LEU* 1.3 59.3 + - - +
544G ILE* 4.2 12.5 - - + +
545G GLU 3.1 7.4 + - - -
546G THR* 2.8 58.7 + - + +
548G PHE* 3.6 28.0 - + + -
584G LEU* 4.1 14.0 - - + +
587G ASP* 3.6 26.9 + - - -
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Residues in contact with LEU 541 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537G LEU* 3.0 34.7 + - + +
540G HIS* 1.3 77.0 - - - +
542G HIS* 1.3 77.3 + - + +
543G ILE 3.6 0.7 - - - -
545G GLU* 3.9 18.2 - - - +
546G THR 5.1 4.3 - - - +
548G PHE* 3.9 31.4 - - + -
553G LEU* 4.7 9.6 - - + -
648G GLU* 3.4 47.1 - - + +
649G LEU* 3.8 6.7 - - + +
652G GLY* 3.9 12.8 - - - +
682G ARG* 5.2 7.6 - - - +
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Residues in contact with HIS 542 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538G TYR* 2.8 61.0 + + + +
541G LEU* 1.3 93.7 + - + +
543G ILE* 1.3 70.1 + - - +
545G GLU* 4.7 3.6 - - - -
648G GLU* 2.7 27.5 + - + +
652G GLY 3.6 20.2 + - - -
653G GLN* 3.7 22.6 - - - -
654G LEU* 3.4 15.0 + - + +
104H LYS* 3.8 18.4 + - - +
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Residues in contact with ILE 543 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538G TYR* 4.3 6.7 - - + -
539G HIS* 3.0 46.0 + - + +
541G LEU 3.6 1.0 - - - -
542G HIS* 1.3 89.8 - - + +
544G ILE* 1.3 63.7 + - + +
545G GLU* 3.2 7.3 + - - +
102H GLU* 3.4 37.0 - - + +
103H ILE* 3.6 30.1 - - - +
104H LYS* 3.3 24.4 - - - +
105H PRO* 5.1 7.7 - - + +
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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
------------------------------------------------------------
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