Contacts of the strand formed by residues 582 - 585 (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 ILE 582 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536G SER* 3.2 4.9 - - - -
537G LEU* 2.8 46.9 + - + -
560G THR* 3.6 32.8 - - + +
577G LEU* 4.3 13.9 - - + -
578G LYS 3.5 15.3 - - - +
579G SER* 3.3 6.3 + - - +
580G ASN 3.3 0.6 - - - -
581G ASN* 1.3 82.3 - - - +
583G PHE* 1.3 63.1 + - - +
584G LEU* 4.8 1.1 - - + -
590G VAL* 3.6 32.8 - - + -
591G LYS 3.7 2.7 - - - -
592G ILE* 5.0 3.4 - - + -
645G VAL* 3.9 25.6 - - + -
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Residues in contact with PHE 583 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514G LEU* 4.6 17.5 - - + -
532G CYS* 4.3 24.5 - - + -
534G GLY 5.8 1.1 - - - +
535G SER* 3.8 4.7 - - - +
536G SER* 3.9 21.3 - - - -
580G ASN 3.3 23.8 - - - -
581G ASN* 3.8 18.2 - - - -
582G ILE* 1.3 74.3 - - - +
584G LEU* 1.3 63.6 + - - +
585G HIS 3.3 3.3 + - - -
589G THR 3.3 1.9 - - - +
590G VAL* 3.3 4.3 - - - +
591G LYS* 2.9 43.2 + - + +
593G GLY* 4.0 17.9 - - - -
594G ASP* 4.7 4.3 - - + -
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Residues in contact with LEU 584 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533G GLU 3.5 5.6 - - - +
534G GLY* 3.9 4.3 - - - -
535G SER 2.9 21.0 + - - +
537G LEU* 5.0 9.4 - - + +
540G HIS* 4.1 12.3 - - + +
548G PHE* 3.5 36.3 - - + -
552G LYS* 5.5 4.3 - - - -
556G ILE* 4.0 22.2 - - + -
582G ILE* 4.8 4.5 - - + -
583G PHE* 1.3 74.6 - - - +
585G HIS* 1.3 60.3 + - - +
586G GLU 3.4 0.9 + - - -
587G ASP* 2.9 42.9 + - + +
588G LEU 5.1 1.1 - - - +
589G THR 3.7 4.7 - - - +
590G VAL* 3.8 25.1 - - + -
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Residues in contact with HIS 585 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511F VAL* 5.6 8.1 - - + +
589F THR* 5.4 4.4 + - - +
530G GLN* 4.6 10.0 + - - -
531G TRP 4.1 14.1 - - - -
532G CYS* 3.5 28.1 - - + -
533G GLU 3.5 8.2 + - - -
583G PHE* 3.3 3.0 + - - +
584G LEU* 1.3 68.2 - - - +
586G GLU* 1.3 94.2 + - + +
587G ASP 2.9 9.6 + - - -
588G LEU* 3.1 11.4 + - + -
589G THR* 3.0 28.4 + - - +
591G LYS* 3.8 37.5 - - + -
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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