Contacts of the helix formed by residues 531 - 540 (chain G) in PDB entry 4P6X
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 THR 531 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529G THR* 3.1 24.1 - - + +
530G PRO* 1.3 78.9 - - - +
532G LEU* 1.3 63.6 + - - +
533G VAL* 3.5 10.5 - - + +
534G SER* 2.9 45.1 + - - +
535G LEU* 3.2 8.1 + - - +
696G GLU* 2.7 25.3 + - - -
699G LYS* 3.3 16.3 + - - -
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Residues in contact with LEU 532 (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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528C LEU* 3.6 34.5 - - + +
530C PRO* 3.5 30.9 - - + +
530G PRO 3.6 0.4 + - - -
531G THR* 1.3 74.6 + - - +
533G VAL* 1.3 59.2 + - - +
535G LEU* 3.1 6.2 + - + +
536G LEU* 2.8 31.2 + - - +
582G PRO* 3.6 13.2 - - + -
692G THR* 3.3 34.3 - - + -
693G TYR* 3.9 17.2 + - + +
696G GLU* 3.3 22.3 + - + +
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Residues in contact with VAL 533 (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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531G THR* 3.5 21.3 - - + +
532G LEU* 1.3 73.8 - - - +
534G SER* 1.3 61.0 + - - +
536G LEU* 3.0 12.5 + - - +
537G GLU* 2.9 27.9 + - - +
661G GLU* 3.7 48.9 - - + +
664G LEU* 3.9 10.7 - - + +
665G CYS* 4.1 10.5 - - - -
696G GLU* 2.8 20.7 + - - +
699G LYS* 5.4 0.9 - - - +
700G ALA* 5.3 4.5 - - + -
703G LYS* 5.6 7.9 - - + +
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Residues in contact with SER 534 (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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535C LEU* 4.0 16.2 - - - +
529G THR 4.6 2.0 + - - -
530G PRO* 4.0 3.6 - - - +
531G THR* 2.9 36.8 + - - +
532G LEU 3.3 0.6 - - - -
533G VAL* 1.3 83.0 - - - +
535G LEU* 1.3 59.7 + - - +
537G GLU* 3.3 22.8 + - - +
538G VAL* 3.4 18.2 + - - +
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Residues in contact with LEU 535 (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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527C GLN 5.5 0.2 - - - +
530C PRO* 4.1 21.3 - - + -
534C SER* 5.2 9.4 - - - +
535C LEU* 3.4 30.7 - - + -
538C VAL* 4.7 4.3 - - + -
531G THR 3.2 8.2 + - - +
532G LEU* 3.1 9.9 + - + +
534G SER* 1.3 78.2 + - - +
536G LEU* 1.3 66.6 + - + +
538G VAL* 3.2 4.7 - - + +
539G ILE* 3.1 40.7 + - + +
580G ALA 4.4 4.7 - - - +
582G PRO* 3.4 40.4 - - + -
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Residues in contact with LEU 536 (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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532G LEU 2.8 16.1 + - - +
533G VAL* 3.0 16.1 + - - +
535G LEU* 1.3 76.9 - - + +
537G GLU* 1.3 61.9 + - - +
539G ILE* 3.4 23.0 - - + +
540G GLU* 3.1 24.9 + - - +
577G TRP* 4.9 4.3 + - + +
581G ILE* 4.4 6.3 - - + -
582G PRO* 5.4 2.5 - - + -
664G LEU* 3.4 46.6 - - + +
665G CYS* 4.0 7.0 - - - +
668G VAL* 3.5 24.5 - - + -
693G TYR* 4.0 25.4 - - + +
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Residues in contact with GLU 537 (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 VAL* 2.9 13.5 + - - +
534G SER* 3.5 16.4 - - - +
535G LEU 3.2 0.6 - - - -
536G LEU* 1.3 78.4 - - - +
538G VAL* 1.3 63.3 + - + +
540G GLU* 3.6 14.8 - - - +
660G TYR* 3.4 36.5 + - + -
661G GLU* 5.1 10.4 - - - +
664G LEU* 3.5 11.5 - - + +
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Residues in contact with VAL 538 (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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535C LEU* 3.5 21.8 - - + -
538C VAL* 3.3 35.4 - - + +
539C ILE* 3.6 28.9 - - + +
580C ALA* 4.8 14.6 - - + +
534G SER 3.6 8.7 - - - +
535G LEU* 3.2 15.7 - - + +
537G GLU* 1.3 81.0 - - + +
539G ILE* 1.3 60.6 + - - +
540G GLU 3.3 4.8 + - - +
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Residues in contact with ILE 539 (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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538C VAL* 4.0 16.8 - - + -
535G LEU* 3.1 37.0 + - + +
536G LEU* 3.4 28.3 - - + +
538G VAL* 1.3 76.3 - - - +
540G GLU* 1.3 66.7 + - - +
541G PRO* 3.1 9.8 - - - +
576G LYS* 4.4 6.8 + - - -
577G TRP* 3.6 33.1 - - + +
580G ALA* 3.8 34.5 - - + +
581G ILE* 4.0 10.3 - - + +
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Residues in contact with GLU 540 (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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536G LEU 3.1 15.0 + - - +
537G GLU 3.6 12.0 - - - +
538G VAL 3.3 5.1 - - - +
539G ILE* 1.3 77.4 - - - +
541G PRO* 1.3 88.7 - - - +
542G GLU* 3.7 1.2 + - - -
577G TRP* 4.0 4.4 + - - -
607G ALA* 5.3 3.5 - - - +
660G TYR* 3.5 21.3 - - + +
663G TYR* 4.1 8.6 + - - -
664G LEU* 3.5 12.2 - - + +
667G LYS* 2.7 39.1 + - - -
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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