Contacts of the helix formed by residues 531 - 540 (chain G) in PDB entry 1O1F
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 GLY 531 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524G GLU 4.7 0.9 - - - -
525G LEU 3.1 18.8 - - - -
526G ILE 3.9 2.7 - - - -
528G MLY 3.0 16.1 + - - +
529G PRO 3.1 0.2 - - - -
530G MET* 1.3 79.0 - - - +
532G ILE* 1.3 55.1 + - - -
533G PHE 3.3 2.2 - - - -
534G SER* 2.8 28.2 + - - -
535G ILE* 3.2 8.9 + - - -
558G HIS* 3.6 9.8 - - - -
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Residues in contact with ILE 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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478G LEU* 4.4 17.7 - - + -
525G LEU* 3.1 22.6 + - + +
526G ILE* 4.4 10.8 - - + +
531G GLY* 1.3 68.6 - - - +
533G PHE* 1.3 60.4 + - + +
535G ILE* 3.4 2.3 + - - +
536G LEU* 2.7 31.4 + - + +
550G PHE* 4.4 6.6 - - + -
554G LEU* 4.1 22.7 - - + -
558G HIS* 4.1 6.4 + - + -
565G PHE* 4.1 20.0 - - + -
579G PHE* 3.7 39.0 - - + -
581G LEU* 4.2 14.4 - - + -
595G TRP* 5.3 2.0 - - + -
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Residues in contact with PHE 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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475G PHE* 4.3 12.6 - + - -
478G LEU* 3.5 37.2 - - + -
479G CYS* 4.3 17.3 - - - -
482G PHE* 4.0 18.6 - + - -
526G ILE* 3.4 36.7 + - + +
527G GLU* 5.1 0.7 - - - -
531G GLY 3.0 1.4 + - - -
532G ILE* 1.3 77.4 - - + +
534G SER* 1.3 51.5 + - - +
536G LEU* 2.8 14.3 + - + +
537G GLU* 2.5 43.2 + - - +
650G SER* 4.1 19.5 - - - -
653G PHE* 4.8 4.5 - + - -
654G ARG* 3.5 41.3 - - + +
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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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3506 SER 2.6 21.1 + - - -
3516 THR* 1.6 55.9 + - - +
3536 GLN* 3.3 11.8 - - - +
3546 GLN* 1.4 67.0 + - - -
526G ILE 4.8 0.4 + - - -
528G MLY 4.4 1.9 + - - -
529G PRO* 4.5 0.2 - - - -
531G GLY 2.8 8.5 + - - -
533G PHE* 1.3 71.9 - - - +
535G ILE* 1.3 46.2 - - - -
537G GLU* 2.7 2.7 + - - +
538G GLU 2.7 3.5 + - - -
654G ARG* 4.9 5.9 + - - +
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Residues in contact with ILE 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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3516 THR* 1.5 51.6 + - + +
3546 GLN* 4.7 5.2 - - + +
468 GLY* 4.8 0.4 - - - -
530G MET* 3.1 34.5 - - + +
531G GLY 3.2 3.1 + - - +
532G ILE 3.9 1.6 - - - +
534G SER* 1.3 68.5 - - - +
536G LEU* 1.3 59.0 + - - +
538G GLU* 4.8 2.2 - - - +
539G GLU* 3.4 14.7 + - - +
550G PHE* 3.9 11.6 - - + -
553G MLY 3.9 36.1 - - + +
554G LEU* 3.4 33.2 - - + -
557G GLU* 4.2 8.5 - - + -
558G HIS* 3.8 15.9 - - + +
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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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475G PHE* 4.2 15.7 - - + -
532G ILE* 2.7 16.6 + - + +
533G PHE* 2.8 23.7 + - + +
535G ILE* 1.3 81.2 - - - +
537G GLU* 1.3 57.9 + - - -
538G GLU 3.3 0.7 + - - -
539G GLU* 3.9 1.2 + - - +
540G CYS* 3.3 19.0 + - - -
550G PHE* 3.2 33.9 - - + -
595G TRP* 3.9 32.3 - - + -
596G LEU* 3.8 17.3 - - + +
599G ASN* 3.6 21.8 - - - +
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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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3496 LEU* 1.7 31.8 - - - +
3506 SER* 0.4 129.9 + - - +
3516 THR 2.5 1.6 - - - -
533G PHE* 2.5 32.4 + - - +
534G SER 2.7 0.8 + - - -
536G LEU* 1.3 73.0 - - - +
538G GLU* 1.3 48.0 - - - +
540G CYS* 3.8 5.0 - - - +
599G ASN* 4.4 0.2 - - - +
641G LYS* 5.1 2.6 + - - -
648G THR* 3.2 11.9 - - - +
650G SER* 2.6 32.3 + - - +
651G ALA* 3.5 6.2 + - - +
654G ARG* 2.9 34.9 + - - -
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Residues in contact with GLU 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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1436 TYR* 3.7 1.7 + - - -
3466 LEU* 4.2 6.5 - - + +
3496 LEU* 1.8 49.4 - - + +
3516 THR* 1.3 105.0 + - - +
3526 PHE* 2.8 18.1 - - + +
3556 MET* 1.9 42.3 - - - +
530G MET* 4.7 2.1 - - - +
535G ILE* 4.8 2.3 - - - +
537G GLU* 1.3 62.7 - - - +
539G GLU* 1.3 53.6 + - - +
540G CYS 2.8 0.2 - - - -
541G MET* 2.4 20.4 + - + +
542G PHE* 4.4 4.8 - - + -
553G MLY 4.3 22.7 - - - +
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Residues in contact with GLU 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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3516 THR* 2.4 6.5 + - - -
458 VAL* 1.3 55.1 - - + +
468 GLY* 3.2 10.4 - - - -
535G ILE* 3.4 14.0 + - - +
536G LEU 4.3 3.1 - - - +
538G GLU* 1.3 76.9 - - - +
540G CYS* 1.3 56.1 + - - +
541G MET 2.8 5.7 + - - -
542G PHE* 3.0 26.1 + - - +
545G ALA* 3.5 13.7 - - + +
549G SER* 2.8 13.8 + - - +
550G PHE* 4.1 11.4 - - + -
553G MLY 3.0 22.5 + - - +
596G LEU* 4.6 11.1 - - + +
600G MLY 3.8 1.6 - - - -
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Residues in contact with CYS 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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3496 LEU* 3.3 3.2 - - - +
536G LEU* 3.3 19.5 + - - -
537G GLU* 3.8 13.2 - - - +
538G GLU 2.7 3.4 + - - -
539G GLU* 1.3 75.0 - - - +
541G MET* 1.3 56.6 + - - +
542G PHE 3.4 0.2 - - - -
596G LEU* 3.8 32.8 - - - -
599G ASN* 4.0 21.1 - - - -
600G MLY 3.3 37.1 - - + +
640G LYS* 6.1 0.7 - - - -
647G GLN 3.9 15.2 - - - +
648G THR* 4.4 2.2 - - - -
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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