Contacts of the helix formed by residues 594 - 601 (chain J) 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 594 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547J ASP* 2.9 13.2 + - - -
593J SER* 1.3 73.8 - - - +
595J TRP* 1.3 64.9 + - - +
596J LEU 3.2 2.7 - - - -
597J GLU* 3.1 12.2 + - - +
598J MLY 2.7 48.5 + - - +
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Residues in contact with TRP 595 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473J ASN 4.5 1.8 - - - -
474J SER* 2.8 19.8 + - - -
475J PHE* 3.0 41.1 - + + +
478J LEU* 4.0 28.3 - - + -
532J ILE* 5.3 1.6 - - + -
536J LEU* 3.9 25.1 - - + -
547J ASP* 4.0 0.8 + - - +
550J PHE* 4.1 23.8 - + + -
579J PHE* 4.4 16.2 - + - -
590J TYR* 4.3 16.4 - - + -
591J ASN 2.8 32.4 + - - -
592J ILE* 3.5 9.4 - - + -
593J SER 3.1 16.5 - - - +
594J GLY* 1.3 83.0 - - - +
596J LEU* 1.3 56.3 + - - +
598J MLY 3.6 7.9 - - - +
599J ASN* 2.6 40.4 + - - +
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Residues in contact with LEU 596 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536J LEU* 3.8 18.4 - - + -
539J GLU* 4.6 11.2 - - + +
540J CYS* 3.8 13.6 - - - -
545J ALA* 3.8 27.6 - - + +
546J THR* 3.5 31.0 - - - +
547J ASP* 3.4 13.7 + - - +
550J PHE* 3.8 27.1 - - + -
594J GLY 3.2 0.4 - - - -
595J TRP* 1.3 80.2 - - - +
597J GLU* 1.3 61.5 + - - +
599J ASN* 3.4 3.5 + - - +
600J MLY 3.2 40.7 + - - +
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Residues in contact with GLU 597 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594J GLY* 3.1 14.0 + - - +
596J LEU* 1.3 75.2 - - - +
598J MLY 1.3 60.4 + - - +
599J ASN 2.9 1.6 - - - -
600J MLY 2.5 33.5 + - - -
601J ASP 3.2 9.2 + - - -
602J PRO* 3.3 31.9 - - + +
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Residues in contact with MLY 598 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J MLY 4.8 10.5 - - - -
431J MLY 6.4 2.0 - - - -
472J PHE* 5.8 3.1 - - - -
474J SER* 4.2 16.4 + - - -
475J PHE* 3.9 22.9 - - + +
476J GLU* 2.7 40.8 + - + +
593J SER 3.6 24.0 - - - -
594J GLY* 2.7 30.9 + - - +
595J TRP* 3.6 6.3 - - - +
597J GLU* 1.3 74.9 + - - +
599J ASN* 1.3 61.0 + - - +
600J MLY 3.4 0.3 + - - -
601J ASP* 3.7 5.9 + - - +
602J PRO* 5.5 0.4 - - - -
649J VAL* 3.2 17.5 - - - +
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Residues in contact with ASN 599 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475J PHE* 3.6 8.3 - - + -
536J LEU* 3.6 25.6 + - + +
537J GLU* 4.4 1.0 - - - +
540J CYS* 4.0 11.4 - - - -
595J TRP 2.6 19.3 + - - +
596J LEU 3.6 4.7 - - - +
598J MLY 1.3 77.2 + - - +
600J MLY 1.3 58.4 + - - +
601J ASP 3.5 0.2 - - - -
647J GLN 4.6 0.2 - - - +
648J THR* 2.8 19.0 + - - -
649J VAL* 2.0 83.3 + - + +
650J SER* 2.7 23.7 + - - -
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Residues in contact with MLY 600 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539J GLU 3.8 3.4 - - - -
540J CYS* 3.3 44.6 - - + +
541J MET 4.7 0.4 - - - -
542J PHE 2.8 33.7 - - - -
543J PRO* 4.1 14.4 - - - -
545J ALA* 4.7 14.6 - - - -
596J LEU* 3.2 28.3 - - - +
597J GLU* 2.5 22.7 + - - +
599J ASN* 1.3 75.2 + - - +
601J ASP* 1.3 68.2 + - - +
602J PRO* 3.3 11.2 - - + -
640J LYS* 3.2 30.3 + - - +
646J PHE 5.3 1.9 - - - +
647J GLN 5.4 4.5 - - - +
649J VAL* 4.8 0.2 - - - -
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Residues in contact with ASP 601 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J MLY 3.5 38.9 + - - -
428J ALA* 6.0 0.3 - - - +
432J ALA* 5.5 0.7 - - - +
436J MLY 3.6 19.6 - - - -
597J GLU 3.2 2.2 + - - -
598J MLY 3.7 3.4 + - - +
599J ASN 3.5 1.6 - - - -
600J MLY 1.3 80.8 + - - +
602J PRO* 1.3 73.4 - - - +
603J LEU* 3.4 23.6 + - - +
640J LYS* 5.0 1.2 + - - -
646J PHE* 6.6 0.2 - - + -
649J VAL* 4.0 16.2 - - + -
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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