Contacts of the helix formed by residues 55 - 61 (chain 1) 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 55 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311 PHE* 4.0 13.7 - - - -
321 PRO* 3.2 36.7 - - - +
341 ILE* 3.4 10.2 + - - +
541 VAL* 1.3 74.4 - - - +
561 ASP* 1.3 64.7 + - - -
581 ALA* 3.2 5.0 + - - +
591 GLN* 3.2 15.9 + - - +
881 HIS* 5.2 1.1 - - - -
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Residues in contact with ASP 56 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301 VAL 4.7 2.0 - - - +
311 PHE* 3.5 20.3 - - - +
321 PRO* 3.7 18.6 - - - +
541 VAL 3.5 1.4 + - - -
551 GLY* 1.3 70.3 - - - -
571 GLU* 1.3 61.1 + - - +
591 GLN* 3.0 6.1 + - + +
601 SER* 2.8 32.2 + - - -
881 HIS* 5.9 0.2 + - - -
931 GLU* 5.0 4.5 - - - +
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Residues in contact with GLU 57 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471 MET* 6.2 0.2 - - - +
501 LYS* 4.8 6.8 + - - -
531 TYR* 3.4 31.4 + - + -
541 VAL 3.6 9.4 + - - +
551 GLY 3.4 1.0 - - - -
561 ASP* 1.3 75.4 - - - +
581 ALA* 1.3 60.0 + - - +
601 SER* 3.2 15.8 + - - +
611 LYS* 2.8 53.3 + - - +
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Residues in contact with ALA 58 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341 ILE* 4.3 7.9 - - + -
361 GLY* 3.9 13.9 - - - +
531 TYR* 3.8 26.6 - - + +
541 VAL* 4.0 2.9 + - - +
551 GLY 3.2 14.2 + - - +
561 ASP 3.1 0.6 - - - -
571 GLU* 1.3 75.9 - - - +
591 GLN* 1.3 67.4 + - - +
621 ARG* 3.3 14.0 + - - -
651 LEU* 3.7 10.1 - - - +
671 LEU* 3.4 23.7 - - + +
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Residues in contact with GLN 59 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 PRO* 4.5 9.3 - - + +
341 ILE* 3.7 21.4 - - - +
551 GLY 3.2 11.6 + - - +
561 ASP* 3.0 12.8 + - + +
581 ALA* 1.3 77.7 - - - +
601 SER* 1.3 62.8 + - - +
621 ARG* 3.0 68.7 + - - +
671 LEU* 3.5 21.3 - - - +
691 TYR* 5.0 4.0 + - - -
2071 GLU* 3.8 9.2 - - - +
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Residues in contact with SER 60 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561 ASP* 2.8 14.3 + - - -
571 GLU* 3.2 17.8 + - - +
591 GLN* 1.3 76.6 - - - +
611 LYS* 1.3 74.5 + - - +
621 ARG* 3.6 3.1 + - - +
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Residues in contact with LYS 61 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441 MET* 3.7 37.3 - - + +
531 TYR* 3.7 32.8 - - + -
571 GLU* 2.8 43.3 + - - +
581 ALA 3.8 2.7 - - - -
591 GLN 3.2 0.8 - - - -
601 SER* 1.3 87.9 + - - +
621 ARG* 1.3 62.0 + - - +
631 GLY 3.1 4.6 + - - -
641 ILE* 3.3 24.1 + - + +
651 LEU* 3.4 18.7 - - + +
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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