Contacts of the helix formed by residues 55 - 61 (chain 0) 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 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310 PHE* 4.0 13.5 - - - -
320 PRO* 3.2 37.4 + - - +
340 ILE* 3.4 11.2 + - - +
540 VAL* 1.3 75.0 - - - +
560 ASP* 1.3 65.2 + - - -
580 ALA* 3.2 5.4 + - - +
590 GLN* 3.2 15.9 + - - +
880 HIS* 5.2 0.9 - - - -
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Residues in contact with ASP 56 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300 VAL 4.7 1.6 - - - +
310 PHE* 3.5 20.3 - - - +
320 PRO* 3.7 17.4 - - - +
540 VAL 3.5 1.4 + - - -
550 GLY* 1.3 69.0 - - - -
570 GLU* 1.3 61.5 + - - +
590 GLN* 3.0 6.2 + - + +
600 SER* 2.8 31.3 + - - -
880 HIS* 5.9 0.2 + - - -
930 GLU* 5.0 4.5 - - - +
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Residues in contact with GLU 57 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470 MET* 6.2 0.2 - - - +
500 LYS* 4.8 7.1 + - - -
530 TYR* 3.4 30.5 + - + -
540 VAL 3.6 9.4 + - - +
550 GLY 3.4 0.8 - - - -
560 ASP* 1.3 76.7 - - + +
580 ALA* 1.3 61.1 + - - +
600 SER* 3.2 16.7 + - - +
610 LYS* 2.8 52.4 + - - +
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Residues in contact with ALA 58 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340 ILE* 4.3 8.3 - - + -
360 GLY* 3.9 13.5 - - - +
530 TYR* 3.8 26.8 - - + +
540 VAL* 4.0 2.7 + - - +
550 GLY 3.2 14.0 + - - +
560 ASP 3.1 1.0 - - - -
570 GLU* 1.3 75.5 - - - +
590 GLN* 1.3 66.7 + - - +
620 ARG* 3.3 13.7 + - - -
650 LEU* 3.7 10.7 - - - +
670 LEU* 3.4 24.1 - - + +
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Residues in contact with GLN 59 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320 PRO* 4.5 10.0 - - + +
340 ILE* 3.7 21.0 - - - +
550 GLY 3.2 11.6 + - - +
560 ASP* 3.0 13.3 + - - +
580 ALA* 1.3 77.7 - - - +
600 SER* 1.3 62.8 + - - +
620 ARG* 3.0 69.8 + - - +
670 LEU* 3.5 22.0 - - - +
690 TYR* 5.0 3.8 + - - -
2070 GLU* 3.8 9.5 - - - +
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Residues in contact with SER 60 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560 ASP* 2.8 14.3 + - - -
570 GLU* 3.2 17.5 + - - +
590 GLN* 1.3 77.2 - - - +
610 LYS* 1.3 74.1 + - - +
620 ARG* 3.6 3.0 + - - +
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Residues in contact with LYS 61 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440 MET* 3.7 38.4 - - + +
530 TYR* 3.8 32.1 - - + -
570 GLU* 2.8 43.0 + - - +
580 ALA 3.8 3.1 - - - -
590 GLN 3.2 0.4 - - - -
600 SER* 1.3 87.0 + - - +
620 ARG* 1.3 62.6 + - - +
630 GLY 3.1 4.1 + - - -
640 ILE* 3.3 24.4 + - + +
650 LEU* 3.4 18.8 - - + +
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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