Contacts of the helix formed by residues 57 - 67 (chain G) in PDB entry 5OF4
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 VAL 57 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400D ARG* 3.4 36.6 - - + +
401D LEU* 5.1 11.7 - - + -
16G MET* 5.9 1.1 - - + -
19G PHE* 3.7 21.9 - - + -
20G LEU* 5.8 3.8 - - + -
23G LEU* 5.6 3.6 - - + -
53G LEU* 3.3 32.8 - - + +
54G GLN 4.7 5.8 - - - +
55G GLU 3.2 0.8 - - - -
56G ARG* 1.3 77.2 - - - +
58G GLY* 1.3 62.8 + - - +
60G LEU* 3.0 6.9 + - - +
61G MET* 3.0 36.6 + - - +
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Residues in contact with GLY 58 (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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400D ARG* 2.9 26.9 - - - +
54G GLN 5.6 0.4 + - - -
55G GLU 4.1 4.3 + - - -
56G ARG 3.5 0.2 - - - -
57G VAL* 1.3 73.9 - - - +
59G GLU* 1.3 57.6 + - - +
60G LEU 3.0 0.2 + - - -
61G MET* 3.0 4.6 + - - -
62G ASP* 3.0 46.5 + - - +
63G GLN 4.3 0.2 + - - -
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Residues in contact with GLU 59 (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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55G GLU* 3.7 10.9 + - - +
56G ARG* 3.1 48.9 + - + +
58G GLY* 1.3 73.2 - - - +
60G LEU* 1.3 55.6 + - - +
62G ASP* 5.7 0.2 - - - -
63G GLN* 4.2 15.1 - - - +
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Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A VAL* 5.6 4.0 - - + -
19G PHE* 3.6 29.6 - - + -
22G TYR* 5.5 12.6 - - + -
23G LEU* 3.7 26.2 - - + -
26G SER* 4.8 8.3 - - - +
56G ARG* 3.3 5.6 + - + +
57G VAL 3.0 3.8 + - - +
59G GLU* 1.3 79.7 - - - +
61G MET* 1.3 53.2 + - - +
62G ASP 3.4 1.6 - - - -
63G GLN* 3.0 11.8 + - + +
64G ASN* 2.5 48.8 + - + +
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Residues in contact with MET 61 (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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519A TYR* 3.6 21.3 - - + +
666A ASP* 3.9 34.4 - - + +
397D GLU* 5.4 1.1 - - + +
400D ARG* 4.2 24.7 - - - +
16G MET* 4.8 14.1 - - + -
19G PHE* 3.6 22.0 - - + -
57G VAL* 3.0 39.3 + - - +
58G GLY* 3.0 3.6 + - - +
60G LEU* 1.3 76.5 - - - +
62G ASP* 1.3 54.2 + - - +
64G ASN* 3.0 11.4 + - - +
65G ALA* 2.6 33.5 + - - +
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Residues in contact with ASP 62 (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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398D ARG* 5.7 3.1 + - - -
400D ARG* 4.6 11.3 + - - -
58G GLY* 3.0 26.4 + - - +
59G GLU* 5.7 0.2 - - - -
61G MET* 1.3 76.4 - - - +
63G GLN* 1.3 59.8 + - + +
65G ALA* 3.0 11.5 + - - +
66G PHE* 3.0 49.9 + - + -
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Residues in contact with GLN 63 (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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59G GLU* 4.2 18.2 - - - +
60G LEU* 3.0 13.9 + - + +
62G ASP* 1.3 74.6 - - + +
64G ASN* 1.3 58.3 + - - +
66G PHE* 3.0 20.6 + - - +
67G SER* 2.9 35.0 + - - -
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Residues in contact with ASN 64 (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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519A TYR* 2.8 37.8 + - - -
522A TYR* 3.3 24.7 + - - -
523A VAL* 3.6 18.2 - - - +
530A ARG* 5.8 0.7 + - - -
666A ASP 3.5 12.9 + - - -
667A THR 5.2 0.2 - - - -
668A GLN* 2.2 26.2 + - - +
60G LEU* 2.5 28.0 + - + +
61G MET* 3.0 15.4 + - - +
63G GLN* 1.3 72.6 - - - +
65G ALA* 1.3 50.3 + - - +
67G SER 4.1 5.2 + - - -
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Residues in contact with ALA 65 (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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666A ASP 5.6 2.2 - - - +
667A THR* 3.7 16.2 - - - +
668A GLN* 2.7 29.1 + - - -
670A MET* 5.8 1.1 - - + -
671A ALA* 3.1 39.1 - - + +
61G MET 2.6 15.0 + - - +
62G ASP* 3.0 18.6 + - - +
64G ASN* 1.3 69.9 - - - +
66G PHE* 1.3 57.4 + - + +
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Residues in contact with PHE 66 (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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668A GLN* 3.2 12.2 + - - +
671A ALA* 3.8 20.9 - - + -
62G ASP* 3.0 31.8 + - + +
63G GLN* 3.0 24.4 + - - +
65G ALA* 1.3 86.4 - - + +
67G SER* 1.3 63.4 + - - +
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Residues in contact with SER 67 (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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526A LYS* 4.8 12.8 - - - +
530A ARG* 3.6 32.8 + - - +
668A GLN* 3.3 12.6 + - - +
63G GLN* 2.9 16.5 + - - -
64G ASN* 4.6 3.8 - - - -
66G PHE* 1.3 82.2 - - - +
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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