Contacts of the helix formed by residues 80 - 89 (chain F) in PDB entry 4XCS
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 SER 80 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78F VAL 3.7 1.4 + - - -
79F ASP* 1.3 77.8 - - - +
81F HIS* 1.3 66.8 + - - +
82F PHE* 3.5 8.4 + - - +
83F SER* 3.1 23.5 + - - -
84F HIS* 3.0 20.8 + - - -
106F SER* 3.6 3.4 - - - -
108F PRO* 4.2 20.3 - - - +
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Residues in contact with HIS 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F THR* 3.8 26.3 + - + +
20F VAL* 3.5 13.8 - - + +
26F PHE* 3.3 46.9 - + + -
80F SER* 1.3 76.3 - - - +
82F PHE* 1.3 86.7 + + - +
84F HIS* 3.4 4.6 + - - -
85F LEU 3.0 21.3 + - - -
106F SER* 3.5 23.4 + - - +
108F PRO* 5.3 0.8 - - - +
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Residues in contact with PHE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PHE* 3.6 29.8 - + - -
80F SER* 3.2 5.9 + - - +
81F HIS* 1.3 109.5 - + - +
83F SER* 1.3 58.8 + - - +
85F LEU* 3.8 14.6 - - + +
86F ALA* 3.0 28.4 + - - +
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Residues in contact with SER 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E CPS 5.7 6.1 - - - -
79F ASP* 2.7 44.5 + - - +
80F SER* 3.1 20.8 + - - -
82F PHE* 1.3 71.9 - - - +
84F HIS* 1.3 66.8 + - - +
86F ALA* 3.1 8.3 + - - +
87F TRP* 2.9 32.3 + - - -
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Residues in contact with HIS 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F VAL* 3.8 14.1 - - + +
48F PHE* 3.4 32.2 - + - -
76F ALA* 4.9 0.4 - - - -
77F SER* 2.8 24.8 + - - -
79F ASP* 3.5 15.0 - - + +
80F SER 3.0 9.1 + - - -
81F HIS* 3.6 8.2 - - - +
82F PHE 3.3 0.2 - - - -
83F SER* 1.3 78.8 + - - +
85F LEU* 1.3 63.2 + - - +
87F TRP* 3.2 5.4 + - - +
88F VAL* 3.0 27.2 + - - +
104F LEU* 3.9 24.9 + - + +
105F VAL 3.1 31.4 - - - -
106F SER* 3.7 19.7 - - - -
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F VAL* 4.0 14.1 - - + +
24F GLY* 3.6 27.8 - - - +
26F PHE* 3.8 25.4 - - + -
81F HIS 3.0 17.1 + - - +
82F PHE* 3.8 16.6 - - + +
83F SER 3.2 0.2 - - - -
84F HIS* 1.3 75.5 - - - +
86F ALA* 1.3 62.1 + - - +
88F VAL* 3.3 11.2 + - + +
89F ASN* 2.9 32.7 + - + +
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E CPS 3.9 27.1 - - + -
82F PHE 3.0 17.9 + - - +
83F SER* 3.1 7.6 + - - +
85F LEU* 1.3 78.2 - - - +
87F TRP* 1.3 55.5 + - - +
89F ASN* 3.4 6.3 + - - +
90F THR* 2.6 34.6 + - - -
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Residues in contact with TRP 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E GLY* 4.5 7.6 - - - -
201E CPS 3.7 55.8 - - + +
47F ASP* 5.4 0.4 + - - -
48F PHE* 3.5 37.3 - + + +
49F THR* 3.6 33.9 - - + +
53F PRO* 4.4 11.4 - - + -
79F ASP* 4.0 12.9 + - - -
83F SER* 2.9 28.7 + - - +
84F HIS* 3.5 9.9 - - - +
86F ALA* 1.3 77.9 - - - +
88F VAL* 1.3 63.2 + - - +
90F THR* 3.1 11.4 + - - +
95F GLY 3.5 21.8 - - - -
96F GLY* 3.9 15.0 - - - -
97F LEU* 3.1 46.0 + - + -
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F VAL* 4.2 17.0 - - + -
22F PRO 6.2 0.2 - - - +
24F GLY* 5.6 3.6 - - - -
84F HIS 3.0 15.1 + - - +
85F LEU* 3.4 21.8 - - + +
87F TRP* 1.3 78.3 - - - +
89F ASN* 1.3 63.5 + - - +
90F THR 3.1 1.7 + - - -
97F LEU* 4.2 5.4 - - + -
98F GLY* 3.2 35.3 - - - +
99F PRO* 3.7 7.6 - - + +
100F MET* 3.8 17.7 - - + +
104F LEU* 3.6 27.4 - - + -
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Residues in contact with ASN 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F LEU* 2.9 25.6 + - + +
86F ALA* 3.6 7.2 - - - +
88F VAL* 1.3 79.7 - - + +
90F THR* 1.3 55.7 + - - +
91F PRO* 3.7 8.1 - - - +
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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