Contacts of the helix formed by residues 80 - 89 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C VAL 3.7 1.8 + - - -
79C ASP* 1.3 78.4 - - - +
81C HIS* 1.3 67.5 + - - +
82C PHE* 3.4 7.2 + - - +
83C SER* 3.1 24.0 + - - -
84C HIS* 3.0 20.3 + - - -
106C SER* 3.7 2.7 - - - -
108C PRO* 4.3 20.7 - - - +
82E PHE* 3.8 23.7 - - - +
83E SER* 5.8 1.4 + - - +
86E ALA* 4.8 5.2 - - - -
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Residues in contact with HIS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ARG* 6.4 0.4 - - - +
161A GLN* 4.7 11.0 + - - -
18C THR* 3.9 26.5 + - + +
19C ALA 5.6 0.2 - - - -
20C VAL* 3.6 9.6 - - + +
26C PHE* 3.4 45.9 - + + -
80C SER* 1.3 75.5 - - - +
82C PHE* 1.3 86.8 + + - +
84C HIS* 3.3 7.8 + - + +
85C LEU 3.0 21.7 + - - -
106C SER* 3.5 23.5 + - - +
108C PRO* 5.3 1.4 - - - +
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ARG* 5.3 1.1 - - - -
161A GLN* 3.6 48.5 - - + -
162A ALA* 4.5 4.9 - - - -
165A PHE* 3.4 41.2 - + + -
26C PHE* 3.6 31.2 - + - -
80C SER* 3.2 6.1 + - - +
81C HIS* 1.3 103.6 - + - +
83C SER* 1.3 64.9 + - - +
85C LEU* 3.3 8.0 + - + +
86C ALA* 3.0 22.7 + - - +
82E PHE* 3.9 20.6 - - + -
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ASP* 2.5 31.6 + - - -
80C SER* 3.1 21.6 + - - -
82C PHE* 1.3 74.3 - - - +
84C HIS* 1.3 65.6 + - - +
86C ALA* 3.0 3.3 + - - +
87C TRP* 2.9 36.2 + - - -
201D CPS 5.0 1.9 - - - +
80E SER* 4.9 3.0 + - - -
82E PHE* 3.6 32.8 - - - -
83E SER* 6.2 0.4 - - - -
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Residues in contact with HIS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 3.7 13.7 - - + -
48C PHE* 3.5 27.8 - + - -
76C ALA 4.9 0.4 - - - -
77C SER* 2.9 30.7 + - - -
79C ASP* 3.6 11.6 - - + +
80C SER 3.0 8.7 + - - -
81C HIS* 3.5 8.3 - - - +
82C PHE 3.3 0.2 - - - -
83C SER* 1.3 78.0 - - - +
85C LEU* 1.3 63.9 + - - +
87C TRP* 3.2 6.7 + - - +
88C VAL* 3.0 28.1 + - - +
104C LEU* 3.8 33.8 - - + +
105C VAL 3.1 21.4 + - - -
106C SER* 3.7 24.0 - - - -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 3.6 31.0 - - + -
172A VAL* 3.7 33.7 - - + -
174A PRO* 4.5 2.5 - - + -
20C VAL* 4.3 5.4 - - + -
24C GLY* 3.9 20.0 - - - +
26C PHE* 4.0 26.9 - - + -
81C HIS 3.0 13.2 + - - +
82C PHE* 3.6 13.9 - - + +
84C HIS* 1.3 73.5 - - - +
86C ALA* 1.3 62.3 + - - +
88C VAL* 3.4 14.7 + - + +
89C ASN* 2.9 33.3 + - + +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 4.1 17.0 - - + -
169A HIS* 5.0 2.7 - - + +
82C PHE 3.0 13.7 + - - +
83C SER 3.5 7.0 - - - +
85C LEU* 1.3 77.1 - - - +
87C TRP* 1.3 55.6 + - - +
89C ASN* 3.3 6.5 + - - +
90C THR* 2.7 33.1 + - - -
201D CPS 3.9 27.1 - - + -
82E PHE* 4.0 11.4 - - + -
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Residues in contact with TRP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ASP* 5.3 0.4 + - - -
48C PHE* 3.5 35.0 - + + +
49C THR* 3.5 29.6 - - + +
53C PRO* 4.4 11.2 - - + -
79C ASP* 4.1 6.6 + - - -
83C SER* 2.9 35.4 + - - -
84C HIS* 3.2 8.7 + - - +
86C ALA* 1.3 77.9 - - - +
88C VAL* 1.3 62.3 + - - +
90C THR* 3.1 11.6 + - - +
95C GLY 3.4 23.1 - - - -
96C GLY* 3.9 14.8 - - - -
97C LEU* 3.1 45.9 + - + -
176D GLY* 4.5 8.3 - - - -
201D CPS 3.6 57.0 - - + +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PRO* 3.8 29.4 - - + +
20C VAL* 4.1 15.9 - - + -
22C PRO 6.0 1.1 - - - +
24C GLY* 5.4 0.4 - - - +
84C HIS 3.0 15.3 + - - +
85C LEU* 3.5 15.5 - - + +
87C TRP* 1.3 77.9 - - - +
89C ASN* 1.3 59.6 + - - +
90C THR 3.1 3.2 + - - -
97C LEU* 4.2 4.9 - - + -
98C GLY* 3.2 35.6 - - - +
99C PRO* 3.7 2.7 - - + -
100C MET* 3.7 19.5 - - + +
104C LEU* 3.6 27.1 - - + -
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Residues in contact with ASN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 5.3 5.2 - - + -
169A HIS* 6.1 1.6 - - - +
170A GLY 5.2 2.4 + - - +
171A GLU 3.0 24.0 + - - -
172A VAL* 3.8 10.4 - - + +
173A CYS 2.7 38.5 + - - +
174A PRO* 3.2 10.1 - - + +
85C LEU* 2.9 22.5 + - + +
86C ALA* 3.6 7.4 - - - +
87C TRP 3.2 0.2 - - - -
88C VAL* 1.3 75.5 - - - +
90C THR* 1.3 57.4 + - - +
91C PRO* 3.8 7.0 - - - +
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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