Contacts of the helix formed by residues 89 - 101 (chain C) in PDB entry 5O65
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 ALA 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C PRO* 1.3 75.0 + - - -
90C GLN* 1.3 66.9 + - - +
91C SER* 3.2 16.6 - - - +
92C VAL* 3.0 20.8 + - + +
93C SER* 3.1 12.5 + - - -
328C ASN 4.9 0.2 - - - +
329C GLU* 3.3 31.4 - - - +
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Residues in contact with GLN 90 (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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88C PRO* 4.4 0.4 - - - +
89C ALA* 1.3 73.9 - - - +
91C SER* 1.3 57.9 + - - +
93C SER* 3.2 8.1 + - - -
94C ASN* 2.8 39.3 + - - +
105C ASN* 5.9 0.7 - - - +
329C GLU* 3.4 27.7 + - - +
330C ARG* 4.2 13.0 - - - +
374C ALA* 3.5 21.0 - - + +
376C SER 3.2 27.5 + - - -
377C GLU* 3.6 36.6 + - + +
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ALA* 3.8 8.1 - - - +
90C GLN* 1.3 76.0 - - - +
92C VAL* 1.3 62.4 + - - +
94C ASN* 3.7 6.3 - - - +
95C LEU* 2.8 35.2 + - - +
326C ALA* 3.7 13.0 - - - +
328C ASN 2.7 28.7 + - - -
329C GLU 3.0 12.1 + - - -
330C ARG* 4.4 5.6 - - - +
331C MSE 3.5 27.6 - - - -
332C SER* 4.1 2.8 - - - -
372C THR* 4.8 1.3 - - - -
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PRO 4.8 6.3 - - - +
89C ALA* 3.0 24.9 + - + +
91C SER* 1.3 78.4 + - - +
93C SER* 1.3 64.5 + - - +
95C LEU* 3.3 9.6 + - + +
96C TYR* 3.0 50.6 + - + -
276C THR* 5.5 1.6 - - - +
326C ALA* 4.0 20.4 - - + -
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PRO 4.3 11.8 - - - -
89C ALA 3.1 12.7 + - - -
90C GLN* 3.5 10.4 - - - -
92C VAL* 1.3 77.6 - - - +
94C ASN* 1.3 62.5 + - - +
96C TYR* 3.4 6.0 + - - +
97C ASN* 3.0 30.7 + - - +
104C GLY 6.2 0.7 - - - -
105C ASN* 3.1 26.2 + - - -
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Residues in contact with ASN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLN* 2.8 28.4 + - - +
91C SER* 3.8 3.1 - - - +
93C SER* 1.3 72.9 - - - +
95C LEU* 1.3 61.7 + - - +
97C ASN* 3.4 11.7 + - - +
98C GLU* 3.0 24.8 + - - +
105C ASN* 3.2 23.4 + - - +
330C ARG 4.9 0.4 + - - -
372C THR* 3.6 25.4 + - + +
374C ALA* 3.8 25.5 - - - +
380C THR* 3.3 31.0 + - + +
405C TYR* 4.8 0.9 + - - -
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Residues in contact with LEU 95 (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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91C SER 2.8 15.2 + - - +
92C VAL* 3.6 17.0 - - + +
94C ASN* 1.3 79.3 - - - +
96C TYR* 1.3 66.1 + - + +
98C GLU* 3.3 7.2 + - - +
99C ALA* 2.9 35.7 + - + +
281C VAL* 3.8 35.0 - - + -
283C PHE* 5.7 0.2 - - + -
324C ALA* 3.7 24.2 - - + -
325C PHE 4.0 3.6 - - - -
326C ALA* 3.9 28.3 - - + +
332C SER* 3.6 25.1 - - - +
372C THR* 4.1 0.8 + - - -
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Residues in contact with TYR 96 (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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92C VAL* 3.0 43.6 + - + +
93C SER* 3.8 5.8 - - - +
95C LEU* 1.3 79.7 - - + +
97C ASN* 1.3 58.9 + - - +
99C ALA* 4.0 3.5 - - - +
100C SER* 2.7 43.8 + - - +
102C PHE 4.7 0.4 - - - +
217C GLU* 2.4 31.5 + - - -
223C ASP* 3.8 23.1 - - + -
274C VAL* 3.3 30.5 - - + -
275C LYS 3.8 0.3 - - - -
276C THR* 2.6 33.9 + - - -
281C VAL* 4.0 12.6 - - + -
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Residues in contact with ASN 97 (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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93C SER* 3.0 19.9 + - - +
94C ASN* 3.5 16.3 + - - +
96C TYR* 1.3 76.3 - - - +
98C GLU* 1.3 59.4 + - - +
101C GLY* 2.8 31.9 + - - -
102C PHE 3.3 19.9 + - - +
103C PHE* 3.5 34.0 - - + +
104C GLY* 3.3 11.6 + - - -
105C ASN* 3.9 16.7 + - - +
405C TYR* 3.2 23.2 + - - -
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Residues in contact with GLU 98 (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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94C ASN 3.0 11.2 + - - +
95C LEU* 3.3 9.9 - - - +
97C ASN* 1.3 82.6 - - - +
99C ALA* 1.3 62.6 + - - +
101C GLY* 4.0 4.2 + - - -
103C PHE* 4.3 13.4 - - - -
334C SER* 6.3 3.6 - - - -
371C MSE 5.5 0.2 - - - +
372C THR* 4.1 15.0 - - + +
382C VAL* 3.6 29.1 - - + +
401C LYS* 2.5 35.1 + - - -
503C LDA 4.9 8.3 + - - -
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Residues in contact with ALA 99 (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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95C LEU* 2.9 20.9 + - + +
96C TYR 4.0 1.1 - - - +
98C GLU* 1.3 77.1 - - - +
100C SER* 1.3 59.3 + - - +
272C SER* 4.1 4.9 + - - -
274C VAL* 4.0 19.8 - - + +
283C PHE* 3.8 46.0 - - + +
284C GLY 5.2 2.9 - - - +
285C SER* 5.3 0.7 - - - -
503C LDA 3.9 16.8 + - - -
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Residues in contact with SER 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 2.7 24.9 + - - +
99C ALA* 1.3 76.6 - - - +
101C GLY* 1.3 61.0 + - - +
102C PHE* 3.0 32.2 + - - +
213C LYS* 6.0 1.1 - - - -
223C ASP* 5.9 3.8 - - - -
225C VAL* 4.7 12.4 - - - +
272C SER* 3.3 28.9 + - - -
274C VAL* 4.0 11.2 - - - -
503C LDA 3.5 9.7 + - - -
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Residues in contact with GLY 101 (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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97C ASN 2.8 13.7 + - - -
98C GLU 4.0 3.0 + - - -
99C ALA 3.7 1.4 - - - -
100C SER* 1.3 78.5 - - - +
102C PHE* 1.3 56.0 + - - +
103C PHE* 3.7 16.1 - - - -
157C ARG* 4.8 1.4 + - - -
165C GLN* 3.1 19.9 + - - -
225C VAL* 6.2 0.7 - - - -
503C LDA 3.9 12.0 + - - -
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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