Contacts of the helix formed by residues 89 - 99 (chain C) in PDB entry 3COG
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 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C PHE* 3.2 2.6 - - - +
88C ALA* 1.3 77.9 - - - +
90C GLY* 1.3 66.0 + - - +
91C LEU 3.5 1.9 + - - -
92C ALA* 2.9 21.8 + - - +
93C ALA 3.0 18.0 + - - -
221C VAL* 3.6 13.5 - - - -
222C MET* 3.6 5.4 - - - +
223C GLY* 3.2 18.4 - - - +
500C PLP 3.3 12.6 + - - -
62D ARG* 4.1 5.2 - - - -
244D GLY* 2.6 29.6 + - - -
246D VAL* 4.7 0.2 - - - -
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Residues in contact with GLY 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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89C SER* 1.3 70.8 - - - +
91C LEU* 1.3 61.3 + - - +
93C ALA* 3.2 2.3 + - - +
94C THR* 3.0 23.8 + - - -
207C MET* 3.2 22.1 - - - +
209C SER* 3.9 5.6 - - - -
222C MET 3.5 4.2 + - - -
223C GLY* 3.8 10.3 - - - -
500C PLP 2.9 28.8 + - - -
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Residues in contact with LEU 91 (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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89C SER* 3.8 4.7 - - - +
90C GLY* 1.3 76.4 - - - +
92C ALA* 1.3 56.8 + - - +
94C THR* 3.1 10.5 + - - +
95C VAL* 2.9 33.0 + - + +
114C TYR* 4.1 9.6 - - + -
116C GLY* 3.7 29.8 - - - +
117C THR* 4.0 8.5 - - - +
119C ARG* 3.8 13.0 - - - +
120C TYR* 5.1 3.1 - - + -
500C PLP 2.9 19.5 + - - +
62D ARG* 3.2 32.3 - - - +
241D ASN 3.4 16.4 - - - +
242D SER 3.6 14.6 - - - +
243D LEU 3.7 9.4 - - - +
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Residues in contact with ALA 92 (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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87C PHE* 4.4 2.0 - - + -
88C ALA 4.3 3.6 - - - +
89C SER* 2.9 30.6 + - - +
91C LEU* 1.3 73.0 - - - +
93C ALA* 1.3 57.4 + - - +
95C VAL* 3.6 4.0 + - - +
96C THR* 2.6 38.4 + - - -
245C ALA* 3.7 27.6 - - + +
243D LEU 3.4 10.7 + - - +
244D GLY 3.6 11.2 - - - +
245D ALA* 4.9 0.2 - - + -
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Residues in contact with ALA 93 (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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87C PHE* 3.8 29.5 - - + +
89C SER 3.0 11.7 + - - +
90C GLY* 3.2 12.3 - - - +
92C ALA* 1.3 77.6 - - - +
94C THR* 1.3 57.0 + - - +
96C THR* 3.3 1.9 + - - -
97C ILE* 2.9 36.8 + - - +
207C MET* 4.3 11.9 - - + -
223C GLY* 4.4 5.2 - - - -
224C LEU 4.4 0.7 - - - +
225C VAL* 3.8 14.5 - - + +
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Residues in contact with THR 94 (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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90C GLY 3.0 14.4 + - - -
91C LEU* 3.1 16.2 + - + +
93C ALA* 1.3 74.0 - - - +
95C VAL* 1.3 63.6 + - - +
97C ILE* 3.5 2.6 + - - +
98C THR* 2.8 29.3 + - - -
117C THR* 4.7 12.5 + - + +
120C TYR* 4.0 22.4 - - + -
121C PHE* 4.0 17.3 - - + -
155C TRP* 3.4 38.5 - - + -
207C MET* 3.6 5.0 - - - +
500C PLP 5.5 0.3 - - - -
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Residues in contact with VAL 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 LEU* 2.9 19.5 + - + +
92C ALA* 3.8 6.3 - - - +
93C ALA 3.4 0.2 - - - -
94C THR* 1.3 75.2 - - - +
96C THR* 1.3 62.5 + - - +
98C THR* 3.2 3.3 + - - -
99C HIS* 2.8 52.0 + - + +
120C TYR* 3.7 35.4 - - + +
243C LEU* 5.0 4.3 - - + -
95D VAL* 5.4 3.6 - - + -
99D HIS* 4.7 3.1 - - + +
242D SER 4.6 0.9 - - - +
243D LEU* 3.7 41.5 - - + +
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Residues in contact with THR 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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87C PHE* 3.7 36.4 - - + -
92C ALA 2.6 23.0 + - - -
93C ALA 3.7 4.0 - - - -
94C THR 3.2 0.2 - - - -
95C VAL* 1.3 76.8 - - - +
97C ILE* 1.3 63.4 + - - +
99C HIS* 3.1 16.1 + - - +
100C LEU* 4.4 0.3 - - - +
236C LEU* 4.6 7.3 - - + +
239C LEU* 3.5 42.8 - - + +
240C GLN 4.1 0.7 - - - +
243C LEU* 4.1 15.7 - - + +
245C ALA* 4.6 7.1 - - - +
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Residues in contact with ILE 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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87C PHE* 6.1 0.2 - - + -
93C ALA 2.9 21.3 + - - +
94C THR 3.8 4.0 - - - +
96C THR* 1.3 76.3 - - - +
98C THR* 1.3 57.1 + - - +
100C LEU* 2.9 34.1 + - + +
101C LEU* 4.4 1.7 + - - +
153C LEU* 4.4 13.8 - - + +
155C TRP* 3.8 28.9 - - + -
183C ILE* 5.8 0.2 - - - +
185C VAL* 3.9 20.4 - - + -
205C ILE* 4.1 28.3 - - + -
207C MET* 4.3 3.8 - - + -
225C VAL* 3.8 23.3 - - + -
236C LEU* 4.0 23.1 - - + -
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Residues in contact with THR 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 THR 2.8 20.1 + - - -
95C VAL 3.5 1.1 - - - -
97C ILE* 1.3 77.5 - - - +
99C HIS* 1.3 56.6 + - + +
100C LEU 3.1 0.2 - - - -
101C LEU* 3.1 26.1 + - - +
107C ILE* 3.8 14.6 - - + -
120C TYR* 3.2 30.9 - - + +
121C PHE* 3.3 22.5 - - - -
125C ALA* 4.2 1.3 - - + -
130C LEU* 3.7 25.4 - - + -
153C LEU* 4.3 9.1 - - - +
155C TRP* 5.4 0.2 - - - -
128D PHE* 4.2 4.9 - - + -
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Residues in contact with HIS 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 VAL* 2.8 46.9 + - + +
96C THR 3.1 11.1 + - - +
98C THR* 1.3 73.4 - - + +
100C LEU* 1.3 59.8 + - - +
101C LEU 3.1 2.9 + - - +
120C TYR* 4.5 5.5 + - - -
239C LEU* 3.5 19.0 - - + +
243C LEU* 3.6 18.2 - - + +
602C GOL 2.7 30.0 + - - -
95D VAL* 4.7 1.7 - - + +
99D HIS* 3.6 29.4 + + - -
120D TYR* 4.8 3.8 + - - -
124D VAL* 3.7 26.9 - - + +
125D ALA* 6.3 0.2 - - - -
128D PHE* 3.7 23.9 - + - -
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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