Contacts of the helix formed by residues 54 - 61 (chain C) in PDB entry 2OOR
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 GLY 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PRO* 1.3 74.9 - - - +
55C TYR* 1.3 65.0 + - - -
57C MET* 3.0 18.9 + - - +
58C ALA 3.5 0.5 + - - -
88C ALA* 4.5 0.4 - - - -
89C GLY 4.3 0.9 - - - -
95C MET* 3.4 18.4 - - - +
128C ILE 3.0 9.3 + - - -
129C GLY 3.2 11.9 - - - -
130C ALA* 3.7 6.0 - - - +
400C TXP 3.3 13.9 - - - -
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Residues in contact with TYR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA 4.7 0.5 + - - -
209B GLU* 3.3 24.6 + - - +
210B GLN* 3.4 28.6 + - + +
213B SER* 3.7 16.6 - - - -
54C GLY* 1.3 70.3 - - - -
56C GLY* 1.3 57.6 + - - +
58C ALA* 3.1 5.3 + - + -
59C VAL* 2.8 49.3 + - + +
89C GLY* 3.8 11.7 - - - +
90C ARG* 3.4 64.6 - - + +
94C HIS* 4.3 5.8 - + - -
129C GLY 3.0 3.8 + - - -
400C TXP 3.0 36.1 + + - +
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Residues in contact with GLY 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 1.3 70.3 - - - +
57C MET* 1.3 59.4 - - - +
59C VAL* 3.9 0.9 - - - -
60C ALA* 3.1 29.8 + - - +
129C GLY* 2.8 19.7 + - - -
191C ALA* 3.7 1.9 - - - +
400C TXP 3.4 46.2 + - - -
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Residues in contact with MET 57 (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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53C PRO* 3.5 23.3 - - + -
54C GLY 3.0 12.4 + - - +
56C GLY* 1.3 75.3 - - - +
58C ALA* 1.3 58.4 + - - +
60C ALA 3.9 0.2 - - - -
61C GLN* 3.0 6.9 + - - -
62C ALA* 3.0 30.3 + - + -
63C GLN* 3.4 40.1 - - + +
66C LEU* 3.6 16.4 - - + -
95C MET* 3.6 15.5 - - + -
98C LEU* 5.3 1.8 - - + -
99C LEU* 3.7 22.0 - - + -
128C ILE* 3.5 39.5 - - + +
129C GLY* 3.7 4.6 - - - -
191C ALA* 4.5 8.1 - - - -
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Residues in contact with ALA 58 (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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213B SER* 3.4 9.3 - - - +
54C GLY 3.5 3.9 + - - +
55C TYR* 3.1 12.4 + - + +
57C MET* 1.3 77.9 - - - +
59C VAL* 1.3 65.9 + - - +
61C GLN* 2.8 27.9 + - - +
94C HIS* 3.3 26.2 - - + +
95C MET* 4.5 3.1 - - + +
98C LEU* 3.3 31.6 - - + +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLU* 4.0 28.9 - - + +
212B GLU* 5.1 4.2 - - - +
213B SER* 3.7 10.4 - - - +
55C TYR* 2.8 61.6 + - + +
56C GLY 4.0 1.1 - - - +
58C ALA* 1.3 74.0 - - - +
60C ALA* 1.3 59.0 + - - +
61C GLN* 3.5 4.7 + - - +
165C ARG* 5.3 2.5 - - - +
400C TXP 3.5 35.0 - - - +
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Residues in contact with ALA 60 (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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56C GLY 3.1 18.8 + - - +
57C MET 4.2 1.8 - - - +
59C VAL* 1.3 76.0 - - - +
61C GLN* 1.3 68.4 + - - +
62C ALA* 4.2 0.7 - - + -
190C ASP* 3.4 25.2 - - - +
191C ALA* 3.8 6.1 - - + -
192C LYS* 3.5 32.1 - - - +
400C TXP 3.6 11.2 - - - +
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Residues in contact with GLN 61 (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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212B GLU 4.1 11.7 - - - +
213B SER 2.8 35.0 + - - -
214B LEU 4.9 0.2 - - - -
215B GLY* 4.1 12.1 + - - +
57C MET 3.0 7.7 + - - -
58C ALA 2.8 19.3 + - - +
59C VAL 4.4 3.1 - - - +
60C ALA* 1.3 80.3 - - - +
62C ALA* 1.3 57.8 + - - +
63C GLN* 3.0 39.4 + - - +
64C HIS* 4.6 8.7 + - + +
65C ALA 5.6 0.2 + - - -
98C LEU* 4.0 6.7 - - - +
101C GLU* 4.3 10.2 - - - +
192C LYS* 3.7 16.1 - - + +
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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