Contacts of the helix formed by residues 295 - 306 (chain C) in PDB entry 2OB1
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 PRO 295 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C LEU* 3.8 27.8 - - + -
293C GLN 3.7 8.3 - - - +
294C ILE* 1.3 91.8 - - + +
296C GLU* 1.3 65.1 + - - +
297C SER* 4.1 15.9 - - - +
298C GLU* 3.0 21.2 + - + +
299C ARG* 3.2 9.6 + - - -
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Residues in contact with GLU 296 (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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294C ILE 3.7 1.2 + - - -
295C PRO* 1.3 72.3 - - - +
297C SER* 1.3 52.2 + - - +
299C ARG* 3.1 37.5 + - - +
300C LYS* 2.8 35.6 + - + +
303C ARG* 3.0 30.1 + - - -
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Residues in contact with SER 297 (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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295C PRO* 3.2 11.9 - - - +
296C GLU* 1.3 78.4 - - - +
298C GLU* 1.3 64.2 + - - +
300C LYS* 3.5 10.2 - - - +
301C ARG* 2.8 28.1 + - - +
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Residues in contact with GLU 298 (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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27C SER* 2.7 21.8 + - - -
28C SER 5.7 0.3 + - - -
29C GLY* 5.8 1.9 + - - -
30C LEU* 4.1 14.4 - - + -
79C TYR* 2.6 30.5 + - - +
294C ILE* 3.6 8.1 - - + -
295C PRO* 3.0 20.2 + - + +
297C SER* 1.3 83.8 + - - +
299C ARG* 1.3 60.4 + - - +
300C LYS 3.2 0.2 - - - -
301C ARG* 2.9 41.8 + - - +
302C LEU* 2.8 36.4 + - - +
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Residues in contact with ARG 299 (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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76C TYR* 4.7 1.0 + - - -
290C PHE* 3.9 41.0 + - + -
291C ASN* 4.1 29.4 + - - +
294C ILE* 3.5 32.5 + - + -
295C PRO 3.2 5.5 + - - -
296C GLU* 3.1 34.4 + - - +
298C GLU* 1.3 76.7 - - - +
300C LYS* 1.3 61.1 + - - +
302C LEU* 3.5 5.5 + - - +
303C ARG* 3.0 45.4 + - - +
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Residues in contact with LYS 300 (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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296C GLU* 2.8 18.8 + - + +
297C SER* 3.5 9.9 - - - +
299C ARG* 1.3 73.8 - - - +
301C ARG* 1.3 67.1 + - - +
303C ARG* 3.2 36.6 + - - +
304C SER* 3.3 10.7 + - - -
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Residues in contact with ARG 301 (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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23C GLY 2.7 28.1 + - - -
24C TYR 2.8 23.2 + - - -
26C PRO 3.9 12.0 + - - -
27C SER* 4.0 3.6 - - - +
79C TYR* 3.7 2.2 - - - -
297C SER 2.8 21.5 + - - +
298C GLU* 2.9 41.0 + - - +
300C LYS* 1.3 71.8 - - - +
302C LEU* 1.3 78.8 + - - +
304C SER* 2.5 31.8 + - - +
305C LEU* 3.6 11.7 - - + +
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Residues in contact with LEU 302 (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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24C TYR* 3.6 34.4 + - + -
76C TYR* 3.6 35.8 + - + +
79C TYR* 3.7 36.3 - - + -
290C PHE* 5.0 5.2 - - + -
294C ILE* 5.6 0.2 - - + -
298C GLU 2.8 25.5 + - - +
299C ARG* 3.9 3.6 - - - +
301C ARG* 1.3 98.7 - - - +
303C ARG* 1.3 60.6 + - - +
305C LEU* 3.0 30.6 + - + +
306C GLN 3.8 5.4 + - - +
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Residues in contact with ARG 303 (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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53A LYS* 3.2 19.9 + - - -
76C TYR* 3.8 11.6 + - - +
290C PHE* 6.3 0.4 - - - -
296C GLU* 3.0 27.3 + - - -
299C ARG* 3.0 37.6 + - - +
300C LYS* 3.2 30.9 + - - +
302C LEU* 1.3 76.0 - - - +
304C SER* 1.3 60.3 + - - +
306C GLN 3.4 9.0 - - - +
308C LEU* 6.5 0.2 - - + -
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Residues in contact with SER 304 (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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50A ILE* 3.4 30.4 - - - +
53A LYS* 3.1 21.2 - - - +
300C LYS 3.3 8.8 + - - -
301C ARG* 2.5 27.4 + - - +
303C ARG* 1.3 76.3 - - - +
305C LEU* 1.3 68.1 + - - +
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Residues in contact with LEU 305 (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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50A ILE* 4.1 24.5 - - + +
53A LYS* 3.9 1.3 - - - -
60A PHE* 3.5 19.4 - - - -
22C VAL* 3.9 27.5 - - + +
23C GLY* 3.6 9.6 - - - +
24C TYR* 3.5 45.5 - - + +
301C ARG* 3.6 16.6 - - + +
302C LEU* 3.0 23.6 + - + +
304C SER* 1.3 90.3 - - - +
306C GLN* 1.3 67.3 + - + +
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Residues in contact with GLN 306 (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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53A LYS* 3.3 10.0 + - - +
60A PHE* 4.4 10.8 - - + -
64A ASP* 4.7 7.2 + - - +
68A ARG* 3.6 25.7 - - - +
22C VAL* 3.7 26.6 - - + +
24C TYR* 2.6 29.1 + - - +
70C SER* 5.5 0.2 + - - -
72C PRO* 3.3 23.6 - - + +
75C ASN* 3.0 25.8 + - - +
76C TYR* 5.4 3.2 + - - -
302C LEU 3.8 4.2 + - - +
303C ARG* 3.4 18.5 - - - +
305C LEU* 1.3 84.7 - - - +
307C PHE* 1.3 63.0 + - - +
308C LEU* 3.6 2.9 + - - +
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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