Contacts of the helix formed by residues 301 - 310 (chain C) in PDB entry 3OFN
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 PHE 301 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299C ASP* 2.9 2.4 - - - -
300C VAL* 1.3 79.8 - - - +
302C TYR* 1.3 57.3 + - + +
303C LEU 3.2 1.1 - - - -
304C HIS* 2.9 8.4 + - - +
305C SER* 2.7 50.8 + - - -
339C TYR* 5.1 2.2 + - - +
343C ASN* 3.7 36.1 - - + +
346C SER* 4.5 11.2 - - - -
347C ILE* 3.6 28.9 - - + -
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Residues in contact with TYR 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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299C ASP* 3.0 30.9 + - + +
301C PHE* 1.3 79.8 - + + +
303C LEU* 1.3 65.9 + - - +
305C SER* 3.2 15.3 - - - -
306C ARG* 2.8 76.6 + - + +
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Residues in contact with LEU 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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246C TYR* 3.4 35.0 - - + +
250C PHE* 3.3 25.4 - - + -
276C GLN* 3.4 24.7 - - - +
277C ALA* 4.4 8.3 - - - -
280C TYR* 3.8 25.4 - - + -
299C ASP* 3.2 12.8 + - - +
300C VAL* 4.2 15.7 - - + -
302C TYR* 1.3 80.4 - - - +
304C HIS* 1.3 90.9 + - + +
306C ARG* 3.5 13.3 - - - +
307C LEU* 3.4 8.1 + - - +
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Residues in contact with HIS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU* 3.5 41.7 + - + +
276C GLN* 3.5 21.3 + - - -
277C ALA* 4.1 4.3 - - + -
300C VAL 3.8 11.9 + - - -
301C PHE* 2.9 5.9 + - - +
303C LEU* 1.3 94.9 - - + +
305C SER* 1.3 61.5 + - - +
307C LEU* 3.3 6.2 + - + +
308C LEU* 2.8 38.0 + - + +
340C ILE* 3.7 26.7 - - + +
343C ASN* 5.2 1.4 - - - +
344C VAL* 3.4 22.0 - - + +
347C ILE* 3.6 18.8 - - + +
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Residues in contact with SER 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C PHE* 2.7 33.7 + - - -
302C TYR* 3.2 26.2 - - - -
304C HIS* 1.3 73.5 - - - +
306C ARG* 1.3 63.5 + - - +
308C LEU* 4.0 0.5 - - - +
309C GLU* 3.1 34.4 + - - +
347C ILE* 3.6 25.0 - - - +
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Residues in contact with ARG 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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52C GLU* 5.6 3.8 + - - -
132C GLN* 3.2 36.5 + - - +
133C VAL 6.1 0.7 - - - -
135C ALA* 4.8 2.1 - - - +
246C TYR* 3.8 21.0 + - - -
250C PHE* 3.8 13.3 - - + -
280C TYR* 5.7 3.6 + - - -
299C ASP* 5.3 4.4 + - - -
302C TYR* 2.8 66.1 + - + +
303C LEU* 3.5 12.4 + - - +
305C SER* 1.3 79.6 + - - +
307C LEU* 1.3 69.5 + - - +
309C GLU* 3.5 10.8 + - - +
310C ARG* 3.6 17.6 + - - +
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Residues in contact with LEU 307 (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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249C PRO* 3.4 37.2 - - + +
250C PHE* 3.5 28.7 - - + -
253C ALA* 4.4 4.4 - - + +
270C TYR* 3.6 33.7 + - + +
273C LEU* 3.7 32.3 - - + -
276C GLN* 4.5 4.3 - - - +
303C LEU 3.4 4.9 + - - +
304C HIS* 3.3 10.3 + - + +
306C ARG* 1.3 82.8 - - - +
308C LEU* 1.3 73.5 + - + +
310C ARG* 3.3 24.7 + - - +
311C ALA* 4.3 1.4 + - - +
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Residues in contact with LEU 308 (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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166C ARG* 2.7 43.3 + - + +
270C TYR* 3.7 33.7 - - + -
273C LEU* 3.9 22.0 - - + -
304C HIS* 2.8 24.6 + - + +
307C LEU* 1.3 75.6 - - + +
309C GLU* 1.3 58.1 + - - +
310C ARG 3.2 2.0 + - - -
311C ALA* 3.7 4.8 + - - +
325C ALA* 3.9 16.2 - - + -
327C PRO* 4.0 17.9 - - + -
344C VAL* 4.3 10.8 - - + -
347C ILE* 3.4 27.8 - - + -
348C THR* 4.3 2.9 - - + -
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Residues in contact with GLU 309 (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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135C ALA* 3.4 19.8 - - + +
136C PRO* 4.0 0.2 - - - +
141C ARG* 3.1 33.1 + - - -
166C ARG* 3.7 21.8 + - - +
305C SER* 3.1 25.0 + - - +
306C ARG* 3.9 5.6 - - - +
307C LEU 3.3 0.6 - - - -
308C LEU* 1.3 77.5 - - - +
310C ARG* 1.3 61.8 + - - +
311C ALA 3.2 4.5 + - - +
347C ILE* 5.7 0.9 - - + -
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Residues in contact with ARG 310 (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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131C ALA 3.1 19.2 + - - -
132C GLN* 4.1 2.6 + - - +
133C VAL* 3.7 32.7 + - - +
135C ALA* 4.2 15.0 - - + -
250C PHE* 3.3 24.4 + - - -
253C ALA* 3.6 12.2 - - + +
254C SER* 2.7 38.2 + - - +
257C GLU* 3.0 38.1 + - - +
260C ARG* 2.7 28.4 + - - +
306C ARG* 3.6 18.2 - - - +
307C LEU* 3.4 13.7 - - - +
308C LEU 3.2 1.0 - - - -
309C GLU* 1.3 75.6 - - - +
311C ALA* 1.3 59.1 + - - +
312C ALA 3.3 1.1 + - - -
323C LEU* 3.8 14.6 - - + +
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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