Contacts of the helix formed by residues 299 - 308 (chain B) in PDB entry 3C9G
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 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B LEU* 4.6 0.7 - - - -
297B ASN 4.3 1.8 - - - +
298B ILE* 1.3 92.6 - - + +
300B PHE* 1.3 68.3 + - - +
301B SER* 3.9 14.6 - - - +
302B ARG* 3.2 37.0 + - + +
303B PHE* 3.3 4.0 + - - +
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ILE* 3.6 31.6 - - + -
255B LEU* 3.8 20.4 - - + -
258B ARG* 3.0 73.3 - - + +
260B GLY 5.6 0.7 - - - -
263B VAL* 3.9 17.5 - - + -
295B LEU* 3.9 17.5 - - + +
299B PRO* 1.3 71.1 - - - +
301B SER* 1.3 61.6 + - - +
303B PHE* 2.6 28.8 + + - +
304B LEU* 2.9 31.6 + - + -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B PRO* 3.9 14.8 - - - +
300B PHE* 1.3 87.3 - - - +
302B ARG* 1.3 69.9 + - - +
304B LEU* 3.3 13.7 + - - +
305B ASP* 3.3 23.5 + - - +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ILE* 4.2 16.1 - - + +
299B PRO* 3.2 34.3 + - + +
300B PHE 3.1 0.6 - - - -
301B SER* 1.3 81.7 + - - +
303B PHE* 1.3 62.7 + - - +
305B ASP* 3.7 4.2 + - - +
306B TYR* 3.3 22.9 + - + +
316B PRO* 4.6 22.6 - - - +
317B VAL 4.9 15.8 - - - +
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Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 4.2 22.7 - - + -
234B LEU* 5.0 2.5 - - + -
254B ILE* 4.2 30.3 - - + -
263B VAL* 4.3 17.5 - - + -
293B PHE* 3.6 34.3 - + + -
295B LEU* 3.5 35.2 - - + -
298B ILE* 4.8 4.2 - - + +
299B PRO 3.3 5.4 + - - +
300B PHE* 2.6 20.3 + + - +
302B ARG* 1.3 73.5 - - - +
304B LEU* 1.3 63.5 + - - -
306B TYR* 3.2 7.3 + + - +
307B ILE* 3.2 51.7 + - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ARG* 3.6 52.9 - - + +
254B ILE* 3.4 28.3 - - + -
255B LEU* 3.4 28.7 - - + -
300B PHE* 2.9 28.4 + - + +
301B SER* 3.6 11.4 - - - +
303B PHE* 1.3 79.4 - - - +
305B ASP* 1.3 58.3 + - - +
307B ILE* 5.3 0.9 - - - -
308B ALA* 2.9 37.2 + - + +
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ARG* 3.2 24.9 + - - -
301B SER* 3.3 20.7 + - - +
302B ARG* 4.3 3.8 - - - +
303B PHE 3.3 0.4 - - - -
304B LEU* 1.3 77.5 - - - +
306B TYR* 1.3 61.6 + - - +
309B PRO* 3.1 33.4 - - + +
310B GLU* 3.9 6.1 + - - +
315B ARG* 4.3 1.4 - - - +
316B PRO* 3.5 30.2 - - + +
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Residues in contact with TYR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU* 4.6 18.2 - - + +
235B ASP* 4.6 7.1 + - - -
238B ARG* 3.1 59.2 + - - -
242B ARG* 3.0 19.5 + - - -
302B ARG* 3.3 18.1 + - + +
303B PHE* 3.2 9.7 + + - +
305B ASP* 1.3 78.4 - - - +
307B ILE* 1.3 76.1 + - + +
315B ARG* 4.9 0.5 - - - -
316B PRO* 3.5 21.5 - - + -
317B VAL* 3.7 29.8 + - + +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU* 4.3 13.7 - - + -
237B PHE* 4.1 24.7 - - + -
238B ARG* 4.2 9.2 - - + +
241B LEU* 3.7 22.1 - - + +
242B ARG* 3.0 27.9 + - - -
247B LEU* 3.8 3.5 - - - +
250B ALA* 5.0 0.9 - - + -
254B ILE* 4.6 17.3 - - + -
303B PHE* 3.2 51.1 + - + +
304B LEU* 4.4 0.7 - - - +
306B TYR* 1.3 100.0 - - + +
308B ALA* 1.3 67.3 + - + +
309B PRO* 3.6 0.9 - - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B LEU* 3.7 15.7 - - + +
250B ALA* 3.7 13.9 - - + -
251B ARG* 3.1 49.9 + - - +
304B LEU* 2.9 20.2 + - + +
307B ILE* 1.3 80.2 - - + +
309B PRO* 1.3 67.0 - - - +
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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