Contacts of the helix formed by residues 299 - 308 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ASN 4.3 3.8 - - - +
298A ILE* 1.3 88.6 - - + +
300A PHE* 1.3 66.3 + - - +
301A SER* 4.6 4.7 - - - +
302A ARG* 2.9 41.3 + - + +
303A PHE* 3.0 10.0 + - - +
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.2 38.9 + - + +
260A GLY 4.2 14.8 - - - +
261A LYS* 5.9 0.2 - - - -
295A LEU* 3.9 20.8 - - + +
298A ILE 3.4 2.8 + - - -
299A PRO* 1.3 71.7 - - - +
301A SER* 1.3 63.3 + - - +
303A PHE* 3.0 13.3 + - - +
304A LEU* 3.0 10.9 + - - +
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.7 11.5 - - - +
299A PRO* 3.2 4.7 - - - +
300A PHE* 1.3 79.6 - - - +
302A ARG* 1.3 61.1 + - - +
304A LEU* 3.6 8.3 - - - +
305A ASP* 3.5 26.2 + - - +
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ILE* 4.5 12.7 - - + +
299A PRO* 2.9 33.7 + - + +
301A SER* 1.3 78.2 - - - +
303A PHE* 1.3 63.8 + - - +
305A ASP* 3.6 6.4 + - - +
306A TYR* 3.2 23.9 + - + +
316A PRO* 4.6 23.4 - - + +
317A VAL 6.0 2.8 - - - -
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Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL* 4.0 17.7 - - + -
234A LEU* 4.1 10.1 - - + -
254A ILE* 4.6 20.2 - - + -
263A VAL* 4.6 7.9 - - + -
293A PHE* 3.7 47.1 - + + -
295A LEU* 3.6 43.1 - - + -
298A ILE* 4.9 6.9 - - + +
299A PRO 3.0 7.0 + - - +
300A PHE 3.0 9.6 + - - +
302A ARG* 1.3 77.4 - - - +
304A LEU* 1.3 64.7 + - - +
306A TYR* 2.9 20.5 + + - +
307A ILE* 3.0 37.5 + - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 3.3 72.2 - - + +
254A ILE* 3.7 24.9 - - + -
255A LEU* 4.1 24.0 - - + -
258A ARG* 4.7 6.7 - - - +
300A PHE 3.0 10.6 + - - +
301A SER* 3.6 12.6 - - - +
302A ARG 3.3 0.2 - - - -
303A PHE* 1.3 79.4 - - - +
305A ASP* 1.3 59.0 + - - +
306A TYR 3.0 1.6 + - - -
307A ILE* 5.3 1.8 - - - -
308A ALA* 2.7 36.5 + - + +
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ARG* 5.3 0.2 + - - -
242A ARG* 5.1 0.2 + - - -
251A ARG* 3.1 28.5 + - - -
301A SER* 3.5 15.7 + - - +
302A ARG* 4.0 8.0 - - - +
303A PHE 3.4 0.8 - - - -
304A LEU* 1.3 76.0 - - - +
306A TYR* 1.3 58.4 + - - +
309A PRO* 3.4 32.8 - - + +
310A GLU* 5.0 3.3 + - - +
314A GLY 4.7 1.3 - - - +
316A PRO* 4.0 18.4 - - + +
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Residues in contact with TYR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 4.2 20.6 - - + +
235A ASP* 4.7 9.2 + - - -
238A ARG* 2.7 81.2 + - - +
242A ARG* 3.2 2.6 + - - -
302A ARG* 3.2 14.8 + - + +
303A PHE* 2.9 17.5 + + - +
305A ASP* 1.3 80.3 - - - +
307A ILE* 1.3 71.5 + - + +
316A PRO* 4.1 27.6 - - + -
317A VAL* 4.3 17.8 - - - +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 3.8 24.7 - - + -
237A PHE* 3.7 17.5 - - + -
238A ARG* 3.5 25.1 - - + +
241A LEU* 3.5 25.8 - - + +
242A ARG* 3.1 27.0 + - - +
247A LEU* 3.8 5.0 - - - +
254A ILE* 4.5 15.9 - - + -
303A PHE* 3.0 37.1 + - + +
304A LEU* 4.2 1.1 - - - +
306A TYR* 1.3 93.7 - - + +
308A ALA* 1.3 59.2 + - + +
309A PRO* 3.5 2.7 - - - +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 3.7 11.0 - - + +
250A ALA* 3.9 11.9 - - + -
251A ARG* 2.9 60.1 + - + +
254A ILE* 4.5 7.6 - - + -
304A LEU* 2.7 16.2 + - + +
307A ILE* 1.3 77.0 - - + +
309A PRO* 1.3 65.1 - - - +
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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