Contacts of the helix formed by residues 300 - 309 (chain A) in PDB entry 3FKS
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 VAL 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ALA* 4.6 9.9 - - + +
280A TYR* 4.9 2.7 - - + -
296A TYR* 3.7 22.7 - - + -
297A PRO* 3.5 24.4 + - + +
298A GLY 3.0 7.0 + - - +
299A ASP* 1.3 76.5 - - - +
301A PHE* 1.3 64.2 + - - +
303A LEU* 3.7 19.0 - - + +
304A HIS* 3.9 12.0 + - - -
339A TYR* 3.3 37.2 - - + +
340A ILE* 3.5 25.4 - - + +
343A ASN* 4.1 6.1 + - - +
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Residues in contact with PHE 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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298A GLY 4.1 1.0 + - - +
300A VAL* 1.3 79.4 - - + +
302A TYR* 1.3 60.1 + - - +
303A LEU 3.1 1.6 - - - -
304A HIS* 3.4 5.0 + - - +
305A SER* 2.9 38.2 + - - -
339A TYR* 5.3 2.7 - - - +
343A ASN* 3.6 38.6 - - + +
346A SER* 3.6 20.9 - - - -
347A ILE* 3.9 6.9 - - + +
222E MET* 3.3 33.9 - - + -
229E ARG* 3.8 19.7 - - - -
260E ARG* 5.2 4.3 - - - -
263E GLN* 3.6 30.1 - - - +
267E GLU* 3.3 26.7 - - - +
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Residues in contact with TYR 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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299A ASP* 3.9 27.4 - - + +
300A VAL 3.5 0.2 - - - -
301A PHE* 1.3 79.4 - - - +
303A LEU* 1.3 59.2 + - - +
305A SER* 3.8 4.7 - - - -
306A ARG* 3.0 69.5 + - + +
19E ALA* 6.3 2.0 - - + -
65E ASP* 5.4 0.2 + - - -
66E GLY* 4.7 11.1 + - - -
222E MET 4.3 4.9 - - - -
223E ASN 3.1 25.8 + - - -
224E GLU 3.9 0.9 - - - -
225E PRO* 3.3 43.0 - - + +
226E PRO* 4.1 14.1 - - + -
229E ARG* 3.8 16.2 - - - +
267E GLU* 4.3 2.6 + - - +
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Residues in contact with LEU 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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246A TYR* 3.5 23.3 - - + -
250A PHE* 3.4 44.1 - - + -
276A GLN* 3.6 16.2 - - - +
277A ALA* 4.5 7.4 - - - -
280A TYR* 3.9 29.2 - - + -
299A ASP 3.5 14.7 + - - +
300A VAL* 3.7 13.7 - - + +
301A PHE 3.1 0.2 - - - -
302A TYR* 1.3 81.8 - - - +
304A HIS* 1.3 84.9 + - + +
306A ARG* 3.8 13.0 - - - +
307A LEU* 3.4 14.4 + - - +
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Residues in contact with HIS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 3.4 47.2 + - + +
276A GLN* 3.5 17.1 + - - -
277A ALA* 4.1 13.9 + - + +
300A VAL 3.9 9.6 + - - +
301A PHE* 3.4 7.6 + - - +
303A LEU* 1.3 100.9 - - + +
305A SER* 1.3 59.1 - - - +
307A LEU* 3.7 6.5 - - - +
308A LEU* 3.1 37.8 + - + +
340A ILE* 4.5 8.2 - - + +
343A ASN* 6.1 2.7 - - + +
344A VAL* 3.2 28.8 - - + +
347A ILE* 4.2 12.3 - - + -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 2.9 26.6 + - - -
302A TYR* 4.0 8.5 - - - -
304A HIS* 1.3 75.6 - - - +
306A ARG* 1.3 66.1 + - - +
309A GLU* 3.2 31.2 + - - +
347A ILE* 3.9 17.0 - - - +
222E MET* 2.7 46.4 + - - +
223E ASN* 4.4 1.7 - - - -
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Residues in contact with ARG 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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52A GLU* 4.4 9.1 + - - -
132A GLN* 3.2 35.0 + - - +
133A VAL 5.2 0.2 - - - +
135A ALA* 5.0 2.3 - - - +
246A TYR* 3.7 19.0 + - - -
250A PHE* 3.9 10.2 - - + -
280A TYR* 5.3 3.8 + - - -
299A ASP* 5.0 6.9 + - - -
302A TYR* 3.0 68.5 + - + +
303A LEU* 3.6 29.3 - - - +
305A SER* 1.3 79.2 - - - +
307A LEU* 1.3 59.9 - - - +
309A GLU* 4.3 1.6 - - - +
310A ARG* 3.0 28.9 + - - +
68E GLU* 4.7 8.1 + - - -
223E ASN* 4.4 9.9 - - - +
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Residues in contact with LEU 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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249A PRO* 3.7 34.8 - - + +
250A PHE* 3.8 16.8 - - + +
253A ALA* 3.7 10.8 - - + -
270A TYR* 3.2 49.6 + - + +
273A LEU* 3.7 26.2 - - + -
276A GLN* 4.5 3.6 - - - +
303A LEU 3.4 10.3 + - - +
304A HIS* 3.7 7.9 - - - +
305A SER 3.2 0.4 - - - -
306A ARG* 1.3 79.0 - - - +
308A LEU* 1.3 68.1 + - + +
310A ARG* 2.9 28.0 + - - +
311A ALA* 4.1 1.2 + - - +
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Residues in contact with LEU 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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166A ARG* 2.9 30.3 + - + -
270A TYR* 4.2 20.4 - - + -
273A LEU* 4.5 10.8 - - + -
304A HIS* 3.1 19.5 + - + +
307A LEU* 1.3 75.7 - - + +
309A GLU* 1.3 57.3 + - - +
310A ARG 2.9 10.9 + - - -
311A ALA* 2.9 15.4 + - - +
325A ALA* 4.2 12.6 - - + -
327A PRO* 3.9 25.1 - - + -
344A VAL* 3.9 27.6 - - + -
347A ILE* 4.3 21.1 - - + -
348A THR* 4.0 12.8 - - + -
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Residues in contact with GLU 309 (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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135A ALA* 3.2 7.0 - - - +
141A ARG* 3.0 28.1 + - - -
166A ARG* 3.3 33.0 + - - +
305A SER* 3.2 31.0 + - - +
306A ARG 4.5 0.2 - - - +
308A LEU* 1.3 74.3 - - - +
310A ARG* 1.3 56.6 + - - +
311A ALA 3.3 2.2 - - - -
347A ILE* 3.9 15.0 - - + +
190E ARG* 4.5 7.5 - - - +
191E THR* 2.9 43.7 + - - -
222E MET* 4.3 10.2 - - + +
223E ASN* 3.8 23.9 - - + +
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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