Contacts of the helix formed by residues 301 - 309 (chain K) 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 PHE 301 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298K GLY 3.9 5.6 + - - +
299K ASP 3.1 0.4 - - - -
300K VAL* 1.3 83.1 - - + +
302K TYR* 1.3 60.0 + - - +
304K HIS* 3.1 7.9 + - - +
305K SER* 3.0 36.7 + - - -
339K TYR* 5.0 1.1 - - - +
343K ASN* 4.1 33.0 - - + +
346K SER* 3.4 20.4 - - - -
347K ILE* 3.9 12.9 - - + +
188O GLY 4.6 0.2 - - - -
222O MET* 4.0 21.1 - - + -
229O ARG* 3.9 15.7 - - - -
260O ARG* 3.2 34.8 - - - -
263O GLN* 3.2 42.4 - - - +
267O GLU* 5.2 0.7 - - - +
311O TYR* 5.8 0.4 - + - -
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Residues in contact with TYR 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299K ASP* 3.1 15.4 + - + +
301K PHE* 1.3 81.5 - - - +
303K LEU* 1.3 61.6 + - - +
304K HIS 3.3 0.2 + - - -
305K SER* 3.1 29.0 + - - -
306K ARG* 3.3 60.2 + - + +
222O MET 3.5 16.4 - - - -
223O ASN 3.9 6.1 + - - -
224O GLU 3.7 12.6 - - - -
225O PRO* 3.5 28.7 - - + +
226O PRO* 4.4 11.0 - - + -
229O ARG* 3.8 12.8 - - - +
267O GLU* 3.8 25.1 + - - +
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Residues in contact with LEU 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K TYR* 3.5 32.5 - - + -
250K PHE* 3.1 37.6 - - + -
276K GLN* 4.3 20.9 - - + +
277K ALA* 4.6 5.2 - - - -
280K TYR* 3.4 43.5 - - + -
299K ASP 3.1 10.3 + - - +
300K VAL* 3.2 17.3 - - + +
301K PHE 3.0 0.6 - - - -
302K TYR* 1.3 78.6 - - - +
304K HIS* 1.3 70.6 + - + +
306K ARG* 3.8 11.6 - - - +
307K LEU* 3.7 5.4 - - - +
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Residues in contact with HIS 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273K LEU* 3.8 34.1 + - + +
276K GLN* 3.3 28.1 + - - -
277K ALA* 4.2 21.9 - - + +
300K VAL* 3.4 24.8 + - + +
301K PHE* 3.1 4.3 + - - +
303K LEU* 1.3 82.8 - - + +
305K SER* 1.3 62.1 + - - +
306K ARG 3.4 1.3 - - - -
307K LEU* 3.7 6.1 - - + -
308K LEU* 2.9 42.7 + - + +
340K ILE* 4.8 7.6 - - + -
343K ASN* 5.4 5.6 - - + +
344K VAL* 4.3 19.0 - - + +
347K ILE* 3.5 16.9 - - + +
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Residues in contact with SER 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301K PHE* 3.0 24.8 + - - -
302K TYR* 3.1 21.3 + - - -
304K HIS* 1.3 79.1 - - - +
306K ARG* 1.3 59.6 + - - +
307K LEU 3.2 0.4 - - - -
309K GLU* 3.2 35.5 + - - +
347K ILE* 3.3 14.7 - - - +
222O MET* 2.9 39.5 + - - -
229O ARG* 4.6 0.2 + - - -
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Residues in contact with ARG 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K GLN* 3.1 42.8 + - - +
133K VAL 4.4 5.5 - - - +
135K ALA* 5.0 1.4 + - - +
246K TYR* 3.8 13.3 + - - -
250K PHE* 3.4 26.8 - - + -
280K TYR* 5.5 2.8 + - - -
299K ASP 5.4 0.2 + - - -
302K TYR* 3.3 72.5 + - + +
303K LEU* 3.8 14.6 - - - +
305K SER* 1.3 78.7 + - - +
307K LEU* 1.3 59.3 + - - +
309K GLU* 4.4 2.0 - - - +
310K ARG* 3.2 28.3 - - - +
223O ASN* 4.3 17.9 - - + +
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Residues in contact with LEU 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249K PRO* 3.4 45.5 - - + +
250K PHE* 3.5 33.4 - - + -
253K ALA* 4.1 5.4 - - + -
270K TYR* 3.6 25.8 + - + +
273K LEU* 3.9 20.2 - - + -
276K GLN* 4.2 8.7 - - - +
303K LEU 3.7 12.1 - - - +
304K HIS* 3.7 6.5 - - + +
305K SER 3.2 0.4 - - - -
306K ARG* 1.3 79.7 - - - +
308K LEU* 1.3 71.7 + - + +
309K GLU 3.3 0.9 - - - -
310K ARG* 3.4 19.5 + - - +
311K ALA* 4.4 1.7 + - - +
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Residues in contact with LEU 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K ARG* 3.0 26.8 - - + +
270K TYR* 4.2 17.3 - - + -
273K LEU* 4.0 13.2 - - + -
304K HIS* 2.9 25.1 + - + +
307K LEU* 1.3 79.6 - - + +
309K GLU* 1.3 61.4 + - - +
311K ALA* 3.2 15.6 + - - +
325K ALA* 4.9 3.8 - - + -
327K PRO* 3.4 25.8 - - + -
344K VAL* 4.0 14.6 - - + -
347K ILE* 3.7 29.2 - - + -
348K THR* 3.5 26.5 - - + -
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Residues in contact with GLU 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K ALA* 3.6 11.8 - - + +
141K ARG* 3.0 24.9 + - - +
166K ARG* 3.4 20.3 + - - +
305K SER 3.2 20.2 + - - +
306K ARG* 4.9 1.1 - - - -
307K LEU 3.3 1.0 - - - -
308K LEU* 1.3 73.1 - - - +
310K ARG* 1.3 57.2 + - - +
311K ALA 2.9 16.3 + - - +
347K ILE* 4.7 0.9 - - + -
190O ARG* 3.5 2.6 - - - -
191O THR* 2.7 46.9 + - - -
222O MET* 3.2 23.1 - - + +
223O ASN* 3.0 34.3 + - + +
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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