Contacts of the helix formed by residues 292 - 296 (chain S) 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 GLY 292 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290S PRO 4.0 0.2 + - - -
291S PRO* 1.3 75.8 - - - +
293S ARG* 1.3 67.6 + - - -
294S GLU 3.3 0.9 + - - -
295S ALA* 3.1 11.3 + - - -
296S TYR 3.3 20.0 + - - -
297S PRO* 4.6 0.8 - - - +
298S GLY* 4.6 9.8 - - - +
270W ALA* 5.6 4.3 - - - -
276W PRO* 5.8 2.9 - - - -
267Y LEU* 3.4 20.6 - - - +
270Y ILE* 5.3 0.5 - - - +
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Residues in contact with ARG 293 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292S GLY* 1.3 69.6 - - - -
294S GLU* 1.3 73.8 + - + +
295S ALA 3.0 1.3 + - - -
296S TYR 3.4 8.4 + - - +
337S SER 4.1 11.3 + - - -
338S ALA* 4.8 1.4 - - - +
339S TYR* 3.3 78.7 + - + +
279W VAL* 5.0 8.6 + - - +
280W GLY* 5.1 11.2 - - - -
259Y ARG* 5.0 15.3 - - - +
263Y ILE* 3.2 48.4 - - + +
267Y LEU* 4.4 12.0 - - - +
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Residues in contact with GLU 294 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281S ARG* 5.1 0.2 + - - -
292S GLY 3.3 1.6 + - - -
293S ARG* 1.3 83.3 + - + +
295S ALA* 1.3 65.0 + - - +
296S TYR* 2.9 44.2 + - + -
338S ALA* 5.2 4.3 - - - +
339S TYR* 3.0 33.1 + - + +
340S ILE* 4.7 1.5 + - - +
278V ALA* 3.4 22.6 - - + +
263Y ILE* 5.6 3.9 - - + +
266Y GLU* 6.3 3.6 - - - -
267Y LEU* 5.3 4.0 - - - +
270Y ILE* 6.2 0.4 - - - -
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Residues in contact with ALA 295 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281S ARG* 3.2 24.0 - - + +
285S LEU* 3.9 16.7 - - + +
291S PRO* 4.4 10.4 - - - +
292S GLY 3.1 13.0 + - - -
293S ARG 3.0 2.4 - - - -
294S GLU* 1.3 80.8 - - - +
296S TYR* 1.3 64.7 + - - +
297S PRO* 3.6 2.6 - - - +
276V PRO 4.6 3.6 - - - +
277V SER* 3.9 10.1 - - - -
278V ALA* 3.5 24.2 - - - +
270Y ILE* 5.1 7.4 - - + +
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Residues in contact with TYR 296 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274S SER 5.4 0.2 - - - -
277S ALA* 3.8 20.4 - - + -
278S VAL* 4.1 15.8 - - + +
281S ARG* 3.0 40.2 + - + -
292S GLY* 3.3 19.3 + - - -
293S ARG 3.4 8.7 + - - +
294S GLU* 2.9 39.2 + - + -
295S ALA* 1.3 78.4 - - - +
297S PRO* 1.3 74.7 - - + +
298S GLY* 4.4 0.2 - - - -
300S VAL* 3.9 23.0 - - + +
339S TYR* 4.2 4.8 + + + -
340S ILE* 3.2 42.5 - - + +
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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
------------------------------------------------------------
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